Menu
▾
▴
sed-ml-discuss — Migrating to google groups: https://groups.google.com/d/forum/sed-ml-discuss
This list is closed, nobody may subscribe to it.
| 2008 |
Jan
(1) |
Feb
(35) |
Mar
(41) |
Apr
(4) |
May
(19) |
Jun
(26) |
Jul
(3) |
Aug
(2) |
Sep
(2) |
Oct
(1) |
Nov
|
Dec
(3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2009 |
Jan
(49) |
Feb
(15) |
Mar
(17) |
Apr
(7) |
May
(26) |
Jun
(1) |
Jul
(5) |
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
| 2010 |
Jan
|
Feb
(1) |
Mar
(29) |
Apr
(4) |
May
(31) |
Jun
(46) |
Jul
|
Aug
(5) |
Sep
(3) |
Oct
(2) |
Nov
(15) |
Dec
|
| 2011 |
Jan
(8) |
Feb
(1) |
Mar
(6) |
Apr
(10) |
May
(17) |
Jun
(23) |
Jul
(5) |
Aug
(3) |
Sep
(28) |
Oct
(41) |
Nov
(20) |
Dec
(1) |
| 2012 |
Jan
(20) |
Feb
(15) |
Mar
(1) |
Apr
(1) |
May
(8) |
Jun
(3) |
Jul
(9) |
Aug
(10) |
Sep
(1) |
Oct
(2) |
Nov
(5) |
Dec
(8) |
| 2013 |
Jan
(2) |
Feb
(1) |
Mar
|
Apr
(16) |
May
(13) |
Jun
(6) |
Jul
(1) |
Aug
(2) |
Sep
(3) |
Oct
(2) |
Nov
(6) |
Dec
(2) |
| 2014 |
Jan
(4) |
Feb
(5) |
Mar
(15) |
Apr
(16) |
May
|
Jun
(6) |
Jul
(3) |
Aug
(2) |
Sep
(1) |
Oct
|
Nov
(13) |
Dec
(8) |
| 2015 |
Jan
(7) |
Feb
|
Mar
(3) |
Apr
|
May
(6) |
Jun
(24) |
Jul
(3) |
Aug
(10) |
Sep
(36) |
Oct
(3) |
Nov
|
Dec
(39) |
| 2016 |
Jan
(9) |
Feb
(38) |
Mar
(25) |
Apr
(3) |
May
(12) |
Jun
(5) |
Jul
(40) |
Aug
(13) |
Sep
(4) |
Oct
|
Nov
|
Dec
(2) |
| 2017 |
Jan
|
Feb
|
Mar
|
Apr
(2) |
May
(29) |
Jun
(26) |
Jul
(12) |
Aug
|
Sep
|
Oct
(4) |
Nov
|
Dec
|
|
From: David N. <dav...@gm...> - 2016-09-20 13:22:51
|
Google doc with meeting notes: https://docs.google.com/document/d/1uNNkjATFUQ78FspKkBTwJ2UmevmCGfovaKI22sr3VF8/edit?usp=sharing Cheers, David. On Tue, Sep 20, 2016 at 8:31 PM, David Nickerson <dav...@gm...> wrote: > Hi all, > > The first SED-ML breakout is about to get underway at COMBINE. Remote > attendance is via BlueJeans, details available on the agenda page: > http://co.mbine.org/events/COMBINE_2016/agenda. > > Hopefully things just work, but if you would like to participate and > have any trouble please reply to this email or contact myself, Frank, > or Lucian directly. > > Cheers, > David. > > > -- > > > David Nickerson > about.me/david.nickerson -- David Nickerson about.me/david.nickerson |
|
From: David N. <dav...@gm...> - 2016-09-20 12:31:34
|
Hi all, The first SED-ML breakout is about to get underway at COMBINE. Remote attendance is via BlueJeans, details available on the agenda page: http://co.mbine.org/events/COMBINE_2016/agenda. Hopefully things just work, but if you would like to participate and have any trouble please reply to this email or contact myself, Frank, or Lucian directly. Cheers, David. -- David Nickerson about.me/david.nickerson |
|
From: Frank T. B. <fbe...@ca...> - 2016-09-16 14:04:57
|
Dear all, Today I want to announce the availability of a library supporting the Combine Archive format. Unlike other libraries that already exist for .NET and Java, this library is written in C++ after the style of libSBML. Support for other languages is available via SWIG (so far I have wrapped only Python, Java and .NET but further languages can be added if needed). https://github.com/sbmlteam/libCombine/releases/tag/0.1.0 At this point I would want to ask for your feedback, concerning any missing features or anything that would help when dealing with the COMBINE archive format. Examples are available online: https://github.com/sbmlteam/libCombine/tree/master/examples Documentation is still quite sparse, and but I have at least generated initial C++ documents here: https://sbmlteam.github.io/libCombine/html/class_combine_archive.html Please provide any feedback and requests you have using the issue tracker under: https://github.com/sbmlteam/libCombine/issues or by contacting me (so we don't swamp the mailing lists) All the best Frank |
|
From: David N. <dav...@gm...> - 2016-08-28 23:34:24
|
COMBINE 2016: 7th Computational Modeling in Biology Network Workshop 19-24 September 2016, Newcastle upon Tyne, UK http://co.mbine.org/events/COMBINE_2016 *Full programme*: http://co.mbine.org/events/COMBINE_2016/agenda The "Computational Modeling in Biology" Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2016 will be a workshop-style event with oral presentations, posters, and breakout sessions. The five meeting days will include talks about the COMBINE standards and associated or related standardization efforts, as well as presentations of tools using these standards. Oral presentations have been selected from the submitted abstracts. In addition, poster sessions will allow people to inform each other about their software and other projects in a setting that fosters interaction and in-depth discussion. == IMPORTANT DATES == COMBINE Workshop: 19-23 September 2016 SBGN Workshop@COMBINE: 24 September 2016 == KEYNOTE SPEAKERS == - Alfonso Bueno-Orovio (Oxford) - Carole Goble (Manchester) - Martin Golebiewski (HITS gGmbH) - Sarah Keating (EMBL-EBI) - Dagmar Iber (ETH Zurich) - Andrew Millar (Edinburgh) - Chris J. Myers (Utah) - David Nickerson (Auckland) - Daryl Shanley (Newcastle) - Yujiang Wang (Newcastle) == REGISTRATION == Delegate registration fee: 195GBP (~ 230EUR, 260USD) Discounted rate for students: 145GBP (~ 170EUR, 195USD) Registration includes lunches, snacks, coffee and tea over the five days and the conference dinner on the 19th. Register here: http://co.mbine.org/events/COMBINE_2016#Registration == TOPICS OF INTEREST == Topics include, but are not limited to: - Data exchange and model standards for systems biology - Graphical notation standards for systems biology - Standards for sharing and analysing biological pathway data - Standards for computational biological models More on the COMBINE standards at http://co.mbine.org/standards == ACKNOWLEDGEMENTS == COMBINE 2016 is generously supported by: - Engineering and Physical Sciences Research Council (UK) [AUDACIOUS project EP/J004111/2] - Interdisciplinary Computing and Complex BioSystems Group (ICOS) - School of Computing Science, Newcastle University - National Science Foundation (USA) == LOCAL CHAIRS == Paolo Zuliani & Anil Wipat, ICOS Group, School of Computing Science, Newcastle University. == LOCAL ORGANISERS == Keith Flanagan & Claire Smith, ICOS Group, School of Computing Science, Newcastle University. == COMBINE COORDINATORS == Gary Bader (Toronto) Martin Golebiewski (Heidelberg) Michael Hucka (Caltech) Nicolas Le Novère (Babraham) Chris J. Myers (Utah) David Nickerson (Auckland) Falk Schreiber (Monash) Dagmar Waltemath (Rostock) |
|
From: Matthias K. <kon...@go...> - 2016-08-18 12:29:34
|
Hi David, I will be at Combine from Tuesday on. I can give more qualified feedback when I worked a bit with the L1V3 library. Matthias On Thu, Aug 18, 2016 at 12:21 PM, David Nickerson <dav...@gm... > wrote: > Just to round this off, it seems that for SED-ML breakout sessions at > COMBINE we could have at least: > > - the SED-ML L1V3 draft spec and trying to get that released, and checking > to see how Matthias gets on using the data features as they are (will you > be at COMBINE Matthias?) > - going through the current bunch of feature requests and trying to come > up with a roadmap for the next version or two of SED-ML, or at least > collating them form various google docs and tracker items into a central > location. > - extending plots, data generators, and post-processing in general. > > Any others that people would like to see? > > Thanks, > David. > > On Fri, Aug 5, 2016 at 12:38 AM, Matthias König <kon...@go...> > wrote: > >> Hi Frank, >> >> perfect. Thanks so much for the support and great work. >> I never tried the L1V3 features, so was unsure if everything is there. >> >> Matthias >> >> On Thu, Aug 4, 2016 at 2:08 PM, Frank T. Bergmann <fbe...@ca...> >> wrote: >> >>> Hello Matthias, >>> >>> the c++ library has supported reading/writing of L1V3 features for at >>> least 7 months now ... please let me know if you find issues with it. And i >>> will try to remedy them: >>> >>> here an example on how to create the new elements: >>> https://github.com/fbergmann/libSEDML/blob/master/examples/c >>> %2B%2B/create_sedml.cpp >>> >>> best >>> Frank >>> >>> On Thu, Aug 4, 2016 at 10:57 AM, Matthias König < >>> kon...@go...> wrote: >>> >>>> Hi David, >>>> this sounds great. >>>> >>>> Is the c++ library supporting L1V3? I.e. https://github.com/fbergmann/l >>>> ibSEDML >>>> Or only the c# library? >>>> >>>> I need python bindings to L1V3. As soon as there is support for L1V3 in >>>> python via the libSEDML c++ library I will implement tool support for >>>> tellurium. >>>> Than there would be a second tool supporting it. >>>> In the process I could test if it does everything I need. Only reading >>>> the specs without having code to work with is not so productive. >>>> >>>> Matthias >>>> >>>> On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson < >>>> dav...@gm...> wrote: >>>> >>>>> Hi Matthias, >>>>> >>>>> The Level 1 version 3 draft specification has been available for a >>>>> couple of years now: http://co.mbine.org/stand >>>>> ards/sed-ml/level-1/version-3/draft-1 - just waiting on a second >>>>> implementation (in addition to Frank's C# libSEDML project) to test things >>>>> out completely before finalising that. I just took a quick look, and there >>>>> is no explicit "what has changed" section that I could see - but one of the >>>>> main changes is the integration of data, including the slicing. Would be >>>>> good to see if those features in the current draft spec would meet your >>>>> needs in that regard. >>>>> >>>>> Otherwise, the main place to look for what people are looking at is >>>>> that google doc capturing the discussions from COMBINE last year and >>>>> HARMONY this year (https://docs.google.com/docum >>>>> ent/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). >>>>> I'm not aware of any further work toward the non-uniform time course beyond >>>>> what is in that document. There is also a bit in there on histograms. >>>>> >>>>> Cheers, >>>>> David. >>>>> >>>>> >>>>> On Thu, Aug 4, 2016 at 7:03 PM, Matthias König < >>>>> kon...@go...> wrote: >>>>> >>>>>> Hi all, >>>>>> where can I find the information about the L1V3 specification. >>>>>> I am especially looking for the parts which describe new features, >>>>>> i.e. what is decided and will definitely come, and what will change from >>>>>> L1V2 to L1V3. >>>>>> I don't want to open discussions if they are already decided on. >>>>>> >>>>>> Things I am very interested in are >>>>>> - support of NonUniformTimeCourses: is this there in L1V3, what is >>>>>> the roadmap here ? >>>>>> - integration of data, how should data be described, how to load >>>>>> data, how to use data to create simulation definitions, how to display data >>>>>> in plots >>>>>> Typical workflows are loading experimental data sets and data sets >>>>>> with parameters from files, than parametrizing the model with data from the >>>>>> files, run tasks, plot simulation data, add experimental data to plot >>>>>> - data slicing, i.e. getting subsets of the data sets (not only by >>>>>> index, but by time or other variable). I.e. I want the simulation data y >>>>>> for x in [x0, x2] (x montone data) -> this becomes important with >>>>>> NonUniformTimeCourses >>>>>> - more plots: heatmaps, contour plots, histograms >>>>>> >>>>>> Matthias >>>>>> >>>>>> >>>>>> On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < >>>>>> dav...@gm...> wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >>>>>>> approaching, September 19-26 in Newcastle, UK, and the organisers are >>>>>>> now soliciting potential topics for breakout sessions. >>>>>>> >>>>>>> If you have any SED-ML topics that you would like to see raised at >>>>>>> COMBINE, please let us know. Or any topics that you think would be >>>>>>> relevant to the wider COMBINE community. >>>>>>> >>>>>>> Cheers, >>>>>>> David. >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> >>>>>>> David Nickerson >>>>>>> about.me/david.nickerson >>>>>>> >>>>>>> ------------------------------------------------------------ >>>>>>> ------------------ >>>>>>> _______________________________________________ >>>>>>> SED-ML-discuss mailing list >>>>>>> SED...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Matthias König >>>>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>>>> https://www.livermetabolism.com >>>>>> kon...@go... >>>>>> Tel: +49 30 20938450 >>>>>> Tel: +49 176 81168480 >>>>>> >>>>>> ------------------------------------------------------------ >>>>>> ------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> SED-ML-discuss mailing list >>>>>> SED...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> [image: David Nickerson on about.me] >>>>> >>>>> David Nickerson >>>>> about.me/david.nickerson >>>>> <http://about.me/david.nickerson> >>>>> >>>>> ------------------------------------------------------------ >>>>> ------------------ >>>>> >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>> >>>> >>>> -- >>>> Matthias König >>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>> https://www.livermetabolism.com >>>> kon...@go... >>>> Tel: +49 30 20938450 >>>> Tel: +49 176 81168480 >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com >> kon...@go... >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > > > [image: David Nickerson on about.me] > > David Nickerson > about.me/david.nickerson > <http://about.me/david.nickerson> > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: David N. <dav...@gm...> - 2016-08-18 10:21:53
|
Just to round this off, it seems that for SED-ML breakout sessions at COMBINE we could have at least: - the SED-ML L1V3 draft spec and trying to get that released, and checking to see how Matthias gets on using the data features as they are (will you be at COMBINE Matthias?) - going through the current bunch of feature requests and trying to come up with a roadmap for the next version or two of SED-ML, or at least collating them form various google docs and tracker items into a central location. - extending plots, data generators, and post-processing in general. Any others that people would like to see? Thanks, David. On Fri, Aug 5, 2016 at 12:38 AM, Matthias König <kon...@go...> wrote: > Hi Frank, > > perfect. Thanks so much for the support and great work. > I never tried the L1V3 features, so was unsure if everything is there. > > Matthias > > On Thu, Aug 4, 2016 at 2:08 PM, Frank T. Bergmann <fbe...@ca...> > wrote: > >> Hello Matthias, >> >> the c++ library has supported reading/writing of L1V3 features for at >> least 7 months now ... please let me know if you find issues with it. And i >> will try to remedy them: >> >> here an example on how to create the new elements: >> https://github.com/fbergmann/libSEDML/blob/master/examples/c >> %2B%2B/create_sedml.cpp >> >> best >> Frank >> >> On Thu, Aug 4, 2016 at 10:57 AM, Matthias König <kon...@go... >> > wrote: >> >>> Hi David, >>> this sounds great. >>> >>> Is the c++ library supporting L1V3? I.e. https://github.com/fbergmann/l >>> ibSEDML >>> Or only the c# library? >>> >>> I need python bindings to L1V3. As soon as there is support for L1V3 in >>> python via the libSEDML c++ library I will implement tool support for >>> tellurium. >>> Than there would be a second tool supporting it. >>> In the process I could test if it does everything I need. Only reading >>> the specs without having code to work with is not so productive. >>> >>> Matthias >>> >>> On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson < >>> dav...@gm...> wrote: >>> >>>> Hi Matthias, >>>> >>>> The Level 1 version 3 draft specification has been available for a >>>> couple of years now: http://co.mbine.org/stand >>>> ards/sed-ml/level-1/version-3/draft-1 - just waiting on a second >>>> implementation (in addition to Frank's C# libSEDML project) to test things >>>> out completely before finalising that. I just took a quick look, and there >>>> is no explicit "what has changed" section that I could see - but one of the >>>> main changes is the integration of data, including the slicing. Would be >>>> good to see if those features in the current draft spec would meet your >>>> needs in that regard. >>>> >>>> Otherwise, the main place to look for what people are looking at is >>>> that google doc capturing the discussions from COMBINE last year and >>>> HARMONY this year (https://docs.google.com/docum >>>> ent/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). >>>> I'm not aware of any further work toward the non-uniform time course beyond >>>> what is in that document. There is also a bit in there on histograms. >>>> >>>> Cheers, >>>> David. >>>> >>>> >>>> On Thu, Aug 4, 2016 at 7:03 PM, Matthias König < >>>> kon...@go...> wrote: >>>> >>>>> Hi all, >>>>> where can I find the information about the L1V3 specification. >>>>> I am especially looking for the parts which describe new features, >>>>> i.e. what is decided and will definitely come, and what will change from >>>>> L1V2 to L1V3. >>>>> I don't want to open discussions if they are already decided on. >>>>> >>>>> Things I am very interested in are >>>>> - support of NonUniformTimeCourses: is this there in L1V3, what is the >>>>> roadmap here ? >>>>> - integration of data, how should data be described, how to load data, >>>>> how to use data to create simulation definitions, how to display data in >>>>> plots >>>>> Typical workflows are loading experimental data sets and data sets >>>>> with parameters from files, than parametrizing the model with data from the >>>>> files, run tasks, plot simulation data, add experimental data to plot >>>>> - data slicing, i.e. getting subsets of the data sets (not only by >>>>> index, but by time or other variable). I.e. I want the simulation data y >>>>> for x in [x0, x2] (x montone data) -> this becomes important with >>>>> NonUniformTimeCourses >>>>> - more plots: heatmaps, contour plots, histograms >>>>> >>>>> Matthias >>>>> >>>>> >>>>> On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < >>>>> dav...@gm...> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >>>>>> approaching, September 19-26 in Newcastle, UK, and the organisers are >>>>>> now soliciting potential topics for breakout sessions. >>>>>> >>>>>> If you have any SED-ML topics that you would like to see raised at >>>>>> COMBINE, please let us know. Or any topics that you think would be >>>>>> relevant to the wider COMBINE community. >>>>>> >>>>>> Cheers, >>>>>> David. >>>>>> >>>>>> -- >>>>>> >>>>>> >>>>>> David Nickerson >>>>>> about.me/david.nickerson >>>>>> >>>>>> ------------------------------------------------------------ >>>>>> ------------------ >>>>>> _______________________________________________ >>>>>> SED-ML-discuss mailing list >>>>>> SED...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Matthias König >>>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>>> https://www.livermetabolism.com >>>>> kon...@go... >>>>> Tel: +49 30 20938450 >>>>> Tel: +49 176 81168480 >>>>> >>>>> ------------------------------------------------------------ >>>>> ------------------ >>>>> >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>> >>>> >>>> -- >>>> >>>> >>>> [image: David Nickerson on about.me] >>>> >>>> David Nickerson >>>> about.me/david.nickerson >>>> <http://about.me/david.nickerson> >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com >>> kon...@go... >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 >>> >>> ------------------------------------------------------------ >>> ------------------ >>> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- [image: David Nickerson on about.me] David Nickerson about.me/david.nickerson <http://about.me/david.nickerson> |
|
From: David N. <dav...@gm...> - 2016-08-10 23:18:45
|
Dear colleagues, We will organize a COMBINE & de.NBI Tutorial 'Modelling and Simulation Tools in Systems Biology‘ on Friday,16 September, 2016 (8:30 - 13:30) as a satellite of the 17th International Conference on Systems Biology (ICSB). Participation is free of charge and registration is open until August 25th: http://co.mbine.org/events/tutorial2016 Please note that the tutorial is at the opening day of the ICSB conference. It will finish in time to allow participants to join the ICSB opening ceremony in the afternoon. Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats. The topics will include: Model setup using different software tools and systems biology platforms Using experimental data for setting up quantitative models Parameter estimation, optimization and model fitting Simulation, analysis and visualization of biochemical models Database supported modelling: integrated data management and model databases Community standards and formats for systems biology models Covered tools, platforms and databases BioModels database: http://www.ebi.ac.uk/biomodels-main/ CellDesigner: http://www.celldesigner.org/ COPASI: http://www.copasi.org JWS Online: http://jjj.biochem.sun.ac.za/ SABIO-RK: http://sabio.h-its.org/ SEEK: http://fair-dom.org/platform/seek/ SYCAMORE: http://sycamore.eml.org You are invited to join us and/or send your students. The target audience are experimentalists and modellers with some very basic experience in modelling and simulation of biological networks and everybody who would like to learn more about the tools and standards. Please feel free to forward this invitation to anybody you would think could be interested to attend. Best regards, Martin Golebiewski (on behalf of all tutors) Martin Golebiewski HITS gGmbH Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone +49 6221 533 281 fax +49 6221 533 298 email mar...@h-... http://www.h-its.org _________________________________________________ Amtsgericht Mannheim / HRB 337446 Managing Director: Dr. Gesa Schönberger Scientific Director: Prof. Dr. Rebecca Wade |
|
From: Matthias K. <kon...@go...> - 2016-08-04 12:38:37
|
Hi Frank, perfect. Thanks so much for the support and great work. I never tried the L1V3 features, so was unsure if everything is there. Matthias On Thu, Aug 4, 2016 at 2:08 PM, Frank T. Bergmann <fbe...@ca...> wrote: > Hello Matthias, > > the c++ library has supported reading/writing of L1V3 features for at > least 7 months now ... please let me know if you find issues with it. And i > will try to remedy them: > > here an example on how to create the new elements: > https://github.com/fbergmann/libSEDML/blob/master/examples/ > c%2B%2B/create_sedml.cpp > > best > Frank > > On Thu, Aug 4, 2016 at 10:57 AM, Matthias König <kon...@go...> > wrote: > >> Hi David, >> this sounds great. >> >> Is the c++ library supporting L1V3? I.e. https://github.com/fbergmann/ >> libSEDML >> Or only the c# library? >> >> I need python bindings to L1V3. As soon as there is support for L1V3 in >> python via the libSEDML c++ library I will implement tool support for >> tellurium. >> Than there would be a second tool supporting it. >> In the process I could test if it does everything I need. Only reading >> the specs without having code to work with is not so productive. >> >> Matthias >> >> On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson < >> dav...@gm...> wrote: >> >>> Hi Matthias, >>> >>> The Level 1 version 3 draft specification has been available for a >>> couple of years now: http://co.mbine.org/standards/sed-ml/level-1/ >>> version-3/draft-1 - just waiting on a second implementation (in >>> addition to Frank's C# libSEDML project) to test things out completely >>> before finalising that. I just took a quick look, and there is no explicit >>> "what has changed" section that I could see - but one of the main changes >>> is the integration of data, including the slicing. Would be good to see if >>> those features in the current draft spec would meet your needs in that >>> regard. >>> >>> Otherwise, the main place to look for what people are looking at is that >>> google doc capturing the discussions from COMBINE last year and HARMONY >>> this year (https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY- >>> fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). I'm not aware of any >>> further work toward the non-uniform time course beyond what is in that >>> document. There is also a bit in there on histograms. >>> >>> Cheers, >>> David. >>> >>> >>> On Thu, Aug 4, 2016 at 7:03 PM, Matthias König <kon...@go... >>> > wrote: >>> >>>> Hi all, >>>> where can I find the information about the L1V3 specification. >>>> I am especially looking for the parts which describe new features, i.e. >>>> what is decided and will definitely come, and what will change from L1V2 to >>>> L1V3. >>>> I don't want to open discussions if they are already decided on. >>>> >>>> Things I am very interested in are >>>> - support of NonUniformTimeCourses: is this there in L1V3, what is the >>>> roadmap here ? >>>> - integration of data, how should data be described, how to load data, >>>> how to use data to create simulation definitions, how to display data in >>>> plots >>>> Typical workflows are loading experimental data sets and data sets with >>>> parameters from files, than parametrizing the model with data from the >>>> files, run tasks, plot simulation data, add experimental data to plot >>>> - data slicing, i.e. getting subsets of the data sets (not only by >>>> index, but by time or other variable). I.e. I want the simulation data y >>>> for x in [x0, x2] (x montone data) -> this becomes important with >>>> NonUniformTimeCourses >>>> - more plots: heatmaps, contour plots, histograms >>>> >>>> Matthias >>>> >>>> >>>> On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < >>>> dav...@gm...> wrote: >>>> >>>>> Hi all, >>>>> >>>>> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >>>>> approaching, September 19-26 in Newcastle, UK, and the organisers are >>>>> now soliciting potential topics for breakout sessions. >>>>> >>>>> If you have any SED-ML topics that you would like to see raised at >>>>> COMBINE, please let us know. Or any topics that you think would be >>>>> relevant to the wider COMBINE community. >>>>> >>>>> Cheers, >>>>> David. >>>>> >>>>> -- >>>>> >>>>> >>>>> David Nickerson >>>>> about.me/david.nickerson >>>>> >>>>> ------------------------------------------------------------ >>>>> ------------------ >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>> >>>> >>>> >>>> -- >>>> Matthias König >>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>> https://www.livermetabolism.com >>>> kon...@go... >>>> Tel: +49 30 20938450 >>>> Tel: +49 176 81168480 >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>> >>> >>> -- >>> >>> >>> [image: David Nickerson on about.me] >>> >>> David Nickerson >>> about.me/david.nickerson >>> <http://about.me/david.nickerson> >>> >>> ------------------------------------------------------------ >>> ------------------ >>> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com >> kon...@go... >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: Frank T. B. <fbe...@ca...> - 2016-08-04 12:08:57
|
Hello Matthias, the c++ library has supported reading/writing of L1V3 features for at least 7 months now ... please let me know if you find issues with it. And i will try to remedy them: here an example on how to create the new elements: https://github.com/fbergmann/libSEDML/blob/master/examples/c%2B%2B/create_sedml.cpp best Frank On Thu, Aug 4, 2016 at 10:57 AM, Matthias König <kon...@go...> wrote: > Hi David, > this sounds great. > > Is the c++ library supporting L1V3? I.e. > https://github.com/fbergmann/libSEDML > Or only the c# library? > > I need python bindings to L1V3. As soon as there is support for L1V3 in > python via the libSEDML c++ library I will implement tool support for > tellurium. > Than there would be a second tool supporting it. > In the process I could test if it does everything I need. Only reading the > specs without having code to work with is not so productive. > > Matthias > > On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson < > dav...@gm...> wrote: > >> Hi Matthias, >> >> The Level 1 version 3 draft specification has been available for a couple >> of years now: >> http://co.mbine.org/standards/sed-ml/level-1/version-3/draft-1 - just >> waiting on a second implementation (in addition to Frank's C# libSEDML >> project) to test things out completely before finalising that. I just took >> a quick look, and there is no explicit "what has changed" section that I >> could see - but one of the main changes is the integration of data, >> including the slicing. Would be good to see if those features in the >> current draft spec would meet your needs in that regard. >> >> Otherwise, the main place to look for what people are looking at is that >> google doc capturing the discussions from COMBINE last year and HARMONY >> this year ( >> https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). >> I'm not aware of any further work toward the non-uniform time course beyond >> what is in that document. There is also a bit in there on histograms. >> >> Cheers, >> David. >> >> >> On Thu, Aug 4, 2016 at 7:03 PM, Matthias König <kon...@go...> >> wrote: >> >>> Hi all, >>> where can I find the information about the L1V3 specification. >>> I am especially looking for the parts which describe new features, i.e. >>> what is decided and will definitely come, and what will change from L1V2 to >>> L1V3. >>> I don't want to open discussions if they are already decided on. >>> >>> Things I am very interested in are >>> - support of NonUniformTimeCourses: is this there in L1V3, what is the >>> roadmap here ? >>> - integration of data, how should data be described, how to load data, >>> how to use data to create simulation definitions, how to display data in >>> plots >>> Typical workflows are loading experimental data sets and data sets with >>> parameters from files, than parametrizing the model with data from the >>> files, run tasks, plot simulation data, add experimental data to plot >>> - data slicing, i.e. getting subsets of the data sets (not only by >>> index, but by time or other variable). I.e. I want the simulation data y >>> for x in [x0, x2] (x montone data) -> this becomes important with >>> NonUniformTimeCourses >>> - more plots: heatmaps, contour plots, histograms >>> >>> Matthias >>> >>> >>> On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < >>> dav...@gm...> wrote: >>> >>>> Hi all, >>>> >>>> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >>>> approaching, September 19-26 in Newcastle, UK, and the organisers are >>>> now soliciting potential topics for breakout sessions. >>>> >>>> If you have any SED-ML topics that you would like to see raised at >>>> COMBINE, please let us know. Or any topics that you think would be >>>> relevant to the wider COMBINE community. >>>> >>>> Cheers, >>>> David. >>>> >>>> -- >>>> >>>> >>>> David Nickerson >>>> about.me/david.nickerson >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com >>> kon...@go... >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> >> >> [image: David Nickerson on about.me] >> >> David Nickerson >> about.me/david.nickerson >> <http://about.me/david.nickerson> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
|
From: Martin P. <acc...@fr...> - 2016-08-04 11:40:03
|
Hi, For everything I used the C++ libSEDML and their Python binding for, it supported all new elements in L1V3. Even though I believe, that not everything is 100% stable and tested yet. However I haven't had any major issue, therefore big thanks to Frank :) Cheers, Martin On 2016-08-04 13:11, David Nickerson wrote: > I'll leave it to Frank to give the definitive answer, but I believe it > is currently on the C# libSEDML that supports L1V3... > > Cheers, > David. > > On Thu, Aug 4, 2016 at 8:57 PM, Matthias König <kon...@go... > <mailto:kon...@go...>> wrote: > > Hi David, > this sounds great. > > Is the c++ library supporting L1V3? I.e. > https://github.com/fbergmann/libSEDML > Or only the c# library? > > I need python bindings to L1V3. As soon as there is support for L1V3 > in python via the libSEDML c++ library I will implement tool support > for tellurium. > Than there would be a second tool supporting it. > In the process I could test if it does everything I need. Only > reading the specs without having code to work with is not so productive. > > Matthias > > On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson > <dav...@gm... <mailto:dav...@gm...>> wrote: > > Hi Matthias, > > The Level 1 version 3 draft specification has been available for > a couple of years > now: http://co.mbine.org/standards/sed-ml/level-1/version-3/draft-1 > - just waiting on a second implementation (in addition to > Frank's C# libSEDML project) to test things out completely > before finalising that. I just took a quick look, and there is > no explicit "what has changed" section that I could see - but > one of the main changes is the integration of data, including > the slicing. Would be good to see if those features in the > current draft spec would meet your needs in that regard. > > Otherwise, the main place to look for what people are looking at > is that google doc capturing the discussions from COMBINE last > year and HARMONY this year > (https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). > I'm not aware of any further work toward the non-uniform time > course beyond what is in that document. There is also a bit in > there on histograms. > > Cheers, > David. > > > On Thu, Aug 4, 2016 at 7:03 PM, Matthias König > <kon...@go... <mailto:kon...@go...>> wrote: > > Hi all, > where can I find the information about the L1V3 specification. > I am especially looking for the parts which describe new > features, i.e. what is decided and will definitely come, and > what will change from L1V2 to L1V3. > I don't want to open discussions if they are already decided > on. > > Things I am very interested in are > - support of NonUniformTimeCourses: is this there in L1V3, > what is the roadmap here ? > - integration of data, how should data be described, how to > load data, how to use data to create simulation definitions, > how to display data in plots > Typical workflows are loading experimental data sets and > data sets with parameters from files, than parametrizing the > model with data from the files, run tasks, plot simulation > data, add experimental data to plot > - data slicing, i.e. getting subsets of the data sets (not > only by index, but by time or other variable). I.e. I want > the simulation data y for x in [x0, x2] (x montone data) -> > this becomes important with NonUniformTimeCourses > - more plots: heatmaps, contour plots, histograms > > Matthias > > > On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson > <dav...@gm... > <mailto:dav...@gm...>> wrote: > > Hi all, > > COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) > is rapidly > approaching, September 19-26 in Newcastle, UK, and the > organisers are > now soliciting potential topics for breakout sessions. > > If you have any SED-ML topics that you would like to see > raised at > COMBINE, please let us know. Or any topics that you > think would be > relevant to the wider COMBINE community. > > Cheers, > David. > > -- > > > David Nickerson > about.me/david.nickerson <http://about.me/david.nickerson> > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... <mailto:kon...@go...> > Tel: +49 30 20938450 > Tel: +49 176 81168480 <tel:%2B49%20176%2081168480> > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > -- > > David Nickerson on about.me > > David Nickerson > about.me/david.nickerson > > > <http://about.me/david.nickerson> > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... <mailto:kon...@go...> > Tel: +49 30 20938450 > Tel: +49 176 81168480 <tel:%2B49%20176%2081168480> > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > -- > > David Nickerson on about.me > > David Nickerson > about.me/david.nickerson > > > <http://about.me/david.nickerson> > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
|
From: David N. <dav...@gm...> - 2016-08-04 11:12:02
|
I'll leave it to Frank to give the definitive answer, but I believe it is currently on the C# libSEDML that supports L1V3... Cheers, David. On Thu, Aug 4, 2016 at 8:57 PM, Matthias König <kon...@go...> wrote: > Hi David, > this sounds great. > > Is the c++ library supporting L1V3? I.e. > https://github.com/fbergmann/libSEDML > Or only the c# library? > > I need python bindings to L1V3. As soon as there is support for L1V3 in > python via the libSEDML c++ library I will implement tool support for > tellurium. > Than there would be a second tool supporting it. > In the process I could test if it does everything I need. Only reading the > specs without having code to work with is not so productive. > > Matthias > > On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson < > dav...@gm...> wrote: > >> Hi Matthias, >> >> The Level 1 version 3 draft specification has been available for a couple >> of years now: >> http://co.mbine.org/standards/sed-ml/level-1/version-3/draft-1 - just >> waiting on a second implementation (in addition to Frank's C# libSEDML >> project) to test things out completely before finalising that. I just took >> a quick look, and there is no explicit "what has changed" section that I >> could see - but one of the main changes is the integration of data, >> including the slicing. Would be good to see if those features in the >> current draft spec would meet your needs in that regard. >> >> Otherwise, the main place to look for what people are looking at is that >> google doc capturing the discussions from COMBINE last year and HARMONY >> this year ( >> https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). >> I'm not aware of any further work toward the non-uniform time course beyond >> what is in that document. There is also a bit in there on histograms. >> >> Cheers, >> David. >> >> >> On Thu, Aug 4, 2016 at 7:03 PM, Matthias König <kon...@go...> >> wrote: >> >>> Hi all, >>> where can I find the information about the L1V3 specification. >>> I am especially looking for the parts which describe new features, i.e. >>> what is decided and will definitely come, and what will change from L1V2 to >>> L1V3. >>> I don't want to open discussions if they are already decided on. >>> >>> Things I am very interested in are >>> - support of NonUniformTimeCourses: is this there in L1V3, what is the >>> roadmap here ? >>> - integration of data, how should data be described, how to load data, >>> how to use data to create simulation definitions, how to display data in >>> plots >>> Typical workflows are loading experimental data sets and data sets with >>> parameters from files, than parametrizing the model with data from the >>> files, run tasks, plot simulation data, add experimental data to plot >>> - data slicing, i.e. getting subsets of the data sets (not only by >>> index, but by time or other variable). I.e. I want the simulation data y >>> for x in [x0, x2] (x montone data) -> this becomes important with >>> NonUniformTimeCourses >>> - more plots: heatmaps, contour plots, histograms >>> >>> Matthias >>> >>> >>> On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < >>> dav...@gm...> wrote: >>> >>>> Hi all, >>>> >>>> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >>>> approaching, September 19-26 in Newcastle, UK, and the organisers are >>>> now soliciting potential topics for breakout sessions. >>>> >>>> If you have any SED-ML topics that you would like to see raised at >>>> COMBINE, please let us know. Or any topics that you think would be >>>> relevant to the wider COMBINE community. >>>> >>>> Cheers, >>>> David. >>>> >>>> -- >>>> >>>> >>>> David Nickerson >>>> about.me/david.nickerson >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com >>> kon...@go... >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> >> >> [image: David Nickerson on about.me] >> >> David Nickerson >> about.me/david.nickerson >> <http://about.me/david.nickerson> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- [image: David Nickerson on about.me] David Nickerson about.me/david.nickerson <http://about.me/david.nickerson> |
|
From: Matthias K. <kon...@go...> - 2016-08-04 08:58:05
|
Hi David, this sounds great. Is the c++ library supporting L1V3? I.e. https://github.com/fbergmann/libSEDML Or only the c# library? I need python bindings to L1V3. As soon as there is support for L1V3 in python via the libSEDML c++ library I will implement tool support for tellurium. Than there would be a second tool supporting it. In the process I could test if it does everything I need. Only reading the specs without having code to work with is not so productive. Matthias On Thu, Aug 4, 2016 at 10:06 AM, David Nickerson <dav...@gm...> wrote: > Hi Matthias, > > The Level 1 version 3 draft specification has been available for a couple > of years now: > http://co.mbine.org/standards/sed-ml/level-1/version-3/draft-1 - just > waiting on a second implementation (in addition to Frank's C# libSEDML > project) to test things out completely before finalising that. I just took > a quick look, and there is no explicit "what has changed" section that I > could see - but one of the main changes is the integration of data, > including the slicing. Would be good to see if those features in the > current draft spec would meet your needs in that regard. > > Otherwise, the main place to look for what people are looking at is that > google doc capturing the discussions from COMBINE last year and HARMONY > this year ( > https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). > I'm not aware of any further work toward the non-uniform time course beyond > what is in that document. There is also a bit in there on histograms. > > Cheers, > David. > > > On Thu, Aug 4, 2016 at 7:03 PM, Matthias König <kon...@go...> > wrote: > >> Hi all, >> where can I find the information about the L1V3 specification. >> I am especially looking for the parts which describe new features, i.e. >> what is decided and will definitely come, and what will change from L1V2 to >> L1V3. >> I don't want to open discussions if they are already decided on. >> >> Things I am very interested in are >> - support of NonUniformTimeCourses: is this there in L1V3, what is the >> roadmap here ? >> - integration of data, how should data be described, how to load data, >> how to use data to create simulation definitions, how to display data in >> plots >> Typical workflows are loading experimental data sets and data sets with >> parameters from files, than parametrizing the model with data from the >> files, run tasks, plot simulation data, add experimental data to plot >> - data slicing, i.e. getting subsets of the data sets (not only by index, >> but by time or other variable). I.e. I want the simulation data y for x in >> [x0, x2] (x montone data) -> this becomes important with >> NonUniformTimeCourses >> - more plots: heatmaps, contour plots, histograms >> >> Matthias >> >> >> On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < >> dav...@gm...> wrote: >> >>> Hi all, >>> >>> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >>> approaching, September 19-26 in Newcastle, UK, and the organisers are >>> now soliciting potential topics for breakout sessions. >>> >>> If you have any SED-ML topics that you would like to see raised at >>> COMBINE, please let us know. Or any topics that you think would be >>> relevant to the wider COMBINE community. >>> >>> Cheers, >>> David. >>> >>> -- >>> >>> >>> David Nickerson >>> about.me/david.nickerson >>> >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com >> kon...@go... >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > > > [image: David Nickerson on about.me] > > David Nickerson > about.me/david.nickerson > <http://about.me/david.nickerson> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: David N. <dav...@gm...> - 2016-08-04 08:06:50
|
Hi Matthias, The Level 1 version 3 draft specification has been available for a couple of years now: http://co.mbine.org/standards/sed-ml/level-1/version-3/draft-1 - just waiting on a second implementation (in addition to Frank's C# libSEDML project) to test things out completely before finalising that. I just took a quick look, and there is no explicit "what has changed" section that I could see - but one of the main changes is the integration of data, including the slicing. Would be good to see if those features in the current draft spec would meet your needs in that regard. Otherwise, the main place to look for what people are looking at is that google doc capturing the discussions from COMBINE last year and HARMONY this year ( https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit?usp=sharing). I'm not aware of any further work toward the non-uniform time course beyond what is in that document. There is also a bit in there on histograms. Cheers, David. On Thu, Aug 4, 2016 at 7:03 PM, Matthias König <kon...@go...> wrote: > Hi all, > where can I find the information about the L1V3 specification. > I am especially looking for the parts which describe new features, i.e. > what is decided and will definitely come, and what will change from L1V2 to > L1V3. > I don't want to open discussions if they are already decided on. > > Things I am very interested in are > - support of NonUniformTimeCourses: is this there in L1V3, what is the > roadmap here ? > - integration of data, how should data be described, how to load data, how > to use data to create simulation definitions, how to display data in plots > Typical workflows are loading experimental data sets and data sets with > parameters from files, than parametrizing the model with data from the > files, run tasks, plot simulation data, add experimental data to plot > - data slicing, i.e. getting subsets of the data sets (not only by index, > but by time or other variable). I.e. I want the simulation data y for x in > [x0, x2] (x montone data) -> this becomes important with > NonUniformTimeCourses > - more plots: heatmaps, contour plots, histograms > > Matthias > > > On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson < > dav...@gm...> wrote: > >> Hi all, >> >> COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly >> approaching, September 19-26 in Newcastle, UK, and the organisers are >> now soliciting potential topics for breakout sessions. >> >> If you have any SED-ML topics that you would like to see raised at >> COMBINE, please let us know. Or any topics that you think would be >> relevant to the wider COMBINE community. >> >> Cheers, >> David. >> >> -- >> >> >> David Nickerson >> about.me/david.nickerson >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > > > ------------------------------------------------------------------------------ > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- [image: David Nickerson on about.me] David Nickerson about.me/david.nickerson <http://about.me/david.nickerson> |
|
From: Matthias K. <kon...@go...> - 2016-08-04 07:03:49
|
Hi all, where can I find the information about the L1V3 specification. I am especially looking for the parts which describe new features, i.e. what is decided and will definitely come, and what will change from L1V2 to L1V3. I don't want to open discussions if they are already decided on. Things I am very interested in are - support of NonUniformTimeCourses: is this there in L1V3, what is the roadmap here ? - integration of data, how should data be described, how to load data, how to use data to create simulation definitions, how to display data in plots Typical workflows are loading experimental data sets and data sets with parameters from files, than parametrizing the model with data from the files, run tasks, plot simulation data, add experimental data to plot - data slicing, i.e. getting subsets of the data sets (not only by index, but by time or other variable). I.e. I want the simulation data y for x in [x0, x2] (x montone data) -> this becomes important with NonUniformTimeCourses - more plots: heatmaps, contour plots, histograms Matthias On Wed, Aug 3, 2016 at 12:42 PM, David Nickerson <dav...@gm...> wrote: > Hi all, > > COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly > approaching, September 19-26 in Newcastle, UK, and the organisers are > now soliciting potential topics for breakout sessions. > > If you have any SED-ML topics that you would like to see raised at > COMBINE, please let us know. Or any topics that you think would be > relevant to the wider COMBINE community. > > Cheers, > David. > > -- > > > David Nickerson > about.me/david.nickerson > > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: David N. <dav...@gm...> - 2016-08-03 20:48:11
|
---------- Forwarded message ---------- From: Golebiewski, Martin <mar...@h-...> Date: Wed, Aug 3, 2016 at 2:44 AM Subject: COMBINE Tutorial at ICSB2016: Modelling and Simulation Tools in Systems Biology - Barcelona (Spain), September 16, 2016 To: "com...@go..." <com...@go...> Cc: "com...@go..." <com...@go...> Dear COMBINE community, We will organize a COMBINE & de.NBI Tutorial 'Modelling and Simulation Tools in Systems Biology‘ on Friday,16 September, 2016 (8:30 - 13:30) as a a satellite of the 17th International Conference on Systems Biology (ICSB). Participation is free of charge and registration is open until August 25th: http://co.mbine.org/events/tutorial2016 Please note that the tutorial is at the opening day of the ICSB conference. It will finish in time to allow participants to join the ICSB opening ceremony in the afternoon. Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats. The topics will include: Model setup using different software tools and systems biology platforms Using experimental data for setting up quantitative models Parameter estimation, optimization and model fitting Simulation, analysis and visualization of biochemical models Database supported modelling: integrated data management and model databases Community standards and formats for systems biology models Covered tools, platforms and databases BioModels database: http://www.ebi.ac.uk/biomodels-main/ CellDesigner: http://www.celldesigner.org/ COPASI: http://www.copasi.org JWS Online: http://jjj.biochem.sun.ac.za/ SABIO-RK: http://sabio.h-its.org/ SEEK: http://fair-dom.org/platform/seek/ SYCAMORE: http://sycamore.eml.org You are invited to join us and/or send your students. The target audience are experimentalists and modellers with some very basic experience in modelling and simulation of biological networks and everybody who would like to learn more about the tools and standards. Please feel free to forward this invitation to anybody you would think could be interested to attend. Best regards, Martin Golebiewski (on behalf of all tutors) Martin Golebiewski HITS gGmbH Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany phone +49 6221 533 281 fax +49 6221 533 298 email mar...@h-... http://www.h-its.org _________________________________________________ Amtsgericht Mannheim / HRB 337446 Managing Director: Dr. Gesa Schönberger Scientific Director: Prof. Dr. Rebecca Wade -- You received this message because you are subscribed to the Google Groups "COMBINE coordination" group. To unsubscribe from this group and stop receiving emails from it, send an email to com...@go.... To post to this group, send email to com...@go.... To view this discussion on the web, visit https://groups.google.com/d/msgid/combine-coord/D3C67E61.2970F%25martin.golebiewski%40h-its.org. For more options, visit https://groups.google.com/d/optout. -- David Nickerson about.me/david.nickerson |
|
From: David N. <dav...@gm...> - 2016-08-03 10:43:13
|
Hi all, COMBINE 2016 (http://co.mbine.org/events/COMBINE_2016) is rapidly approaching, September 19-26 in Newcastle, UK, and the organisers are now soliciting potential topics for breakout sessions. If you have any SED-ML topics that you would like to see raised at COMBINE, please let us know. Or any topics that you think would be relevant to the wider COMBINE community. Cheers, David. -- David Nickerson about.me/david.nickerson |
|
From: Chris J. M. <my...@ec...> - 2016-07-14 14:44:43
|
-1 :-) If we don't make this change now, we never will and it will always hamper scaling. Chris Sent from my iPhone > On Jul 14, 2016, at 12:59 AM, Matthias König <kon...@go...> wrote: > > +1 for no change > >> On Wed, Jul 13, 2016 at 8:56 PM, Frank T. Bergmann <fbe...@ca...> wrote: >> i agree, not changing anything seems to be the right thing for me as well. >> >> Frank >> >>> On Wed, Jul 13, 2016 at 12:18 AM, David Nickerson <dav...@gm...> wrote: >>> I'd have to say that at this point I'm not really seeing any super-strong cases for either approach. Both Chris' and Matthias' use-cases seem equally valid, but could both be solved in the implementation if the spec didn't change/changed. The uniqueness or non-uniqueness in the spec just makes things more convenient in each case. >>> >>> For myself, I guess I would currently be leaning toward Herbert's view that this isn't really a critical change and we're better off putting resources into other proposals and implementations. >>> >>> Cheers, >>> David. >>> >>> >>> >>>> On Wed, Jul 13, 2016 at 2:18 AM, Matthias König <kon...@go...> wrote: >>>> Hi Chris, >>>> you are right. I could also do this via looking in the right list if it is only about resolving the sedml structure. >>>> >>>> But I am not only using the ids for looking up the related objects in the SEDML, but for instance for instance I am creating a network graph from the sedml xml structure where I require to have unique node ids for all nodes. >>>> Because metaids are often not set I rely on the unique ids for node ids. >>>> >>>> M >>>> >>>> >>>> >>>> >>>> >>>>> On Tue, Jul 12, 2016 at 1:12 AM, Chris Myers <my...@ec...> wrote: >>>>> Hi Dave, >>>>> >>>>> SED-ML already does support this. Every object has both a metaId and an id. The metaId is required to be unique in the document. So, if it is important to a software to have unique ids, that software could assign all metaIds a unique value and use the metaIds to look things up. >>>>> >>>>> As for the referencing syntax, I think this is good, but I wonder if we can avoid the tags. If we include them, it is getting quite close to XPath. The reason you would need the tags is if the scoping was very tight. For example, a DataGenerator has Variables and Parameters. If they each are scoped separately, they could have identical ids, and you would need the tags. However, if all child objects are in the same scope, then you would not be allowed to have the same id for a Variable and Parameter in the same DataGenerator, so you would not need the tags. Actually, we certainly must have Variable and Parameter in the same scope, since they can both be referred to in the Math element. However, a Variable from a different DataGenerator cannot, so it is not needed for Variables in two different DataGenerators to be in the same scope. >>>>> >>>>> Cheers, >>>>> >>>>> Chris >>>>> >>>>>> On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au...> wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>> Could this discussion be resolved by extending SED-ML to include a `name` attribute that is unique amongst a given class of XML elements (and keep `id` as unique within a document)?? >>>>>> >>>>>> Then what about combining an element's tag name with the value of its name attribute (if it has one) with '.' and then combining these named tags with `/` to produce relative URIs? As an example, in the XML document: >>>>>> >>>>>> <A> >>>>>> <B name="name_b1"> >>>>>> <C> >>>>>> <D name="name_d"/> >>>>>> </C> >>>>>> </B> >>>>>> <B name="name_b2"> >>>>>> <C> >>>>>> <D name="name_d" id="123"/> >>>>>> </C> >>>>>> </B> >>>>>> </A> >>>>>> >>>>>> the element with an id of "123" could be referred to both as `#123` or `/A/B.name_b2/C/D.name_d`. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Dave >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> On 11/07/16 7:45 PM, Matthias König wrote: >>>>>>> Hi Chris, >>>>>>> I am using the python bindings to libsedml. >>>>>>> Sorry for the confusion with the model. >>>>>>> >>>>>>> Here the correct example using the SedDocument (code just for demonstration, not working example). >>>>>>> Via the function one can get the element based on the id independent of the class. This is quit useful if one does not want to question all the listOfs. >>>>>>> I use this a lot in libsbml which has an analogue function, but also in libsedml to quickly O(1) lookup an object without the need to look in all listOfs. >>>>>>> >>>>>>> import libsedml >>>>>>> >>>>>>> sid = "abd" >>>>>>> doc = libsedml.SedDocument() >>>>>>> element = doc.getElementBySId(sid) >>>>>>> Matthias >>>>>>> >>>>>>>> On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec...> wrote: >>>>>>>> Agreed. I would just like to gauge the pros and cons. >>>>>>>> >>>>>>>> I’m not sure what you mean by model = Model(). Is this just the Model elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, and there Model is only the Model elements of SED-ML. Within any single class, there would still be unique ids. >>>>>>>> >>>>>>>> Chris >>>>>>>> >>>>>>>> >>>>>>>>> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go...> wrote: >>>>>>>>> >>>>>>>>> Hi Chris, >>>>>>>>> the method is >>>>>>>>> model = Model() >>>>>>>>> model.getElementBySId(sid) >>>>>>>>> I use this method to get my unique objects based on unique ids and to store things in HashMaps with ids as keys. >>>>>>>>> As soon as keys, i.e. ids are not unique anymore, the objects in the hashmaps are overwritten (this is a silent difficult bug, because all code will work, but will not give the correct results). >>>>>>>>> Anybody storing anything for lookup via id will have similar issues. >>>>>>>>> >>>>>>>>> @Chris I don't have a problem to rewrite code, but I fear similar lookups via id will be part of many code bases. So the unique id constraint should only be changed if the advantages are much larger than the costs. >>>>>>>>> >>>>>>>>> Matthias >>>>>>>>> >>>>>>>>> >>>>>>>>> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec...> wrote: >>>>>>>>>> Lucian, if you had read the whole message, I do mention what Matthias said. My concern with his statement is I’m not sure why he is using Id’s for annotations. In SBML, they are linked to meta-ids, which would still be globally unique. If this is the only use by anyone in the community of the global unique property, then I still think this is worthy of discussion. Namely, is using id’s in this way correct? If not, is there another use case for global ids that is important to people? If so, how much effort is it to loosen this requirement. >>>>>>>>>> >>>>>>>>>> Maintaining global id uniqueness in a large document places a huge burden on software. There is a reason why programming languages use scoping rules, so you don’t need global variable uniqueness. With this rule, every time you mint an id, you must check if it is in use somewhere else, and if so have a scheme to try again. Currently, there is no easy way to do this in jlibSEDML. >>>>>>>>>> >>>>>>>>>> I think the jury is still out on whether this rule adds more burden on software developers than not having this rule. Having this rule means my code is broken, and there is no clean and easy way to fix it currently. There are not a lot of SED-ML implementations yet, so if we are to ever consider changing this rule, it should be sooner than later before more implementations come to rely on it. >>>>>>>>>> >>>>>>>>>> If having this rule helps more people than it hurts, we will clearly keep it, but if it is the other way around, we need to consider removing it. So far, Matthias has explained how his code relies on the rule, and I’ve explained that my code is flawed due to this rule. How do others feel about the rule and its impact on their code? >>>>>>>>>> >>>>>>>>>> Chris >>>>>>>>>> >>>>>>>>>>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm...> wrote: >>>>>>>>>>> >>>>>>>>>>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec...> wrote: >>>>>>>>>>> > >>>>>>>>>>> > But will it really break things? >>>>>>>>>>> >>>>>>>>>>> Yes, Matthias said it would break his code. >>>>>>>>>>> >>>>>>>>>>> -Lucian >>>>>>>>>>> >>>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>>>>>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>>>>>>>> present their vision of the future. This family event has something for >>>>>>>>>>> everyone, including kids. Get more information and register today. >>>>>>>>>>> http://sdm.link/attshape_______________________________________________ >>>>>>>>>>> SED-ML-discuss mailing list >>>>>>>>>>> SED...@li... >>>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>>>>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>>>>>>> present their vision of the future. This family event has something for >>>>>>>>>> everyone, including kids. Get more information and register today. >>>>>>>>>> http://sdm.link/attshape >>>>>>>>>> _______________________________________________ >>>>>>>>>> SED-ML-discuss mailing list >>>>>>>>>> SED...@li... >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Matthias König >>>>>>>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>>>>>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>>>>>>> https://www.livermetabolism.com >>>>>>>>> kon...@go... >>>>>>>>> Tel: +49 30 20938450 >>>>>>>>> Tel: +49 176 81168480 >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>>>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>>>>>> present their vision of the future. This family event has something for >>>>>>>>> everyone, including kids. Get more information and register today. >>>>>>>>> http://sdm.link/attshape_______________________________________________ >>>>>>>>> SED-ML-discuss mailing list >>>>>>>>> SED...@li... >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>>>>> present their vision of the future. This family event has something for >>>>>>>> everyone, including kids. Get more information and register today. >>>>>>>> http://sdm.link/attshape >>>>>>>> _______________________________________________ >>>>>>>> SED-ML-discuss mailing list >>>>>>>> SED...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Matthias König >>>>>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>>>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>>>>> https://www.livermetabolism.com >>>>>>> kon...@go... >>>>>>> Tel: +49 30 20938450 >>>>>>> Tel: +49 176 81168480 >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>>>> present their vision of the future. This family event has something for >>>>>>> everyone, including kids. Get more information and register today. >>>>>>> http://sdm.link/attshape >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> SED-ML-discuss mailing list >>>>>>> SED...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>>> present their vision of the future. This family event has something for >>>>>> everyone, including kids. Get more information and register today. >>>>>> http://sdm.link/attshape_______________________________________________ >>>>>> SED-ML-discuss mailing list >>>>>> SED...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >>>>> patterns at an interface-level. Reveals which users, apps, and protocols are >>>>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>>>> J-Flow, sFlow and other flows. Make informed decisions using capacity planning >>>>> reports.http://sdm.link/zohodev2dev >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>> >>>> >>>> >>>> -- >>>> Matthias König >>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>> https://www.livermetabolism.com >>>> kon...@go... >>>> Tel: +49 30 20938450 >>>> Tel: +49 176 81168480 >>>> >>>> ------------------------------------------------------------------------------ >>>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >>>> patterns at an interface-level. Reveals which users, apps, and protocols are >>>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>>> J-Flow, sFlow and other flows. Make informed decisions using capacity planning >>>> reports.http://sdm.link/zohodev2dev >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>> >>> >>> >>> -- >>> >>> >>> >>> David Nickerson >>> about.me/david.nickerson >>> >>> >>> ------------------------------------------------------------------------------ >>> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >>> patterns at an interface-level. Reveals which users, apps, and protocols are >>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>> J-Flow, sFlow and other flows. Make informed decisions using capacity planning >>> reports.http://sdm.link/zohodev2dev >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic >> patterns at an interface-level. Reveals which users, apps, and protocols are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity planning >> reports.http://sdm.link/zohodev2dev >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
|
From: Matthias K. <kon...@go...> - 2016-07-14 07:59:43
|
+1 for no change On Wed, Jul 13, 2016 at 8:56 PM, Frank T. Bergmann <fbe...@ca...> wrote: > i agree, not changing anything seems to be the right thing for me as well. > > Frank > > On Wed, Jul 13, 2016 at 12:18 AM, David Nickerson < > dav...@gm...> wrote: > >> I'd have to say that at this point I'm not really seeing any super-strong >> cases for either approach. Both Chris' and Matthias' use-cases seem equally >> valid, but could both be solved in the implementation if the spec didn't >> change/changed. The uniqueness or non-uniqueness in the spec just makes >> things more convenient in each case. >> >> For myself, I guess I would currently be leaning toward Herbert's view >> that this isn't really a critical change and we're better off putting >> resources into other proposals and implementations. >> >> Cheers, >> David. >> >> >> >> On Wed, Jul 13, 2016 at 2:18 AM, Matthias König <kon...@go... >> > wrote: >> >>> Hi Chris, >>> you are right. I could also do this via looking in the right list if it >>> is only about resolving the sedml structure. >>> >>> But I am not only using the ids for looking up the related objects in >>> the SEDML, but for instance for instance I am creating a network graph from >>> the sedml xml structure where I require to have unique node ids for all >>> nodes. >>> Because metaids are often not set I rely on the unique ids for node ids. >>> >>> M >>> >>> >>> >>> >>> >>> On Tue, Jul 12, 2016 at 1:12 AM, Chris Myers <my...@ec...> wrote: >>> >>>> Hi Dave, >>>> >>>> SED-ML already does support this. Every object has both a metaId and >>>> an id. The metaId is required to be unique in the document. So, if it is >>>> important to a software to have unique ids, that software could assign all >>>> metaIds a unique value and use the metaIds to look things up. >>>> >>>> As for the referencing syntax, I think this is good, but I wonder if we >>>> can avoid the tags. If we include them, it is getting quite close to >>>> XPath. The reason you would need the tags is if the scoping was very >>>> tight. For example, a DataGenerator has Variables and Parameters. If they >>>> each are scoped separately, they could have identical ids, and you would >>>> need the tags. However, if all child objects are in the same scope, then >>>> you would not be allowed to have the same id for a Variable and Parameter >>>> in the same DataGenerator, so you would not need the tags. Actually, we >>>> certainly must have Variable and Parameter in the same scope, since they >>>> can both be referred to in the Math element. However, a Variable from a >>>> different DataGenerator cannot, so it is not needed for Variables in two >>>> different DataGenerators to be in the same scope. >>>> >>>> Cheers, >>>> >>>> Chris >>>> >>>> On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au...> >>>> wrote: >>>> >>>> Hi, >>>> >>>> Could this discussion be resolved by extending SED-ML to include a >>>> `name` attribute that is unique amongst a given class of XML elements (and >>>> keep `id` as unique within a document)?? >>>> >>>> Then what about combining an element's tag name with the value of its >>>> name attribute (if it has one) with '.' and then combining these named tags >>>> with `/` to produce relative URIs? As an example, in the XML document: >>>> >>>> <A> >>>> <B name="name_b1"> >>>> <C> >>>> <D name="name_d"/> >>>> </C> >>>> </B> >>>> <B name="name_b2"> >>>> <C> >>>> <D name="name_d" id="123"/> >>>> </C> >>>> </B> >>>> </A> >>>> >>>> the element with an id of "123" could be referred to both as `#123` or >>>> `/A/B.name_b2/C/D.name_d`. >>>> >>>> >>>> >>>> >>>> Best regards, >>>> >>>> Dave >>>> >>>> >>>> >>>> >>>> >>>> On 11/07/16 7:45 PM, Matthias König wrote: >>>> >>>> Hi Chris, >>>> I am using the python bindings to libsedml. >>>> Sorry for the confusion with the model. >>>> >>>> Here the correct example using the SedDocument (code just for >>>> demonstration, not working example). >>>> Via the function one can get the element based on the id independent of >>>> the class. This is quit useful if one does not want to question all the >>>> listOfs. >>>> I use this a lot in libsbml which has an analogue function, but also in >>>> libsedml to quickly O(1) lookup an object without the need to look in all >>>> listOfs. >>>> >>>> import libsedml >>>> >>>> sid = "abd"doc = libsedml.SedDocument() >>>> element = doc.getElementBySId(sid) >>>> >>>> Matthias >>>> >>>> On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec...> >>>> wrote: >>>> >>>>> Agreed. I would just like to gauge the pros and cons. >>>>> >>>>> I’m not sure what you mean by model = Model(). Is this just the Model >>>>> elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, >>>>> and there Model is only the Model elements of SED-ML. Within any single >>>>> class, there would still be unique ids. >>>>> >>>>> Chris >>>>> >>>>> >>>>> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go...> >>>>> wrote: >>>>> >>>>> Hi Chris, >>>>> the method is >>>>> >>>>> model = Model()model.getElementBySId(sid) >>>>> >>>>> I use this method to get my unique objects based on unique ids and to >>>>> store things in HashMaps with ids as keys. >>>>> As soon as keys, i.e. ids are not unique anymore, the objects in the >>>>> hashmaps are overwritten (this is a silent difficult bug, because all code >>>>> will work, but will not give the correct results). >>>>> Anybody storing anything for lookup via id will have similar issues. >>>>> >>>>> @Chris I don't have a problem to rewrite code, but I fear similar >>>>> lookups via id will be part of many code bases. So the unique id constraint >>>>> should only be changed if the advantages are much larger than the costs. >>>>> >>>>> Matthias >>>>> >>>>> >>>>> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec...> >>>>> wrote: >>>>> >>>>>> Lucian, if you had read the whole message, I do mention what Matthias >>>>>> said. My concern with his statement is I’m not sure why he is using Id’s >>>>>> for annotations. In SBML, they are linked to meta-ids, which would still >>>>>> be globally unique. If this is the only use by anyone in the community of >>>>>> the global unique property, then I still think this is worthy of >>>>>> discussion. Namely, is using id’s in this way correct? If not, is there >>>>>> another use case for global ids that is important to people? If so, how >>>>>> much effort is it to loosen this requirement. >>>>>> >>>>>> Maintaining global id uniqueness in a large document places a huge >>>>>> burden on software. There is a reason why programming languages use scoping >>>>>> rules, so you don’t need global variable uniqueness. With this rule, every >>>>>> time you mint an id, you must check if it is in use somewhere else, and if >>>>>> so have a scheme to try again. Currently, there is no easy way to do this >>>>>> in jlibSEDML. >>>>>> >>>>>> I think the jury is still out on whether this rule adds more burden >>>>>> on software developers than not having this rule. Having this rule means >>>>>> my code is broken, and there is no clean and easy way to fix it currently. >>>>>> There are not a lot of SED-ML implementations yet, so if we are to ever >>>>>> consider changing this rule, it should be sooner than later before more >>>>>> implementations come to rely on it. >>>>>> >>>>>> If having this rule helps more people than it hurts, we will clearly >>>>>> keep it, but if it is the other way around, we need to consider removing >>>>>> it. So far, Matthias has explained how his code relies on the rule, and >>>>>> I’ve explained that my code is flawed due to this rule. How do others feel >>>>>> about the rule and its impact on their code? >>>>>> >>>>>> Chris >>>>>> >>>>>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm...> >>>>>> wrote: >>>>>> >>>>>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec...> wrote: >>>>>> > >>>>>> > But will it really break things? >>>>>> >>>>>> Yes, Matthias said it would break his code. >>>>>> >>>>>> -Lucian >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in >>>>>> San >>>>>> Francisco, CA to explore cutting-edge tech and listen to tech >>>>>> luminaries >>>>>> present their vision of the future. This family event has something >>>>>> for >>>>>> everyone, including kids. Get more information and register today. >>>>>> >>>>>> http://sdm.link/attshape_______________________________________________ >>>>>> SED-ML-discuss mailing list >>>>>> SED...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in >>>>>> San >>>>>> Francisco, CA to explore cutting-edge tech and listen to tech >>>>>> luminaries >>>>>> present their vision of the future. This family event has something >>>>>> for >>>>>> everyone, including kids. Get more information and register today. >>>>>> http://sdm.link/attshape >>>>>> _______________________________________________ >>>>>> SED-ML-discuss mailing list >>>>>> SED...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Matthias König >>>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>>> https://www.livermetabolism.com >>>>> kon...@go... >>>>> Tel: +49 30 20938450 >>>>> Tel: +49 176 81168480 <%2B49%20176%2081168480> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>> Francisco, CA to explore cutting-edge tech and listen to tech >>>>> luminaries >>>>> present their vision of the future. This family event has something for >>>>> everyone, including kids. Get more information and register today. >>>>> http://sdm.link/attshape_______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>> Francisco, CA to explore cutting-edge tech and listen to tech >>>>> luminaries >>>>> present their vision of the future. This family event has something for >>>>> everyone, including kids. Get more information and register today. >>>>> http://sdm.link/attshape >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>> >>>> >>>> -- >>>> Matthias König >>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>> https://www.livermetabolism.com >>>> kon...@go... >>>> Tel: +49 30 20938450 >>>> Tel: +49 176 81168480 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today.http://sdm.link/attshape >>>> >>>> >>>> >>>> _______________________________________________ >>>> SED-ML-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape_______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> What NetFlow Analyzer can do for you? Monitors network bandwidth and >>>> traffic >>>> patterns at an interface-level. Reveals which users, apps, and >>>> protocols are >>>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>>> J-Flow, sFlow and other flows. Make informed decisions using capacity >>>> planning >>>> reports.http://sdm.link/zohodev2dev >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com >>> kon...@go... >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 >>> >>> >>> ------------------------------------------------------------------------------ >>> What NetFlow Analyzer can do for you? Monitors network bandwidth and >>> traffic >>> patterns at an interface-level. Reveals which users, apps, and protocols >>> are >>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>> J-Flow, sFlow and other flows. Make informed decisions using capacity >>> planning >>> reports.http://sdm.link/zohodev2dev >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> >> >> [image: David Nickerson on about.me] >> >> David Nickerson >> about.me/david.nickerson >> <http://about.me/david.nickerson> >> >> >> ------------------------------------------------------------------------------ >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: Frank T. B. <fbe...@ca...> - 2016-07-13 18:56:27
|
i agree, not changing anything seems to be the right thing for me as well. Frank On Wed, Jul 13, 2016 at 12:18 AM, David Nickerson <dav...@gm... > wrote: > I'd have to say that at this point I'm not really seeing any super-strong > cases for either approach. Both Chris' and Matthias' use-cases seem equally > valid, but could both be solved in the implementation if the spec didn't > change/changed. The uniqueness or non-uniqueness in the spec just makes > things more convenient in each case. > > For myself, I guess I would currently be leaning toward Herbert's view > that this isn't really a critical change and we're better off putting > resources into other proposals and implementations. > > Cheers, > David. > > > > On Wed, Jul 13, 2016 at 2:18 AM, Matthias König <kon...@go...> > wrote: > >> Hi Chris, >> you are right. I could also do this via looking in the right list if it >> is only about resolving the sedml structure. >> >> But I am not only using the ids for looking up the related objects in the >> SEDML, but for instance for instance I am creating a network graph from the >> sedml xml structure where I require to have unique node ids for all nodes. >> Because metaids are often not set I rely on the unique ids for node ids. >> >> M >> >> >> >> >> >> On Tue, Jul 12, 2016 at 1:12 AM, Chris Myers <my...@ec...> wrote: >> >>> Hi Dave, >>> >>> SED-ML already does support this. Every object has both a metaId and an >>> id. The metaId is required to be unique in the document. So, if it is >>> important to a software to have unique ids, that software could assign all >>> metaIds a unique value and use the metaIds to look things up. >>> >>> As for the referencing syntax, I think this is good, but I wonder if we >>> can avoid the tags. If we include them, it is getting quite close to >>> XPath. The reason you would need the tags is if the scoping was very >>> tight. For example, a DataGenerator has Variables and Parameters. If they >>> each are scoped separately, they could have identical ids, and you would >>> need the tags. However, if all child objects are in the same scope, then >>> you would not be allowed to have the same id for a Variable and Parameter >>> in the same DataGenerator, so you would not need the tags. Actually, we >>> certainly must have Variable and Parameter in the same scope, since they >>> can both be referred to in the Math element. However, a Variable from a >>> different DataGenerator cannot, so it is not needed for Variables in two >>> different DataGenerators to be in the same scope. >>> >>> Cheers, >>> >>> Chris >>> >>> On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au...> >>> wrote: >>> >>> Hi, >>> >>> Could this discussion be resolved by extending SED-ML to include a >>> `name` attribute that is unique amongst a given class of XML elements (and >>> keep `id` as unique within a document)?? >>> >>> Then what about combining an element's tag name with the value of its >>> name attribute (if it has one) with '.' and then combining these named tags >>> with `/` to produce relative URIs? As an example, in the XML document: >>> >>> <A> >>> <B name="name_b1"> >>> <C> >>> <D name="name_d"/> >>> </C> >>> </B> >>> <B name="name_b2"> >>> <C> >>> <D name="name_d" id="123"/> >>> </C> >>> </B> >>> </A> >>> >>> the element with an id of "123" could be referred to both as `#123` or >>> `/A/B.name_b2/C/D.name_d`. >>> >>> >>> >>> >>> Best regards, >>> >>> Dave >>> >>> >>> >>> >>> >>> On 11/07/16 7:45 PM, Matthias König wrote: >>> >>> Hi Chris, >>> I am using the python bindings to libsedml. >>> Sorry for the confusion with the model. >>> >>> Here the correct example using the SedDocument (code just for >>> demonstration, not working example). >>> Via the function one can get the element based on the id independent of >>> the class. This is quit useful if one does not want to question all the >>> listOfs. >>> I use this a lot in libsbml which has an analogue function, but also in >>> libsedml to quickly O(1) lookup an object without the need to look in all >>> listOfs. >>> >>> import libsedml >>> >>> sid = "abd"doc = libsedml.SedDocument() >>> element = doc.getElementBySId(sid) >>> >>> Matthias >>> >>> On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec...> wrote: >>> >>>> Agreed. I would just like to gauge the pros and cons. >>>> >>>> I’m not sure what you mean by model = Model(). Is this just the Model >>>> elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, >>>> and there Model is only the Model elements of SED-ML. Within any single >>>> class, there would still be unique ids. >>>> >>>> Chris >>>> >>>> >>>> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go...> >>>> wrote: >>>> >>>> Hi Chris, >>>> the method is >>>> >>>> model = Model()model.getElementBySId(sid) >>>> >>>> I use this method to get my unique objects based on unique ids and to >>>> store things in HashMaps with ids as keys. >>>> As soon as keys, i.e. ids are not unique anymore, the objects in the >>>> hashmaps are overwritten (this is a silent difficult bug, because all code >>>> will work, but will not give the correct results). >>>> Anybody storing anything for lookup via id will have similar issues. >>>> >>>> @Chris I don't have a problem to rewrite code, but I fear similar >>>> lookups via id will be part of many code bases. So the unique id constraint >>>> should only be changed if the advantages are much larger than the costs. >>>> >>>> Matthias >>>> >>>> >>>> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec...> >>>> wrote: >>>> >>>>> Lucian, if you had read the whole message, I do mention what Matthias >>>>> said. My concern with his statement is I’m not sure why he is using Id’s >>>>> for annotations. In SBML, they are linked to meta-ids, which would still >>>>> be globally unique. If this is the only use by anyone in the community of >>>>> the global unique property, then I still think this is worthy of >>>>> discussion. Namely, is using id’s in this way correct? If not, is there >>>>> another use case for global ids that is important to people? If so, how >>>>> much effort is it to loosen this requirement. >>>>> >>>>> Maintaining global id uniqueness in a large document places a huge >>>>> burden on software. There is a reason why programming languages use scoping >>>>> rules, so you don’t need global variable uniqueness. With this rule, every >>>>> time you mint an id, you must check if it is in use somewhere else, and if >>>>> so have a scheme to try again. Currently, there is no easy way to do this >>>>> in jlibSEDML. >>>>> >>>>> I think the jury is still out on whether this rule adds more burden on >>>>> software developers than not having this rule. Having this rule means my >>>>> code is broken, and there is no clean and easy way to fix it currently. >>>>> There are not a lot of SED-ML implementations yet, so if we are to ever >>>>> consider changing this rule, it should be sooner than later before more >>>>> implementations come to rely on it. >>>>> >>>>> If having this rule helps more people than it hurts, we will clearly >>>>> keep it, but if it is the other way around, we need to consider removing >>>>> it. So far, Matthias has explained how his code relies on the rule, and >>>>> I’ve explained that my code is flawed due to this rule. How do others feel >>>>> about the rule and its impact on their code? >>>>> >>>>> Chris >>>>> >>>>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm...> >>>>> wrote: >>>>> >>>>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec...> wrote: >>>>> > >>>>> > But will it really break things? >>>>> >>>>> Yes, Matthias said it would break his code. >>>>> >>>>> -Lucian >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>> Francisco, CA to explore cutting-edge tech and listen to tech >>>>> luminaries >>>>> present their vision of the future. This family event has something for >>>>> everyone, including kids. Get more information and register today. >>>>> http://sdm.link/attshape_______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>> Francisco, CA to explore cutting-edge tech and listen to tech >>>>> luminaries >>>>> present their vision of the future. This family event has something for >>>>> everyone, including kids. Get more information and register today. >>>>> http://sdm.link/attshape >>>>> _______________________________________________ >>>>> SED-ML-discuss mailing list >>>>> SED...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>>> >>>>> >>>> >>>> >>>> -- >>>> Matthias König >>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>> https://www.livermetabolism.com >>>> kon...@go... >>>> Tel: +49 30 20938450 >>>> Tel: +49 176 81168480 <%2B49%20176%2081168480> >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape_______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com >>> kon...@go... >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today.http://sdm.link/attshape >>> >>> >>> >>> _______________________________________________ >>> SED-ML-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape_______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> What NetFlow Analyzer can do for you? Monitors network bandwidth and >>> traffic >>> patterns at an interface-level. Reveals which users, apps, and protocols >>> are >>> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >>> J-Flow, sFlow and other flows. Make informed decisions using capacity >>> planning >>> reports.http://sdm.link/zohodev2dev >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com >> kon...@go... >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 >> >> >> ------------------------------------------------------------------------------ >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > > > [image: David Nickerson on about.me] > > David Nickerson > about.me/david.nickerson > <http://about.me/david.nickerson> > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
|
From: Chris M. <my...@ec...> - 2016-07-12 23:38:12
|
Hi, I’ve added more comments to the document below based on our experience mapping SED-ML to iBioSim. Version 2.9 of iBioSim found here: http://www.async.ece.utah.edu/ibiosim <http://www.async.ece.utah.edu/ibiosim> has substantially improved SED-ML support though many things have to be encoded in annotations as described in the document linked below. We can import a SED-ML with associated models or a SED-ML archive. Each iBioSim project has a single SED-ML file that encodes the AnalysisViews as Tasks and graphs as Outputs. This SED-ML file can be found in the project directory as <projectName>.sedml. The main items that iBioSim does not support are: 1) Math in DataGenerators other than simple <ci> terms. 2) RepeatedTasks except that we do allow stochastic runs to be repeated using a Task with an AlgorithmParameter specifying number of runs (mis-using KISAO number of samples term for this, need a new term). 3) Steady-state simulation (except for FBA which is supported). 4) 3D Plots. Comments are very welcome. Cheers, Chris > On Jun 7, 2016, at 6:13 PM, David Nickerson <dav...@gm...> wrote: > > Hi all, > > A reminder that the SED-ML discussion at COMBINE last year is > available here: > https://docs.google.com/document/d/1dgm6hGCK8MbxlrkXY-fdU1Y9UTph4G7WQ_Xjhq6HipU/edit > > Cheers, > David. > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
|
From: Chris M. <my...@ec...> - 2016-07-12 22:34:33
|
We have the same issue with SBML. We need the metaIds to do annotations. So, when we open an SBML file, we assign unique metaIds to every SBML element first thing. This approach could likely solve your issue too. Chris > On Jul 12, 2016, at 8:18 AM, Matthias König <kon...@go...> wrote: > > Hi Chris, > you are right. I could also do this via looking in the right list if it is only about resolving the sedml structure. > > But I am not only using the ids for looking up the related objects in the SEDML, but for instance for instance I am creating a network graph from the sedml xml structure where I require to have unique node ids for all nodes. > Because metaids are often not set I rely on the unique ids for node ids. > > M > > > > > > On Tue, Jul 12, 2016 at 1:12 AM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: > Hi Dave, > > SED-ML already does support this. Every object has both a metaId and an id. The metaId is required to be unique in the document. So, if it is important to a software to have unique ids, that software could assign all metaIds a unique value and use the metaIds to look things up. > > As for the referencing syntax, I think this is good, but I wonder if we can avoid the tags. If we include them, it is getting quite close to XPath. The reason you would need the tags is if the scoping was very tight. For example, a DataGenerator has Variables and Parameters. If they each are scoped separately, they could have identical ids, and you would need the tags. However, if all child objects are in the same scope, then you would not be allowed to have the same id for a Variable and Parameter in the same DataGenerator, so you would not need the tags. Actually, we certainly must have Variable and Parameter in the same scope, since they can both be referred to in the Math element. However, a Variable from a different DataGenerator cannot, so it is not needed for Variables in two different DataGenerators to be in the same scope. > > Cheers, > > Chris > >> On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au... <mailto:d.b...@au...>> wrote: >> >> Hi, >> >> Could this discussion be resolved by extending SED-ML to include a `name` attribute that is unique amongst a given class of XML elements (and keep `id` as unique within a document)?? >> >> Then what about combining an element's tag name with the value of its name attribute (if it has one) with '.' and then combining these named tags with `/` to produce relative URIs? As an example, in the XML document: >> >> <A> >> <B name="name_b1"> >> <C> >> <D name="name_d"/> >> </C> >> </B> >> <B name="name_b2"> >> <C> >> <D name="name_d" id="123"/> >> </C> >> </B> >> </A> >> >> the element with an id of "123" could be referred to both as `#123` or `/A/B.name_b2/C/D.name_d`. >> >> >> >> >> Best regards, >> >> Dave >> >> >> >> >> >> On 11/07/16 7:45 PM, Matthias König wrote: >>> Hi Chris, >>> I am using the python bindings to libsedml. >>> Sorry for the confusion with the model. >>> >>> Here the correct example using the SedDocument (code just for demonstration, not working example). >>> Via the function one can get the element based on the id independent of the class. This is quit useful if one does not want to question all the listOfs. >>> I use this a lot in libsbml which has an analogue function, but also in libsedml to quickly O(1) lookup an object without the need to look in all listOfs. >>> >>> import libsedml >>> >>> sid = "abd" >>> doc = libsedml.SedDocument() >>> element = doc.getElementBySId(sid) >>> Matthias >>> >>> On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: >>> Agreed. I would just like to gauge the pros and cons. >>> >>> I’m not sure what you mean by model = Model(). Is this just the Model elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, and there Model is only the Model elements of SED-ML. Within any single class, there would still be unique ids. >>> >>> Chris >>> >>> >>>> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go... <mailto:kon...@go...>> wrote: >>>> >>>> Hi Chris, >>>> the method is >>>> model = Model() >>>> model.getElementBySId(sid) >>>> I use this method to get my unique objects based on unique ids and to store things in HashMaps with ids as keys. >>>> As soon as keys, i.e. ids are not unique anymore, the objects in the hashmaps are overwritten (this is a silent difficult bug, because all code will work, but will not give the correct results). >>>> Anybody storing anything for lookup via id will have similar issues. >>>> >>>> @Chris I don't have a problem to rewrite code, but I fear similar lookups via id will be part of many code bases. So the unique id constraint should only be changed if the advantages are much larger than the costs. >>>> >>>> Matthias >>>> >>>> >>>> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: >>>> Lucian, if you had read the whole message, I do mention what Matthias said. My concern with his statement is I’m not sure why he is using Id’s for annotations. In SBML, they are linked to meta-ids, which would still be globally unique. If this is the only use by anyone in the community of the global unique property, then I still think this is worthy of discussion. Namely, is using id’s in this way correct? If not, is there another use case for global ids that is important to people? If so, how much effort is it to loosen this requirement. >>>> >>>> Maintaining global id uniqueness in a large document places a huge burden on software. There is a reason why programming languages use scoping rules, so you don’t need global variable uniqueness. With this rule, every time you mint an id, you must check if it is in use somewhere else, and if so have a scheme to try again. Currently, there is no easy way to do this in jlibSEDML. >>>> >>>> I think the jury is still out on whether this rule adds more burden on software developers than not having this rule. Having this rule means my code is broken, and there is no clean and easy way to fix it currently. There are not a lot of SED-ML implementations yet, so if we are to ever consider changing this rule, it should be sooner than later before more implementations come to rely on it. >>>> >>>> If having this rule helps more people than it hurts, we will clearly keep it, but if it is the other way around, we need to consider removing it. So far, Matthias has explained how his code relies on the rule, and I’ve explained that my code is flawed due to this rule. How do others feel about the rule and its impact on their code? >>>> >>>> Chris >>>> >>>>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: >>>>> >>>>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec... <mailto:my...@ec...>> wrote: >>>>> > >>>>> > But will it really break things? >>>>> >>>>> Yes, Matthias said it would break his code. >>>>> >>>>> -Lucian >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>>> present their vision of the future. This family event has something for >>>>> everyone, including kids. Get more information and register today. >>>>> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >>>>> SED-ML-discuss mailing list >>>>> SED...@li... <mailto:SED...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape <http://sdm.link/attshape> >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... <mailto:SED...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>>> >>>> >>>> >>>> >>>> -- >>>> Matthias König >>>> Junior Group Leader LiSym - Systems Medicine of the Liver >>>> Humboldt-University Berlin, Institute for Theoretical Biology >>>> https://www.livermetabolism.com <https://www.livermetabolism.com/> >>>> kon...@go... <mailto:kon...@go...> >>>> Tel: +49 30 20938450 >>>> Tel: +49 176 81168480 <tel:%2B49%20176%2081168480> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >>>> SED-ML-discuss mailing list >>>> SED...@li... <mailto:SED...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape <http://sdm.link/attshape> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... <mailto:SED...@li...> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>> >>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com <https://www.livermetabolism.com/> >>> kon...@go... <mailto:kon...@go...> >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 <tel:%2B49%20176%2081168480> >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape <http://sdm.link/attshape> >>> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... <mailto:SED...@li...> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev <http://sdm.link/zohodev2dev> > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com <https://www.livermetabolism.com/> > kon...@go... <mailto:kon...@go...> > Tel: +49 30 20938450 > Tel: +49 176 81168480 > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
|
From: David N. <dav...@gm...> - 2016-07-12 22:19:21
|
I'd have to say that at this point I'm not really seeing any super-strong cases for either approach. Both Chris' and Matthias' use-cases seem equally valid, but could both be solved in the implementation if the spec didn't change/changed. The uniqueness or non-uniqueness in the spec just makes things more convenient in each case. For myself, I guess I would currently be leaning toward Herbert's view that this isn't really a critical change and we're better off putting resources into other proposals and implementations. Cheers, David. On Wed, Jul 13, 2016 at 2:18 AM, Matthias König <kon...@go...> wrote: > Hi Chris, > you are right. I could also do this via looking in the right list if it is > only about resolving the sedml structure. > > But I am not only using the ids for looking up the related objects in the > SEDML, but for instance for instance I am creating a network graph from the > sedml xml structure where I require to have unique node ids for all nodes. > Because metaids are often not set I rely on the unique ids for node ids. > > M > > > > > > On Tue, Jul 12, 2016 at 1:12 AM, Chris Myers <my...@ec...> wrote: > >> Hi Dave, >> >> SED-ML already does support this. Every object has both a metaId and an >> id. The metaId is required to be unique in the document. So, if it is >> important to a software to have unique ids, that software could assign all >> metaIds a unique value and use the metaIds to look things up. >> >> As for the referencing syntax, I think this is good, but I wonder if we >> can avoid the tags. If we include them, it is getting quite close to >> XPath. The reason you would need the tags is if the scoping was very >> tight. For example, a DataGenerator has Variables and Parameters. If they >> each are scoped separately, they could have identical ids, and you would >> need the tags. However, if all child objects are in the same scope, then >> you would not be allowed to have the same id for a Variable and Parameter >> in the same DataGenerator, so you would not need the tags. Actually, we >> certainly must have Variable and Parameter in the same scope, since they >> can both be referred to in the Math element. However, a Variable from a >> different DataGenerator cannot, so it is not needed for Variables in two >> different DataGenerators to be in the same scope. >> >> Cheers, >> >> Chris >> >> On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au...> >> wrote: >> >> Hi, >> >> Could this discussion be resolved by extending SED-ML to include a `name` >> attribute that is unique amongst a given class of XML elements (and keep >> `id` as unique within a document)?? >> >> Then what about combining an element's tag name with the value of its >> name attribute (if it has one) with '.' and then combining these named tags >> with `/` to produce relative URIs? As an example, in the XML document: >> >> <A> >> <B name="name_b1"> >> <C> >> <D name="name_d"/> >> </C> >> </B> >> <B name="name_b2"> >> <C> >> <D name="name_d" id="123"/> >> </C> >> </B> >> </A> >> >> the element with an id of "123" could be referred to both as `#123` or >> `/A/B.name_b2/C/D.name_d`. >> >> >> >> >> Best regards, >> >> Dave >> >> >> >> >> >> On 11/07/16 7:45 PM, Matthias König wrote: >> >> Hi Chris, >> I am using the python bindings to libsedml. >> Sorry for the confusion with the model. >> >> Here the correct example using the SedDocument (code just for >> demonstration, not working example). >> Via the function one can get the element based on the id independent of >> the class. This is quit useful if one does not want to question all the >> listOfs. >> I use this a lot in libsbml which has an analogue function, but also in >> libsedml to quickly O(1) lookup an object without the need to look in all >> listOfs. >> >> import libsedml >> >> sid = "abd"doc = libsedml.SedDocument() >> element = doc.getElementBySId(sid) >> >> Matthias >> >> On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec...> wrote: >> >>> Agreed. I would just like to gauge the pros and cons. >>> >>> I’m not sure what you mean by model = Model(). Is this just the Model >>> elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, >>> and there Model is only the Model elements of SED-ML. Within any single >>> class, there would still be unique ids. >>> >>> Chris >>> >>> >>> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go...> >>> wrote: >>> >>> Hi Chris, >>> the method is >>> >>> model = Model()model.getElementBySId(sid) >>> >>> I use this method to get my unique objects based on unique ids and to >>> store things in HashMaps with ids as keys. >>> As soon as keys, i.e. ids are not unique anymore, the objects in the >>> hashmaps are overwritten (this is a silent difficult bug, because all code >>> will work, but will not give the correct results). >>> Anybody storing anything for lookup via id will have similar issues. >>> >>> @Chris I don't have a problem to rewrite code, but I fear similar >>> lookups via id will be part of many code bases. So the unique id constraint >>> should only be changed if the advantages are much larger than the costs. >>> >>> Matthias >>> >>> >>> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec...> >>> wrote: >>> >>>> Lucian, if you had read the whole message, I do mention what Matthias >>>> said. My concern with his statement is I’m not sure why he is using Id’s >>>> for annotations. In SBML, they are linked to meta-ids, which would still >>>> be globally unique. If this is the only use by anyone in the community of >>>> the global unique property, then I still think this is worthy of >>>> discussion. Namely, is using id’s in this way correct? If not, is there >>>> another use case for global ids that is important to people? If so, how >>>> much effort is it to loosen this requirement. >>>> >>>> Maintaining global id uniqueness in a large document places a huge >>>> burden on software. There is a reason why programming languages use scoping >>>> rules, so you don’t need global variable uniqueness. With this rule, every >>>> time you mint an id, you must check if it is in use somewhere else, and if >>>> so have a scheme to try again. Currently, there is no easy way to do this >>>> in jlibSEDML. >>>> >>>> I think the jury is still out on whether this rule adds more burden on >>>> software developers than not having this rule. Having this rule means my >>>> code is broken, and there is no clean and easy way to fix it currently. >>>> There are not a lot of SED-ML implementations yet, so if we are to ever >>>> consider changing this rule, it should be sooner than later before more >>>> implementations come to rely on it. >>>> >>>> If having this rule helps more people than it hurts, we will clearly >>>> keep it, but if it is the other way around, we need to consider removing >>>> it. So far, Matthias has explained how his code relies on the rule, and >>>> I’ve explained that my code is flawed due to this rule. How do others feel >>>> about the rule and its impact on their code? >>>> >>>> Chris >>>> >>>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm...> >>>> wrote: >>>> >>>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec...> wrote: >>>> > >>>> > But will it really break things? >>>> >>>> Yes, Matthias said it would break his code. >>>> >>>> -Lucian >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape_______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>>> >>>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com >>> kon...@go... >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 <%2B49%20176%2081168480> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape_______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com >> kon...@go... >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today.http://sdm.link/attshape >> >> >> >> _______________________________________________ >> SED-ML-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape_______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> >> ------------------------------------------------------------------------------ >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- [image: David Nickerson on about.me] David Nickerson about.me/david.nickerson <http://about.me/david.nickerson> |
|
From: Matthias K. <kon...@go...> - 2016-07-12 14:18:24
|
Hi Chris, you are right. I could also do this via looking in the right list if it is only about resolving the sedml structure. But I am not only using the ids for looking up the related objects in the SEDML, but for instance for instance I am creating a network graph from the sedml xml structure where I require to have unique node ids for all nodes. Because metaids are often not set I rely on the unique ids for node ids. M On Tue, Jul 12, 2016 at 1:12 AM, Chris Myers <my...@ec...> wrote: > Hi Dave, > > SED-ML already does support this. Every object has both a metaId and an > id. The metaId is required to be unique in the document. So, if it is > important to a software to have unique ids, that software could assign all > metaIds a unique value and use the metaIds to look things up. > > As for the referencing syntax, I think this is good, but I wonder if we > can avoid the tags. If we include them, it is getting quite close to > XPath. The reason you would need the tags is if the scoping was very > tight. For example, a DataGenerator has Variables and Parameters. If they > each are scoped separately, they could have identical ids, and you would > need the tags. However, if all child objects are in the same scope, then > you would not be allowed to have the same id for a Variable and Parameter > in the same DataGenerator, so you would not need the tags. Actually, we > certainly must have Variable and Parameter in the same scope, since they > can both be referred to in the Math element. However, a Variable from a > different DataGenerator cannot, so it is not needed for Variables in two > different DataGenerators to be in the same scope. > > Cheers, > > Chris > > On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au...> wrote: > > Hi, > > Could this discussion be resolved by extending SED-ML to include a `name` > attribute that is unique amongst a given class of XML elements (and keep > `id` as unique within a document)?? > > Then what about combining an element's tag name with the value of its name > attribute (if it has one) with '.' and then combining these named tags with > `/` to produce relative URIs? As an example, in the XML document: > > <A> > <B name="name_b1"> > <C> > <D name="name_d"/> > </C> > </B> > <B name="name_b2"> > <C> > <D name="name_d" id="123"/> > </C> > </B> > </A> > > the element with an id of "123" could be referred to both as `#123` or > `/A/B.name_b2/C/D.name_d`. > > > > > Best regards, > > Dave > > > > > > On 11/07/16 7:45 PM, Matthias König wrote: > > Hi Chris, > I am using the python bindings to libsedml. > Sorry for the confusion with the model. > > Here the correct example using the SedDocument (code just for > demonstration, not working example). > Via the function one can get the element based on the id independent of > the class. This is quit useful if one does not want to question all the > listOfs. > I use this a lot in libsbml which has an analogue function, but also in > libsedml to quickly O(1) lookup an object without the need to look in all > listOfs. > > import libsedml > > sid = "abd"doc = libsedml.SedDocument() > element = doc.getElementBySId(sid) > > Matthias > > On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec...> wrote: > >> Agreed. I would just like to gauge the pros and cons. >> >> I’m not sure what you mean by model = Model(). Is this just the Model >> elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, >> and there Model is only the Model elements of SED-ML. Within any single >> class, there would still be unique ids. >> >> Chris >> >> >> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go...> >> wrote: >> >> Hi Chris, >> the method is >> >> model = Model()model.getElementBySId(sid) >> >> I use this method to get my unique objects based on unique ids and to >> store things in HashMaps with ids as keys. >> As soon as keys, i.e. ids are not unique anymore, the objects in the >> hashmaps are overwritten (this is a silent difficult bug, because all code >> will work, but will not give the correct results). >> Anybody storing anything for lookup via id will have similar issues. >> >> @Chris I don't have a problem to rewrite code, but I fear similar lookups >> via id will be part of many code bases. So the unique id constraint should >> only be changed if the advantages are much larger than the costs. >> >> Matthias >> >> >> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec...> wrote: >> >>> Lucian, if you had read the whole message, I do mention what Matthias >>> said. My concern with his statement is I’m not sure why he is using Id’s >>> for annotations. In SBML, they are linked to meta-ids, which would still >>> be globally unique. If this is the only use by anyone in the community of >>> the global unique property, then I still think this is worthy of >>> discussion. Namely, is using id’s in this way correct? If not, is there >>> another use case for global ids that is important to people? If so, how >>> much effort is it to loosen this requirement. >>> >>> Maintaining global id uniqueness in a large document places a huge >>> burden on software. There is a reason why programming languages use scoping >>> rules, so you don’t need global variable uniqueness. With this rule, every >>> time you mint an id, you must check if it is in use somewhere else, and if >>> so have a scheme to try again. Currently, there is no easy way to do this >>> in jlibSEDML. >>> >>> I think the jury is still out on whether this rule adds more burden on >>> software developers than not having this rule. Having this rule means my >>> code is broken, and there is no clean and easy way to fix it currently. >>> There are not a lot of SED-ML implementations yet, so if we are to ever >>> consider changing this rule, it should be sooner than later before more >>> implementations come to rely on it. >>> >>> If having this rule helps more people than it hurts, we will clearly >>> keep it, but if it is the other way around, we need to consider removing >>> it. So far, Matthias has explained how his code relies on the rule, and >>> I’ve explained that my code is flawed due to this rule. How do others feel >>> about the rule and its impact on their code? >>> >>> Chris >>> >>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm...> >>> wrote: >>> >>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec...> wrote: >>> > >>> > But will it really break things? >>> >>> Yes, Matthias said it would break his code. >>> >>> -Lucian >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape_______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com >> kon...@go... >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 <%2B49%20176%2081168480> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape_______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com > kon...@go... > Tel: +49 30 20938450 > Tel: +49 176 81168480 > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today.http://sdm.link/attshape > > > > _______________________________________________ > SED-ML-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: Chris M. <my...@ec...> - 2016-07-11 23:12:32
|
Hi Dave, SED-ML already does support this. Every object has both a metaId and an id. The metaId is required to be unique in the document. So, if it is important to a software to have unique ids, that software could assign all metaIds a unique value and use the metaIds to look things up. As for the referencing syntax, I think this is good, but I wonder if we can avoid the tags. If we include them, it is getting quite close to XPath. The reason you would need the tags is if the scoping was very tight. For example, a DataGenerator has Variables and Parameters. If they each are scoped separately, they could have identical ids, and you would need the tags. However, if all child objects are in the same scope, then you would not be allowed to have the same id for a Variable and Parameter in the same DataGenerator, so you would not need the tags. Actually, we certainly must have Variable and Parameter in the same scope, since they can both be referred to in the Math element. However, a Variable from a different DataGenerator cannot, so it is not needed for Variables in two different DataGenerators to be in the same scope. Cheers, Chris > On Jul 11, 2016, at 3:52 PM, David Brooks <d.b...@au...> wrote: > > Hi, > > Could this discussion be resolved by extending SED-ML to include a `name` attribute that is unique amongst a given class of XML elements (and keep `id` as unique within a document)?? > > Then what about combining an element's tag name with the value of its name attribute (if it has one) with '.' and then combining these named tags with `/` to produce relative URIs? As an example, in the XML document: > > <A> > <B name="name_b1"> > <C> > <D name="name_d"/> > </C> > </B> > <B name="name_b2"> > <C> > <D name="name_d" id="123"/> > </C> > </B> > </A> > > the element with an id of "123" could be referred to both as `#123` or `/A/B.name_b2/C/D.name_d`. > > > > > Best regards, > > Dave > > > > > > On 11/07/16 7:45 PM, Matthias König wrote: >> Hi Chris, >> I am using the python bindings to libsedml. >> Sorry for the confusion with the model. >> >> Here the correct example using the SedDocument (code just for demonstration, not working example). >> Via the function one can get the element based on the id independent of the class. This is quit useful if one does not want to question all the listOfs. >> I use this a lot in libsbml which has an analogue function, but also in libsedml to quickly O(1) lookup an object without the need to look in all listOfs. >> >> import libsedml >> >> sid = "abd" >> doc = libsedml.SedDocument() >> element = doc.getElementBySId(sid) >> Matthias >> >> On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: >> Agreed. I would just like to gauge the pros and cons. >> >> I’m not sure what you mean by model = Model(). Is this just the Model elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, and there Model is only the Model elements of SED-ML. Within any single class, there would still be unique ids. >> >> Chris >> >> >>> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go... <mailto:kon...@go...>> wrote: >>> >>> Hi Chris, >>> the method is >>> model = Model() >>> model.getElementBySId(sid) >>> I use this method to get my unique objects based on unique ids and to store things in HashMaps with ids as keys. >>> As soon as keys, i.e. ids are not unique anymore, the objects in the hashmaps are overwritten (this is a silent difficult bug, because all code will work, but will not give the correct results). >>> Anybody storing anything for lookup via id will have similar issues. >>> >>> @Chris I don't have a problem to rewrite code, but I fear similar lookups via id will be part of many code bases. So the unique id constraint should only be changed if the advantages are much larger than the costs. >>> >>> Matthias >>> >>> >>> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: >>> Lucian, if you had read the whole message, I do mention what Matthias said. My concern with his statement is I’m not sure why he is using Id’s for annotations. In SBML, they are linked to meta-ids, which would still be globally unique. If this is the only use by anyone in the community of the global unique property, then I still think this is worthy of discussion. Namely, is using id’s in this way correct? If not, is there another use case for global ids that is important to people? If so, how much effort is it to loosen this requirement. >>> >>> Maintaining global id uniqueness in a large document places a huge burden on software. There is a reason why programming languages use scoping rules, so you don’t need global variable uniqueness. With this rule, every time you mint an id, you must check if it is in use somewhere else, and if so have a scheme to try again. Currently, there is no easy way to do this in jlibSEDML. >>> >>> I think the jury is still out on whether this rule adds more burden on software developers than not having this rule. Having this rule means my code is broken, and there is no clean and easy way to fix it currently. There are not a lot of SED-ML implementations yet, so if we are to ever consider changing this rule, it should be sooner than later before more implementations come to rely on it. >>> >>> If having this rule helps more people than it hurts, we will clearly keep it, but if it is the other way around, we need to consider removing it. So far, Matthias has explained how his code relies on the rule, and I’ve explained that my code is flawed due to this rule. How do others feel about the rule and its impact on their code? >>> >>> Chris >>> >>>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: >>>> >>>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec... <mailto:my...@ec...>> wrote: >>>> > >>>> > But will it really break things? >>>> >>>> Yes, Matthias said it would break his code. >>>> >>>> -Lucian >>>> >>>> ------------------------------------------------------------------------------ >>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>>> present their vision of the future. This family event has something for >>>> everyone, including kids. Get more information and register today. >>>> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >>>> SED-ML-discuss mailing list >>>> SED...@li... <mailto:SED...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>> >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape <http://sdm.link/attshape> >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... <mailto:SED...@li...> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>> >>> >>> >>> >>> -- >>> Matthias König >>> Junior Group Leader LiSym - Systems Medicine of the Liver >>> Humboldt-University Berlin, Institute for Theoretical Biology >>> https://www.livermetabolism.com <https://www.livermetabolism.com/> >>> kon...@go... <mailto:kon...@go...> >>> Tel: +49 30 20938450 >>> Tel: +49 176 81168480 <tel:%2B49%20176%2081168480> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >>> SED-ML-discuss mailing list >>> SED...@li... <mailto:SED...@li...> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape <http://sdm.link/attshape> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> >> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com <https://www.livermetabolism.com/> >> kon...@go... <mailto:kon...@go...> >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape <http://sdm.link/attshape> >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
|
From: Chris M. <my...@ec...> - 2016-07-11 23:05:23
|
Hi Matthias, My confusion is why do you need to search by id in the first place? At every point in which I’m searching by id, I know what I’m looking for. For example, when I’m working on a task, I use the modelReference to get the Model and the simulationReference to get the Simulation. Same for TaskId’s in variables, or variables in DataGenerator math. There is no overloading of references, so it is always straightforward to use the appropriate get method from the appropriate list. I’ve used the get by id method that you mention in libsbml that you mention, but in that case, it is necessary because references can refer to many different types of objects. So far as I can see, SED-ML does not overload references. Cheers, Chris > On Jul 11, 2016, at 12:45 PM, Matthias König <kon...@go...> wrote: > > Hi Chris, > I am using the python bindings to libsedml. > Sorry for the confusion with the model. > > Here the correct example using the SedDocument (code just for demonstration, not working example). > Via the function one can get the element based on the id independent of the class. This is quit useful if one does not want to question all the listOfs. > I use this a lot in libsbml which has an analogue function, but also in libsedml to quickly O(1) lookup an object without the need to look in all listOfs. > > import libsedml > > sid = "abd" > doc = libsedml.SedDocument() > element = doc.getElementBySId(sid) > Matthias > > On Mon, Jul 11, 2016 at 3:56 PM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: > Agreed. I would just like to gauge the pros and cons. > > I’m not sure what you mean by model = Model(). Is this just the Model elements of SED-ML or are you getting all SED-ML objects? I use jlibSEDML, and there Model is only the Model elements of SED-ML. Within any single class, there would still be unique ids. > > Chris > > >> On Jul 11, 2016, at 1:23 AM, Matthias König <kon...@go... <mailto:kon...@go...>> wrote: >> >> Hi Chris, >> the method is >> model = Model() >> model.getElementBySId(sid) >> I use this method to get my unique objects based on unique ids and to store things in HashMaps with ids as keys. >> As soon as keys, i.e. ids are not unique anymore, the objects in the hashmaps are overwritten (this is a silent difficult bug, because all code will work, but will not give the correct results). >> Anybody storing anything for lookup via id will have similar issues. >> >> @Chris I don't have a problem to rewrite code, but I fear similar lookups via id will be part of many code bases. So the unique id constraint should only be changed if the advantages are much larger than the costs. >> >> Matthias >> >> >> On Sun, Jul 10, 2016 at 12:11 AM, Chris Myers <my...@ec... <mailto:my...@ec...>> wrote: >> Lucian, if you had read the whole message, I do mention what Matthias said. My concern with his statement is I’m not sure why he is using Id’s for annotations. In SBML, they are linked to meta-ids, which would still be globally unique. If this is the only use by anyone in the community of the global unique property, then I still think this is worthy of discussion. Namely, is using id’s in this way correct? If not, is there another use case for global ids that is important to people? If so, how much effort is it to loosen this requirement. >> >> Maintaining global id uniqueness in a large document places a huge burden on software. There is a reason why programming languages use scoping rules, so you don’t need global variable uniqueness. With this rule, every time you mint an id, you must check if it is in use somewhere else, and if so have a scheme to try again. Currently, there is no easy way to do this in jlibSEDML. >> >> I think the jury is still out on whether this rule adds more burden on software developers than not having this rule. Having this rule means my code is broken, and there is no clean and easy way to fix it currently. There are not a lot of SED-ML implementations yet, so if we are to ever consider changing this rule, it should be sooner than later before more implementations come to rely on it. >> >> If having this rule helps more people than it hurts, we will clearly keep it, but if it is the other way around, we need to consider removing it. So far, Matthias has explained how his code relies on the rule, and I’ve explained that my code is flawed due to this rule. How do others feel about the rule and its impact on their code? >> >> Chris >> >>> On Jul 9, 2016, at 3:57 PM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: >>> >>> On Jul 9, 2016 1:10 PM, "Chris Myers" <my...@ec... <mailto:my...@ec...>> wrote: >>> > >>> > But will it really break things? >>> >>> Yes, Matthias said it would break his code. >>> >>> -Lucian >>> >>> ------------------------------------------------------------------------------ >>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >>> present their vision of the future. This family event has something for >>> everyone, including kids. Get more information and register today. >>> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >>> SED-ML-discuss mailing list >>> SED...@li... <mailto:SED...@li...> >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape <http://sdm.link/attshape> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >> >> >> >> >> -- >> Matthias König >> Junior Group Leader LiSym - Systems Medicine of the Liver >> Humboldt-University Berlin, Institute for Theoretical Biology >> https://www.livermetabolism.com <https://www.livermetabolism.com/> >> kon...@go... <mailto:kon...@go...> >> Tel: +49 30 20938450 >> Tel: +49 176 81168480 <tel:%2B49%20176%2081168480> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape_______________________________________________ <http://sdm.link/attshape_______________________________________________> >> SED-ML-discuss mailing list >> SED...@li... <mailto:SED...@li...> >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape <http://sdm.link/attshape> > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... <mailto:SED...@li...> > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> > > > > > -- > Matthias König > Junior Group Leader LiSym - Systems Medicine of the Liver > Humboldt-University Berlin, Institute for Theoretical Biology > https://www.livermetabolism.com <https://www.livermetabolism.com/> > kon...@go... <mailto:kon...@go...> > Tel: +49 30 20938450 > Tel: +49 176 81168480 > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
14 messages has been excluded from this view by a project administrator.
