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: <da...@eb...> - 2009-03-06 09:10:00
|
Hej Richard, good idea to have a manifest (whatever it will look like in the end). > Other than that, the format Frank proposed seems quite effective - > Frank I hope to be able to test out some .miase files generated by the > java library on your website soon (at least before the Biomodels > meeting). I am not sure, but I suppose that I missed a mail/discussion or alike here, what is 'the format Frank proposed' ? :-) Dagmar |
From: Frank B. <fbergman@u.washington.edu> - 2009-03-06 02:30:49
|
Hello Richard, i've been thinking about manifests. In my first implementation i decided against it, the task of actually reading the experiment description seemed negligible as compared to the updating effort that would have to be done in order to change a given miase file. Reading the notes from the sed ml, should be simple enough. The one thing that a manifest should provide is a unique identification of *which* XML file the experiment description is. I would obstain from putting the Model Names into the description as even something as simple as Model.getName implies an understanding of the API's needed to correctly interpret the model description language for encoded models. Which is not guaranteed at the moment. > to parse all the files - what does anyone think of a manifest to be > included in the archive? as said above, I think if we have a manifest it should be very rudimentary, it should contain - the name of the experiment desciption file - the types of models encoded, (i.e: SBML/CellML...), this would allow tools at a glance to refuse files (or warn users) we never talked about the format of experimental data, but that would be the things to be described here, be it CVS, SBRML or whatever I think of manifests similar as to jar files, it tells me precisely what i need to know in order to run (the experiment description) successfully > > If we agreed that the manifest was the 'first' file in the archive > then tools wouldn't even have to unzip all the files to find it. thats actually harder to do (in some api's) than to agree on a predefined fileName. If we need a manifest then 'MANIFEST' seems as good a name as any. Which begs the next question, which format should the manifest take? For all those reasons decided not to include a manifest in the first place. > > > Other than that, the format Frank proposed seems quite effective - > Frank I hope to be able to test out some .miase files generated by the > java library on your website soon (at least before the Biomodels > meeting). That would be great, thanks best Frank > > > > Thanks > Richard > > > > > > > > > > -- > Dr Richard Adams > Senior Software Developer, > Computational Systems Biology Group, > University of Edinburgh > Tel: 0131 650 8281/8285 > email : ric...@ed... > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
From: Richard A. <ra...@st...> - 2009-03-05 17:54:03
|
Hello, I'm hoping to be able to generate and read .miase files in the near future using the java library in sourceforge. Since I'm also developing a client tool I was thinking it would be nice to be able to view a summary of the contents of the .miase archive without having to parse all the files - what does anyone think of a manifest to be included in the archive? It could contain: 1. A short decription of the sedml file (e.g., in the example .sedml file based on biomodel12 there is a top-level notes annotation called 'from periodicity to chaos'. Actually couldn't the SedML root object have a basic name/ description rather than relying on a note? 2. The names of any model files included e.g., for sbml models, it could be the string resulting from Model.getName(). 3. Some other optional info e.g., date generated etc If we agreed that the manifest was the 'first' file in the archive then tools wouldn't even have to unzip all the files to find it. Other than that, the format Frank proposed seems quite effective - Frank I hope to be able to test out some .miase files generated by the java library on your website soon (at least before the Biomodels meeting). Thanks Richard -- Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Henning S. <he...@hs...> - 2009-03-04 21:06:23
|
Hi, I think it is not much of an issue for the biotech/pharma industry since people there use tools they purchase or are open source. License fees for the use of patent protected technology usually needs to be paid by the tool developing and selling companies. So it is rather an issue for Mathworks or even for Copasi, which also is sold to companies. But also for any companies who ever will implement support for SedML in their software products. But, honestly, who will be able to tell Mathworks that they need to pay license fees because they have an event handling feature inbuilt in their integrators (already far longer than the filing date of this patent). Henning -----Original Message----- From: Moraru,Ion [mailto:Mo...@NE...] Sent: Mittwoch, 4. März 2009 21:12 To: le...@eb...; mia...@li...; hen...@no... Subject: Re: [Miase-discuss] SBML/sedML Patent Issue Guys, Entelos is patenting all sorts of stuff ostensibly to protect their Physiolab product. These are not only patents on various standard modeling and simulation methods, but also on models themselves (e.g. models of type 1 diabetes physiology in islet cells etc.). The patents read like nobody else will be allowed to model whatever physiology they are modeling. Ridiculuos, and probably has no significance for academic research - but it may have some significance for the industry if you are in the business of modeling... I would like to hear more comments from modelers in biotech/pharma companies. Ion >-----Original Message----- >From: Nicolas Le novère [mailto:le...@eb...] >Sent: Wednesday, March 04, 2009 1:35 PM >To: hen...@no... >Cc: mia...@li... >Subject: Re: [Miase-discuss] SBML/sedML Patent Issue > >As a matter of principle, I think if you do not get money on >something, you are not sued. But that was not my point. My >point was that SEDML/SBML are not software to instantiate >simulations as described in the patent, but description of the >procedure. If they could sue us or people using SED-ML, they >could sue most authors of books on simulation .... > >hen...@no... wrote: >> >> >> Hi Nicholas, >> >> are you sure it only applies to commercial companies using >the software? >> In my opinion also non-profit organization are not allowed >to develop >> and distribute software (and any other things) that violate topics >> covered by patents. And this certainly applies in this case to all >> SBML software simulating events ... if used and produced at >> universities or in companies (and all possible combinations). >> >> /Henning >> >> >> >> >> *Nicolas Le novère <le...@eb...>* >> >> 04.03.2009 15:20 >> Please respond to >> le...@eb... >> >> >> >> To >> hen...@no... >> cc >> mh...@ca..., mia...@li... >> Subject >> Re: SBML/sedML Patent Issue >> >> >> >> >> >> >> >> >> Henning, >> >> Thanks a lot for the information. I think this does not affect us >> because it deals with running the sequence experiments and not >> describing the sequence. But we should keep an eye if we >want SEDML to >> be used by companies (they already use simulators using SBML events >> ...) >> >> hen...@no... wrote: >> > >> > Hi Mike and Nicholas, >> > >> > hope both of you are doing fine! Here in Basel everything >is ok and >> the > rate of development on the toolbox has > gotten even >higher :) >> Just need to convince my bosses to make it > publicly available at >> some point in time. >> > >> > During my work here something came up which might have an >impact on >> SBML > and sedML in terms of "intellectual property". >> > >> > Are you aware of the following patent by Entelos: >> > http://www.google.com/patents?vid=USPAT6983237 >> > >> > What they patented are "sequenced experiments". This >means you run >> one > experiment on a model until a certain > time, then based on >> the last statevector you update the states and > parameters >(manually >> or automatically by a script / program / etc.) > of the >model and run >> this second experiment and so forth. >> > >> > This procedure has been used for many years and is >certainly not new. >> > Especially for very time consuming simulations > one often >> simulates until a certain time, saves the statevector and >can > then >> from there simulate different scenarios. >> > I guess almost every modeler has used this idea at some point in >> time > (especiall in the older days with slower > computers). >> > >> > Anyway, initially I thought that this only covers single >experiment >> > descriptions that then are run in a sequence. >> > Now, I heard from Entelos that they think their patent >also covers >> > changes of parameters or states DURING a > simulation experiment, >> which are implemented using events. >> > >> > Since SBML allows to change states and parameters using events >> during > simulations all users simulating such SBML > models would >> in principle need to pay license fees to Entelos :) Same of >> course >> for sedML users, since some of the > experimental settings might be >> implemented using events. >> > >> > One good thing: its only a US patent and similar things >are not > >> patentable in Europe (afaik). >> > >> > It would be great if you could check out the patent too >and let me >> know > what you think. In my view a patent like this should > > not be >> around for too long, since it in principle subjects all SBML > > tools >> to license fees to Entelos. >> > >> > All the best, >> > Henning >> > >> > >> >> >> -- >> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, >> Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, >> Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, >> MSN:nle...@ho... http://www.ebi.ac.uk/~lenov/, >> http://www.ebi.ac.uk/compneur/ >> >> >> > > >-- >Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, >Wellcome-Trust Genome Campus, Hinxton CB101SD UK, >Mob:+447833147074, Tel:+441223494521 Fax:468, >Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... >http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > >--------------------------------------------------------------- >--------------- >Open Source Business Conference (OSBC), March 24-25, 2009, San >Francisco, CA >-OSBC tackles the biggest issue in open source: Open Sourcing >the Enterprise >-Strategies to boost innovation and cut costs with open source >participation >-Receive a $600 discount off the registration fee with the >source code: SFAD >http://p.sf.net/sfu/XcvMzF8H >_______________________________________________ >Miase-discuss mailing list >Mia...@li... >https://lists.sourceforge.net/lists/listinfo/miase-discuss > ---------------------------------------------------------------------------- -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ Miase-discuss mailing list Mia...@li... https://lists.sourceforge.net/lists/listinfo/miase-discuss |
From: Moraru,Ion <Mo...@NE...> - 2009-03-04 20:26:47
|
Guys, Entelos is patenting all sorts of stuff ostensibly to protect their Physiolab product. These are not only patents on various standard modeling and simulation methods, but also on models themselves (e.g. models of type 1 diabetes physiology in islet cells etc.). The patents read like nobody else will be allowed to model whatever physiology they are modeling. Ridiculuos, and probably has no significance for academic research - but it may have some significance for the industry if you are in the business of modeling... I would like to hear more comments from modelers in biotech/pharma companies. Ion >-----Original Message----- >From: Nicolas Le novère [mailto:le...@eb...] >Sent: Wednesday, March 04, 2009 1:35 PM >To: hen...@no... >Cc: mia...@li... >Subject: Re: [Miase-discuss] SBML/sedML Patent Issue > >As a matter of principle, I think if you do not get money on >something, you are not sued. But that was not my point. My >point was that SEDML/SBML are not software to instantiate >simulations as described in the patent, but description of the >procedure. If they could sue us or people using SED-ML, they >could sue most authors of books on simulation .... > >hen...@no... wrote: >> >> >> Hi Nicholas, >> >> are you sure it only applies to commercial companies using >the software? >> In my opinion also non-profit organization are not allowed >to develop >> and distribute software (and any other things) that violate topics >> covered by patents. And this certainly applies in this case to all >> SBML software simulating events ... if used and produced at >> universities or in companies (and all possible combinations). >> >> /Henning >> >> >> >> >> *Nicolas Le novère <le...@eb...>* >> >> 04.03.2009 15:20 >> Please respond to >> le...@eb... >> >> >> >> To >> hen...@no... >> cc >> mh...@ca..., mia...@li... >> Subject >> Re: SBML/sedML Patent Issue >> >> >> >> >> >> >> >> >> Henning, >> >> Thanks a lot for the information. I think this does not affect us >> because it deals with running the sequence experiments and not >> describing the sequence. But we should keep an eye if we >want SEDML to >> be used by companies (they already use simulators using SBML events >> ...) >> >> hen...@no... wrote: >> > >> > Hi Mike and Nicholas, >> > >> > hope both of you are doing fine! Here in Basel everything >is ok and >> the > rate of development on the toolbox has > gotten even >higher :) >> Just need to convince my bosses to make it > publicly available at >> some point in time. >> > >> > During my work here something came up which might have an >impact on >> SBML > and sedML in terms of "intellectual property". >> > >> > Are you aware of the following patent by Entelos: >> > http://www.google.com/patents?vid=USPAT6983237 >> > >> > What they patented are "sequenced experiments". This >means you run >> one > experiment on a model until a certain > time, then based on >> the last statevector you update the states and > parameters >(manually >> or automatically by a script / program / etc.) > of the >model and run >> this second experiment and so forth. >> > >> > This procedure has been used for many years and is >certainly not new. >> > Especially for very time consuming simulations > one often >> simulates until a certain time, saves the statevector and >can > then >> from there simulate different scenarios. >> > I guess almost every modeler has used this idea at some point in >> time > (especiall in the older days with slower > computers). >> > >> > Anyway, initially I thought that this only covers single >experiment >> > descriptions that then are run in a sequence. >> > Now, I heard from Entelos that they think their patent >also covers >> > changes of parameters or states DURING a > simulation experiment, >> which are implemented using events. >> > >> > Since SBML allows to change states and parameters using events >> during > simulations all users simulating such SBML > models would >> in principle need to pay license fees to Entelos :) Same of >> course >> for sedML users, since some of the > experimental settings might be >> implemented using events. >> > >> > One good thing: its only a US patent and similar things >are not > >> patentable in Europe (afaik). >> > >> > It would be great if you could check out the patent too >and let me >> know > what you think. In my view a patent like this should > > not be >> around for too long, since it in principle subjects all SBML > > tools >> to license fees to Entelos. >> > >> > All the best, >> > Henning >> > >> > >> >> >> -- >> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, >> Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, >> Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, >> MSN:nle...@ho... http://www.ebi.ac.uk/~lenov/, >> http://www.ebi.ac.uk/compneur/ >> >> >> > > >-- >Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, >Wellcome-Trust Genome Campus, Hinxton CB101SD UK, >Mob:+447833147074, Tel:+441223494521 Fax:468, >Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... >http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > >--------------------------------------------------------------- >--------------- >Open Source Business Conference (OSBC), March 24-25, 2009, San >Francisco, CA >-OSBC tackles the biggest issue in open source: Open Sourcing >the Enterprise >-Strategies to boost innovation and cut costs with open source >participation >-Receive a $600 discount off the registration fee with the >source code: SFAD >http://p.sf.net/sfu/XcvMzF8H >_______________________________________________ >Miase-discuss mailing list >Mia...@li... >https://lists.sourceforge.net/lists/listinfo/miase-discuss > |
From: Nicolas Le n. <le...@eb...> - 2009-03-04 18:35:30
|
As a matter of principle, I think if you do not get money on something, you are not sued. But that was not my point. My point was that SEDML/SBML are not software to instantiate simulations as described in the patent, but description of the procedure. If they could sue us or people using SED-ML, they could sue most authors of books on simulation .... hen...@no... wrote: > > > Hi Nicholas, > > are you sure it only applies to commercial companies using the software? > In my opinion also non-profit organization are not allowed to > develop and distribute software (and any other things) that violate > topics covered by patents. And this certainly applies in this case to > all SBML software simulating events ... if used and produced at > universities or in companies (and all possible combinations). > > /Henning > > > > > *Nicolas Le novère <le...@eb...>* > > 04.03.2009 15:20 > Please respond to > le...@eb... > > > > To > hen...@no... > cc > mh...@ca..., mia...@li... > Subject > Re: SBML/sedML Patent Issue > > > > > > > > > Henning, > > Thanks a lot for the information. I think this does not affect us because > it deals with running the sequence experiments and not describing the > sequence. But we should keep an eye if we want SEDML to be used by > companies (they already use simulators using SBML events ...) > > hen...@no... wrote: > > > > Hi Mike and Nicholas, > > > > hope both of you are doing fine! Here in Basel everything is ok and the > > rate of development on the toolbox has > > gotten even higher :) Just need to convince my bosses to make it > > publicly available at some point in time. > > > > During my work here something came up which might have an impact on SBML > > and sedML in terms of "intellectual property". > > > > Are you aware of the following patent by Entelos: > > http://www.google.com/patents?vid=USPAT6983237 > > > > What they patented are "sequenced experiments". This means you run one > > experiment on a model until a certain > > time, then based on the last statevector you update the states and > > parameters (manually or automatically by a script / program / etc.) > > of the model and run this second experiment and so forth. > > > > This procedure has been used for many years and is certainly not new. > > Especially for very time consuming simulations > > one often simulates until a certain time, saves the statevector and can > > then from there simulate different scenarios. > > I guess almost every modeler has used this idea at some point in time > > (especiall in the older days with slower > > computers). > > > > Anyway, initially I thought that this only covers single experiment > > descriptions that then are run in a sequence. > > Now, I heard from Entelos that they think their patent also covers > > changes of parameters or states DURING a > > simulation experiment, which are implemented using events. > > > > Since SBML allows to change states and parameters using events during > > simulations all users simulating such SBML > > models would in principle need to pay license fees to Entelos :) Same of > > course for sedML users, since some of the > > experimental settings might be implemented using events. > > > > One good thing: its only a US patent and similar things are not > > patentable in Europe (afaik). > > > > It would be great if you could check out the patent too and let me know > > what you think. In my view a patent like this should > > not be around for too long, since it in principle subjects all SBML > > tools to license fees to Entelos. > > > > All the best, > > Henning > > > > > > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ |
From: <hen...@no...> - 2009-03-04 14:33:15
|
Hi Nicholas, are you sure it only applies to commercial companies using the software? In my opinion also non-profit organization are not allowed to develop and distribute software (and any other things) that violate topics covered by patents. And this certainly applies in this case to all SBML software simulating events ... if used and produced at universities or in companies (and all possible combinations). /Henning Nicolas Le novère <le...@eb...> 04.03.2009 15:20 Please respond to le...@eb... To hen...@no... cc mh...@ca..., mia...@li... Subject Re: SBML/sedML Patent Issue Henning, Thanks a lot for the information. I think this does not affect us because it deals with running the sequence experiments and not describing the sequence. But we should keep an eye if we want SEDML to be used by companies (they already use simulators using SBML events ...) hen...@no... wrote: > > Hi Mike and Nicholas, > > hope both of you are doing fine! Here in Basel everything is ok and the > rate of development on the toolbox has > gotten even higher :) Just need to convince my bosses to make it > publicly available at some point in time. > > During my work here something came up which might have an impact on SBML > and sedML in terms of "intellectual property". > > Are you aware of the following patent by Entelos: > http://www.google.com/patents?vid=USPAT6983237 > > What they patented are "sequenced experiments". This means you run one > experiment on a model until a certain > time, then based on the last statevector you update the states and > parameters (manually or automatically by a script / program / etc.) > of the model and run this second experiment and so forth. > > This procedure has been used for many years and is certainly not new. > Especially for very time consuming simulations > one often simulates until a certain time, saves the statevector and can > then from there simulate different scenarios. > I guess almost every modeler has used this idea at some point in time > (especiall in the older days with slower > computers). > > Anyway, initially I thought that this only covers single experiment > descriptions that then are run in a sequence. > Now, I heard from Entelos that they think their patent also covers > changes of parameters or states DURING a > simulation experiment, which are implemented using events. > > Since SBML allows to change states and parameters using events during > simulations all users simulating such SBML > models would in principle need to pay license fees to Entelos :) Same of > course for sedML users, since some of the > experimental settings might be implemented using events. > > One good thing: its only a US patent and similar things are not > patentable in Europe (afaik). > > It would be great if you could check out the patent too and let me know > what you think. In my view a patent like this should > not be around for too long, since it in principle subjects all SBML > tools to license fees to Entelos. > > All the best, > Henning > > -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ |
From: Nicolas Le n. <le...@eb...> - 2009-03-04 14:19:59
|
Henning, Thanks a lot for the information. I think this does not affect us because it deals with running the sequence experiments and not describing the sequence. But we should keep an eye if we want SEDML to be used by companies (they already use simulators using SBML events ...) hen...@no... wrote: > > Hi Mike and Nicholas, > > hope both of you are doing fine! Here in Basel everything is ok and the > rate of development on the toolbox has > gotten even higher :) Just need to convince my bosses to make it > publicly available at some point in time. > > During my work here something came up which might have an impact on SBML > and sedML in terms of "intellectual property". > > Are you aware of the following patent by Entelos: > http://www.google.com/patents?vid=USPAT6983237 > > What they patented are "sequenced experiments". This means you run one > experiment on a model until a certain > time, then based on the last statevector you update the states and > parameters (manually or automatically by a script / program / etc.) > of the model and run this second experiment and so forth. > > This procedure has been used for many years and is certainly not new. > Especially for very time consuming simulations > one often simulates until a certain time, saves the statevector and can > then from there simulate different scenarios. > I guess almost every modeler has used this idea at some point in time > (especiall in the older days with slower > computers). > > Anyway, initially I thought that this only covers single experiment > descriptions that then are run in a sequence. > Now, I heard from Entelos that they think their patent also covers > changes of parameters or states DURING a > simulation experiment, which are implemented using events. > > Since SBML allows to change states and parameters using events during > simulations all users simulating such SBML > models would in principle need to pay license fees to Entelos :) Same of > course for sedML users, since some of the > experimental settings might be implemented using events. > > One good thing: its only a US patent and similar things are not > patentable in Europe (afaik). > > It would be great if you could check out the patent too and let me know > what you think. In my view a patent like this should > not be around for too long, since it in principle subjects all SBML > tools to license fees to Entelos. > > All the best, > Henning > > -- Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ |
From: Frank B. <fbergman@u.washington.edu> - 2009-02-18 03:06:37
|
> > Do I understand it correctly that the 'annotation' we are > talking about is the following in the sbml-mathml schema?: > Yes I believe those were the lines. Though I'm not sure as to the precise error message. Richard could you post it? > > I'm not sure what to suggest as far as the jaxb issue is > concerned. I haven't looked at the jaxb code, but it seems > strange that jaxb would not let a person specify some sort > of prefix at the software level, so that it can be told to > generate alternate names for chosen elements. I agree there has to be a way this can be handled at the software level. If not it might be something to be taken up with the jaxb community :) ... For now however we have a working solution with keeping the processing instructions separate. Best Frank |
From: Michael H. <mh...@ca...> - 2009-02-18 01:24:44
|
fbergman> if renaming is to be done, i think it should be fbergman> on the math-ML level. I consider notes and fbergman> annotation for Sed-ML vital, but not at the fbergman> math- ml level. That would limit all changes to fbergman> the sbml-mathml.xsd file. Maybe Mike could chip fbergman> in, how this feature is used in SBML. Hi, Do I understand it correctly that the 'annotation' we are talking about is the following in the sbml-mathml schema?: <xs:complexType name="Annotation"> <xs:simpleContent> <xs:extension base="xs:string"> <xs:attributeGroup ref="AnnotationAttributes"/> </xs:extension> </xs:simpleContent> </xs:complexType> If so, then this is not something we have much control over -- it's part of the definition of MathML 2.0 (it's not even an SBML issue). The <annotation> and <annotation-xml> constructs are involved in the definition of MathML's <semantics> element. At present, I don't think there is a lot of use of <semantics> and its associated constructs in SBML software; however, it *is* used by SBO, in the rate law MathML expressions. It's pretty vital in that role. (Although, now that I look at it, it doesn't seem that <annotation> and <annotation-xml> per se are being used in the SBO terms I've looked at, only <semantics>.) I'm not sure what to suggest as far as the jaxb issue is concerned. I haven't looked at the jaxb code, but it seems strange that jaxb would not let a person specify some sort of prefix at the software level, so that it can be told to generate alternate names for chosen elements. One could rename them to "mathml-annotation" or some such then. MH |
From: Frank B. <fbergman@u.washington.edu> - 2009-02-17 16:42:51
|
On Feb 17, 2009, at 5:18 AM, Dagmar Köhn wrote: > Did you consider the option of renaming the annotation and notes > element > to something else in SED-ML if we run into namespace conflicts? if renaming is to be done, i think it should be on the math-ML level. I consider notes and annotation for Sed-ML vital, but not at the math- ml level. That would limit all changes to the sbml-mathml.xsd file. Maybe Mike could chip in, how this feature is used in SBML. Frank > > > Dagmar > > > Frank Bergmann wrote: >> Personally I don't mind, as I would not consume the schema as such. >> Though >> your concerns are valid at which point would we stop adding non- >> critical >> elements. For the problem at hand it might make more sense to take >> 'notes' >> and 'annotation' out from the sbml-math schema. I would prefer to >> have the >> sed-ml file annotated, rather than the math-ml ... >> >> If that won't work, perhaps you could keep the JAXB annotations >> separate >> from the miase schema in jlibsedml, perhaps having your ant script >> merge the >> two. >> >> What do you think? >> >> Best >> Frank >> >> >>> -----Original Message----- >>> From: Richard Adams [mailto:ra...@st...] >>> Sent: Monday, February 16, 2009 8:08 AM >>> To: mia...@li... >>> Subject: [Miase-discuss] Schema annotations >>> >>> >>> Sorry, probably didn't explain very well - the .xsd schema >>> definition >>> allows application specific annotations. The changes to the schema >>> I'm >>> proposing would >>> not be included in .miase files, but in the schema itself, inside >>> the >>> notes and annotation element definitions. >>> >>> The problem arises, as JAXB comes across 'notes' and 'annotation' >>> defined in both sbml-mathml and sedml schemas. When generating >>> classes >>> from the schema, it gets confused as it attempts to create classes >>> of >>> the same name twice. To prevent this happening, you can add a >>> processing instruction in the notes element declaration in the sedml >>> schema, saying 'don't create another notes class for this notes >>> element, create a class called 'SedmlNotes instead'. >>> >>> Just looking through the JAXB docs, there doesn't seem to be an >>> obvious solution readily available, e.g., to make the classes in two >>> different packages, >>> which would prevent the need for these annotations. >>> >>> Basically, there are a quite a lot of processing instructions which >>> could be included, for example, specifying java collection classes, >>> method names, class names, javadoc. Some of these, but not all, >>> can be >>> put in an external file, called a binding file, so I'm just thinking >>> that these schema annotations could pollute the schema definition >>> somewhat. >>> >>> Cheers >>> Richard >>> >>> >>> >>> >>>> I'm sorry, i don't quite see the issue ... the schema right now >>>> says >>>> that you are free to put under the annotation element pretty much >>>> anything, and as far as MIASE goes, it will be ignored. The same >>>> goes >>>> for the notes section. >>>> >>>> i've never used jaxb so I'm not sure what the issues are. Could you >>>> explain further? >>>> >>> best >>> Frank >>> >>> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: >>> >>> >>>> Hi all, >>>> Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> >>>> elements >>>> into a schema for tool-specific customization of schema processing. >>>> Is this tolerable in the sed-ml schema, or would it clutter up the >>>> schema too much? >>>> >>>> Just wondered as Dagmar's last change ( to add the notes/annotation >>>> elements) causes a namespace conflict to the JAXB schema parser >>>> with >>>> the elements of the same name defined in sbml-mathml. One way round >>>> this is to add this jaxb specific annotations in the .xsd file to >>>> produce classes with different names. An alternative is to specify >>>> instructions in a separate 'binding' file, this would be ideal but >>>> I've not got it to work yet. >>>> >>>> Basically it would add: >>>> >>>> <xs:annotation> >>>> <xs:appinfo> >>>> <jxb:class name="SedMLNotes"> >>>> </jxb:class> >>>> </xs:appinfo> >>>> >>> -- >>> Dr Richard Adams >>> Senior Software Developer, >>> Computational Systems Biology Group, >>> University of Edinburgh >>> Tel: 0131 650 8281/8285 >>> email : ric...@ed... >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336. >>> >>> >>> >>> ----------------------------------------------------------------------- >>> ------- >>> Open Source Business Conference (OSBC), March 24-25, 2009, San >>> Francisco, CA >>> -OSBC tackles the biggest issue in open source: Open Sourcing the >>> Enterprise >>> -Strategies to boost innovation and cut costs with open source >>> participation >>> -Receive a $600 discount off the registration fee with the source >>> code: >>> SFAD >>> http://p.sf.net/sfu/XcvMzF8H >>> _______________________________________________ >>> Miase-discuss mailing list >>> Mia...@li... >>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>> >> >> >> ------------------------------------------------------------------------------ >> Open Source Business Conference (OSBC), March 24-25, 2009, San >> Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source >> code: SFAD >> http://p.sf.net/sfu/XcvMzF8H >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss >> > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
From: Richard A. <ra...@st...> - 2009-02-17 15:54:04
|
But the concept - of needing a human readable and machine readable exegesis of an element - is still needed. Possible 'note' could be replaced with 'comment'? Harder to think of a replacement for 'annotation'. Richard > Richard Adams wrote: >> >> Yes, that's another option, although using the same terms people >> are familiar with from sbml is probably desirable, and its up to >> the implementation to deal with it. > > True as well - although I thought actually that a disadvantage of > using "annotation" and "notes" was that it is too close to SBML - and > we definitely want other people to join as well, not only SBMLer ;-) > > The problem that I rather see is that it is hard to find appropriate > other terms... > > Oh, and can you try to answer to the list - I think only I got your > mail this time. I remember Nicolas had the same problem when using the > "reply" button, but can't remember how he solved it!? > Dagmar > >> >> >>> Did you consider the option of renaming the annotation and notes element >>> to something else in SED-ML if we run into namespace conflicts? >>> >>> Dagmar >>> >>> >>> Frank Bergmann wrote: >>>> Personally I don't mind, as I would not consume the schema as such. Though >>>> your concerns are valid at which point would we stop adding non-critical >>>> elements. For the problem at hand it might make more sense to take 'notes' >>>> and 'annotation' out from the sbml-math schema. I would prefer to have the >>>> sed-ml file annotated, rather than the math-ml ... >>>> >>>> If that won't work, perhaps you could keep the JAXB annotations separate >>>> from the miase schema in jlibsedml, perhaps having your ant >>>> script merge the >>>> two. >>>> >>>> What do you think? >>>> >>>> Best >>>> Frank >>>> >>>> >>>>> -----Original Message----- >>>>> From: Richard Adams [mailto:ra...@st...] >>>>> Sent: Monday, February 16, 2009 8:08 AM >>>>> To: mia...@li... >>>>> Subject: [Miase-discuss] Schema annotations >>>>> >>>>> >>>>> Sorry, probably didn't explain very well - the .xsd schema definition >>>>> allows application specific annotations. The changes to the schema I'm >>>>> proposing would >>>>> not be included in .miase files, but in the schema itself, inside the >>>>> notes and annotation element definitions. >>>>> >>>>> The problem arises, as JAXB comes across 'notes' and 'annotation' >>>>> defined in both sbml-mathml and sedml schemas. When generating classes >>>>> from the schema, it gets confused as it attempts to create classes of >>>>> the same name twice. To prevent this happening, you can add a >>>>> processing instruction in the notes element declaration in the sedml >>>>> schema, saying 'don't create another notes class for this notes >>>>> element, create a class called 'SedmlNotes instead'. >>>>> >>>>> Just looking through the JAXB docs, there doesn't seem to be an >>>>> obvious solution readily available, e.g., to make the classes in two >>>>> different packages, >>>>> which would prevent the need for these annotations. >>>>> >>>>> Basically, there are a quite a lot of processing instructions which >>>>> could be included, for example, specifying java collection classes, >>>>> method names, class names, javadoc. Some of these, but not all, can be >>>>> put in an external file, called a binding file, so I'm just thinking >>>>> that these schema annotations could pollute the schema definition >>>>> somewhat. >>>>> >>>>> Cheers >>>>> Richard >>>>> >>>>> >>>>> >>>>> >>>>>> I'm sorry, i don't quite see the issue ... the schema right now says >>>>>> that you are free to put under the annotation element pretty much >>>>>> anything, and as far as MIASE goes, it will be ignored. The same goes >>>>>> for the notes section. >>>>>> >>>>>> i've never used jaxb so I'm not sure what the issues are. Could you >>>>>> explain further? >>>>>> >>>>> best >>>>> Frank >>>>> >>>>> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: >>>>> >>>>> >>>>>> Hi all, >>>>>> Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> >>>>>> elements >>>>>> into a schema for tool-specific customization of schema processing. >>>>>> Is this tolerable in the sed-ml schema, or would it clutter up the >>>>>> schema too much? >>>>>> >>>>>> Just wondered as Dagmar's last change ( to add the notes/annotation >>>>>> elements) causes a namespace conflict to the JAXB schema parser with >>>>>> the elements of the same name defined in sbml-mathml. One way round >>>>>> this is to add this jaxb specific annotations in the .xsd file to >>>>>> produce classes with different names. An alternative is to specify >>>>>> instructions in a separate 'binding' file, this would be ideal but >>>>>> I've not got it to work yet. >>>>>> >>>>>> Basically it would add: >>>>>> >>>>>> <xs:annotation> >>>>>> <xs:appinfo> >>>>>> <jxb:class name="SedMLNotes"> >>>>>> </jxb:class> >>>>>> </xs:appinfo> >>>>>> >>>>> -- >>>>> Dr Richard Adams >>>>> Senior Software Developer, >>>>> Computational Systems Biology Group, >>>>> University of Edinburgh >>>>> Tel: 0131 650 8281/8285 >>>>> email : ric...@ed... >>>>> >>>>> -- >>>>> The University of Edinburgh is a charitable body, registered in >>>>> Scotland, with registration number SC005336. >>>>> >>>>> >>>>> >>>>> ----------------------------------------------------------------------- >>>>> ------- >>>>> Open Source Business Conference (OSBC), March 24-25, 2009, San >>>>> Francisco, CA >>>>> -OSBC tackles the biggest issue in open source: Open Sourcing the >>>>> Enterprise >>>>> -Strategies to boost innovation and cut costs with open source >>>>> participation >>>>> -Receive a $600 discount off the registration fee with the source code: >>>>> SFAD >>>>> http://p.sf.net/sfu/XcvMzF8H >>>>> _______________________________________________ >>>>> Miase-discuss mailing list >>>>> Mia...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, >>>> CA >>>> -OSBC tackles the biggest issue in open source: Open Sourcing the >>>> Enterprise >>>> -Strategies to boost innovation and cut costs with open source >>>> participation >>>> -Receive a $600 discount off the registration fee with the source >>>> code: SFAD >>>> http://p.sf.net/sfu/XcvMzF8H >>>> _______________________________________________ >>>> Miase-discuss mailing list >>>> Mia...@li... >>>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>>> >>> >>> >>> ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, >>> CA >>> -OSBC tackles the biggest issue in open source: Open Sourcing the >>> Enterprise >>> -Strategies to boost innovation and cut costs with open source >>> participation >>> -Receive a $600 discount off the registration fee with the source >>> code: SFAD >>> http://p.sf.net/sfu/XcvMzF8H >>> _______________________________________________ >>> Miase-discuss mailing list >>> Mia...@li... >>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>> >>> >> >> >> -- Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Dagmar K. <da...@eb...> - 2009-02-17 13:18:38
|
Did you consider the option of renaming the annotation and notes element to something else in SED-ML if we run into namespace conflicts? Dagmar Frank Bergmann wrote: > Personally I don't mind, as I would not consume the schema as such. Though > your concerns are valid at which point would we stop adding non-critical > elements. For the problem at hand it might make more sense to take 'notes' > and 'annotation' out from the sbml-math schema. I would prefer to have the > sed-ml file annotated, rather than the math-ml ... > > If that won't work, perhaps you could keep the JAXB annotations separate > from the miase schema in jlibsedml, perhaps having your ant script merge the > two. > > What do you think? > > Best > Frank > > >> -----Original Message----- >> From: Richard Adams [mailto:ra...@st...] >> Sent: Monday, February 16, 2009 8:08 AM >> To: mia...@li... >> Subject: [Miase-discuss] Schema annotations >> >> >> Sorry, probably didn't explain very well - the .xsd schema definition >> allows application specific annotations. The changes to the schema I'm >> proposing would >> not be included in .miase files, but in the schema itself, inside the >> notes and annotation element definitions. >> >> The problem arises, as JAXB comes across 'notes' and 'annotation' >> defined in both sbml-mathml and sedml schemas. When generating classes >> from the schema, it gets confused as it attempts to create classes of >> the same name twice. To prevent this happening, you can add a >> processing instruction in the notes element declaration in the sedml >> schema, saying 'don't create another notes class for this notes >> element, create a class called 'SedmlNotes instead'. >> >> Just looking through the JAXB docs, there doesn't seem to be an >> obvious solution readily available, e.g., to make the classes in two >> different packages, >> which would prevent the need for these annotations. >> >> Basically, there are a quite a lot of processing instructions which >> could be included, for example, specifying java collection classes, >> method names, class names, javadoc. Some of these, but not all, can be >> put in an external file, called a binding file, so I'm just thinking >> that these schema annotations could pollute the schema definition >> somewhat. >> >> Cheers >> Richard >> >> >> >> >>> I'm sorry, i don't quite see the issue ... the schema right now says >>> that you are free to put under the annotation element pretty much >>> anything, and as far as MIASE goes, it will be ignored. The same goes >>> for the notes section. >>> >>> i've never used jaxb so I'm not sure what the issues are. Could you >>> explain further? >>> >> best >> Frank >> >> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: >> >> >>> Hi all, >>> Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> >>> elements >>> into a schema for tool-specific customization of schema processing. >>> Is this tolerable in the sed-ml schema, or would it clutter up the >>> schema too much? >>> >>> Just wondered as Dagmar's last change ( to add the notes/annotation >>> elements) causes a namespace conflict to the JAXB schema parser with >>> the elements of the same name defined in sbml-mathml. One way round >>> this is to add this jaxb specific annotations in the .xsd file to >>> produce classes with different names. An alternative is to specify >>> instructions in a separate 'binding' file, this would be ideal but >>> I've not got it to work yet. >>> >>> Basically it would add: >>> >>> <xs:annotation> >>> <xs:appinfo> >>> <jxb:class name="SedMLNotes"> >>> </jxb:class> >>> </xs:appinfo> >>> >> -- >> Dr Richard Adams >> Senior Software Developer, >> Computational Systems Biology Group, >> University of Edinburgh >> Tel: 0131 650 8281/8285 >> email : ric...@ed... >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> >> ----------------------------------------------------------------------- >> ------- >> Open Source Business Conference (OSBC), March 24-25, 2009, San >> Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source code: >> SFAD >> http://p.sf.net/sfu/XcvMzF8H >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss >> > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss > |
From: Richard A. <ra...@st...> - 2009-02-17 11:21:25
|
Quoting Frank Bergmann <fbergman@u.washington.edu>: > Personally I don't mind, as I would not consume the schema as such. Though > your concerns are valid at which point would we stop adding non-critical > elements. For the problem at hand it might make more sense to take 'notes' > and 'annotation' out from the sbml-math schema. I would prefer to have the > sed-ml file annotated, rather than the math-ml ... > > If that won't work, perhaps you could keep the JAXB annotations separate > from the miase schema in jlibsedml, perhaps having your ant script merge the > two. I think that could be the best all round solution for now, it keeps the main schema nice and clean - while 'notes' and 'annotation' may not be essential for the mathml elements it probably sets a bad precedent to start altering the schema to fit in with the whims of implementations. > Richard > What do you think? > > Best > Frank > >> -----Original Message----- >> From: Richard Adams [mailto:ra...@st...] >> Sent: Monday, February 16, 2009 8:08 AM >> To: mia...@li... >> Subject: [Miase-discuss] Schema annotations >> >> >> Sorry, probably didn't explain very well - the .xsd schema definition >> allows application specific annotations. The changes to the schema I'm >> proposing would >> not be included in .miase files, but in the schema itself, inside the >> notes and annotation element definitions. >> >> The problem arises, as JAXB comes across 'notes' and 'annotation' >> defined in both sbml-mathml and sedml schemas. When generating classes >> from the schema, it gets confused as it attempts to create classes of >> the same name twice. To prevent this happening, you can add a >> processing instruction in the notes element declaration in the sedml >> schema, saying 'don't create another notes class for this notes >> element, create a class called 'SedmlNotes instead'. >> >> Just looking through the JAXB docs, there doesn't seem to be an >> obvious solution readily available, e.g., to make the classes in two >> different packages, >> which would prevent the need for these annotations. >> >> Basically, there are a quite a lot of processing instructions which >> could be included, for example, specifying java collection classes, >> method names, class names, javadoc. Some of these, but not all, can be >> put in an external file, called a binding file, so I'm just thinking >> that these schema annotations could pollute the schema definition >> somewhat. >> >> Cheers >> Richard >> >> >> >> > I'm sorry, i don't quite see the issue ... the schema right now says >> > that you are free to put under the annotation element pretty much >> > anything, and as far as MIASE goes, it will be ignored. The same goes >> > for the notes section. >> >> > i've never used jaxb so I'm not sure what the issues are. Could you >> > explain further? >> >> best >> Frank >> >> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: >> >> > >> > Hi all, >> > Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> >> > elements >> > into a schema for tool-specific customization of schema processing. >> > Is this tolerable in the sed-ml schema, or would it clutter up the >> > schema too much? >> > >> > Just wondered as Dagmar's last change ( to add the notes/annotation >> > elements) causes a namespace conflict to the JAXB schema parser with >> > the elements of the same name defined in sbml-mathml. One way round >> > this is to add this jaxb specific annotations in the .xsd file to >> > produce classes with different names. An alternative is to specify >> > instructions in a separate 'binding' file, this would be ideal but >> > I've not got it to work yet. >> > >> > Basically it would add: >> > >> > <xs:annotation> >> > <xs:appinfo> >> > <jxb:class name="SedMLNotes"> >> > </jxb:class> >> > </xs:appinfo> >> >> -- >> Dr Richard Adams >> Senior Software Developer, >> Computational Systems Biology Group, >> University of Edinburgh >> Tel: 0131 650 8281/8285 >> email : ric...@ed... >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> >> ----------------------------------------------------------------------- >> ------- >> Open Source Business Conference (OSBC), March 24-25, 2009, San >> Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source code: >> SFAD >> http://p.sf.net/sfu/XcvMzF8H >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss > > -- Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Richard A. <ra...@st...> - 2009-02-17 11:21:22
|
Quoting Frank Bergmann <fbergman@u.washington.edu>: > Personally I don't mind, as I would not consume the schema as such. Though > your concerns are valid at which point would we stop adding non-critical > elements. For the problem at hand it might make more sense to take 'notes' > and 'annotation' out from the sbml-math schema. I would prefer to have the > sed-ml file annotated, rather than the math-ml ... > > If that won't work, perhaps you could keep the JAXB annotations separate > from the miase schema in jlibsedml, perhaps having your ant script merge the > two. I think that could be the best all round solution for now, it keeps the main schema nice and clean - while 'notes' and 'annotation' may not be essential for the mathml elements it probably sets a bad precedent to start altering the schema to fit in with the whims of implementations. > Richard > What do you think? > > Best > Frank > >> -----Original Message----- >> From: Richard Adams [mailto:ra...@st...] >> Sent: Monday, February 16, 2009 8:08 AM >> To: mia...@li... >> Subject: [Miase-discuss] Schema annotations >> >> >> Sorry, probably didn't explain very well - the .xsd schema definition >> allows application specific annotations. The changes to the schema I'm >> proposing would >> not be included in .miase files, but in the schema itself, inside the >> notes and annotation element definitions. >> >> The problem arises, as JAXB comes across 'notes' and 'annotation' >> defined in both sbml-mathml and sedml schemas. When generating classes >> from the schema, it gets confused as it attempts to create classes of >> the same name twice. To prevent this happening, you can add a >> processing instruction in the notes element declaration in the sedml >> schema, saying 'don't create another notes class for this notes >> element, create a class called 'SedmlNotes instead'. >> >> Just looking through the JAXB docs, there doesn't seem to be an >> obvious solution readily available, e.g., to make the classes in two >> different packages, >> which would prevent the need for these annotations. >> >> Basically, there are a quite a lot of processing instructions which >> could be included, for example, specifying java collection classes, >> method names, class names, javadoc. Some of these, but not all, can be >> put in an external file, called a binding file, so I'm just thinking >> that these schema annotations could pollute the schema definition >> somewhat. >> >> Cheers >> Richard >> >> >> >> > I'm sorry, i don't quite see the issue ... the schema right now says >> > that you are free to put under the annotation element pretty much >> > anything, and as far as MIASE goes, it will be ignored. The same goes >> > for the notes section. >> >> > i've never used jaxb so I'm not sure what the issues are. Could you >> > explain further? >> >> best >> Frank >> >> On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: >> >> > >> > Hi all, >> > Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> >> > elements >> > into a schema for tool-specific customization of schema processing. >> > Is this tolerable in the sed-ml schema, or would it clutter up the >> > schema too much? >> > >> > Just wondered as Dagmar's last change ( to add the notes/annotation >> > elements) causes a namespace conflict to the JAXB schema parser with >> > the elements of the same name defined in sbml-mathml. One way round >> > this is to add this jaxb specific annotations in the .xsd file to >> > produce classes with different names. An alternative is to specify >> > instructions in a separate 'binding' file, this would be ideal but >> > I've not got it to work yet. >> > >> > Basically it would add: >> > >> > <xs:annotation> >> > <xs:appinfo> >> > <jxb:class name="SedMLNotes"> >> > </jxb:class> >> > </xs:appinfo> >> >> -- >> Dr Richard Adams >> Senior Software Developer, >> Computational Systems Biology Group, >> University of Edinburgh >> Tel: 0131 650 8281/8285 >> email : ric...@ed... >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> >> ----------------------------------------------------------------------- >> ------- >> Open Source Business Conference (OSBC), March 24-25, 2009, San >> Francisco, CA >> -OSBC tackles the biggest issue in open source: Open Sourcing the >> Enterprise >> -Strategies to boost innovation and cut costs with open source >> participation >> -Receive a $600 discount off the registration fee with the source code: >> SFAD >> http://p.sf.net/sfu/XcvMzF8H >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss > > -- Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Frank B. <fbergman@u.washington.edu> - 2009-02-17 00:09:10
|
Personally I don't mind, as I would not consume the schema as such. Though your concerns are valid at which point would we stop adding non-critical elements. For the problem at hand it might make more sense to take 'notes' and 'annotation' out from the sbml-math schema. I would prefer to have the sed-ml file annotated, rather than the math-ml ... If that won't work, perhaps you could keep the JAXB annotations separate from the miase schema in jlibsedml, perhaps having your ant script merge the two. What do you think? Best Frank > -----Original Message----- > From: Richard Adams [mailto:ra...@st...] > Sent: Monday, February 16, 2009 8:08 AM > To: mia...@li... > Subject: [Miase-discuss] Schema annotations > > > Sorry, probably didn't explain very well - the .xsd schema definition > allows application specific annotations. The changes to the schema I'm > proposing would > not be included in .miase files, but in the schema itself, inside the > notes and annotation element definitions. > > The problem arises, as JAXB comes across 'notes' and 'annotation' > defined in both sbml-mathml and sedml schemas. When generating classes > from the schema, it gets confused as it attempts to create classes of > the same name twice. To prevent this happening, you can add a > processing instruction in the notes element declaration in the sedml > schema, saying 'don't create another notes class for this notes > element, create a class called 'SedmlNotes instead'. > > Just looking through the JAXB docs, there doesn't seem to be an > obvious solution readily available, e.g., to make the classes in two > different packages, > which would prevent the need for these annotations. > > Basically, there are a quite a lot of processing instructions which > could be included, for example, specifying java collection classes, > method names, class names, javadoc. Some of these, but not all, can be > put in an external file, called a binding file, so I'm just thinking > that these schema annotations could pollute the schema definition > somewhat. > > Cheers > Richard > > > > > I'm sorry, i don't quite see the issue ... the schema right now says > > that you are free to put under the annotation element pretty much > > anything, and as far as MIASE goes, it will be ignored. The same goes > > for the notes section. > > > i've never used jaxb so I'm not sure what the issues are. Could you > > explain further? > > best > Frank > > On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: > > > > > Hi all, > > Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> > > elements > > into a schema for tool-specific customization of schema processing. > > Is this tolerable in the sed-ml schema, or would it clutter up the > > schema too much? > > > > Just wondered as Dagmar's last change ( to add the notes/annotation > > elements) causes a namespace conflict to the JAXB schema parser with > > the elements of the same name defined in sbml-mathml. One way round > > this is to add this jaxb specific annotations in the .xsd file to > > produce classes with different names. An alternative is to specify > > instructions in a separate 'binding' file, this would be ideal but > > I've not got it to work yet. > > > > Basically it would add: > > > > <xs:annotation> > > <xs:appinfo> > > <jxb:class name="SedMLNotes"> > > </jxb:class> > > </xs:appinfo> > > -- > Dr Richard Adams > Senior Software Developer, > Computational Systems Biology Group, > University of Edinburgh > Tel: 0131 650 8281/8285 > email : ric...@ed... > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > ----------------------------------------------------------------------- > ------- > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source code: > SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
From: Richard A. <ra...@st...> - 2009-02-16 21:27:30
|
Hi all, There is a skeletal validator for example sedml files available here : http://www.bioinformatics.ed.ac.uk:8080/SBSVisualWebApp/html/sedml/ based upon the current version 0 schema. It validates against the schema and highlights schema errors. It's pretty basic at present - no line numbers for XML well-formedness errors or 'semantic' errors - but the two example files in SVN pass OK. If you're preparing an example file, please give it a go, and let me know if it doesn't behave as expected. Richard Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Richard A. <ra...@st...> - 2009-02-16 21:25:24
|
Hi all, There is a skeletal validator for example sedml files available here : http://www.bioinformatics.ed.ac.uk:8080/SBSVisualWebApp/html/sedml/ based upon the current version 0 schema. It validates against the schema and highlights schema errors. It's pretty basic at present - no line numbers for XML well-formedness errors or 'semantic' errors - but the two example files in SVN pass OK. If you're preparing an example file, please give it a go, and let me know if it doesn't behave as expected. Richard Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Richard A. <ra...@st...> - 2009-02-16 16:44:02
|
Sorry, probably didn't explain very well - the .xsd schema definition allows application specific annotations. The changes to the schema I'm proposing would not be included in .miase files, but in the schema itself, inside the notes and annotation element definitions. The problem arises, as JAXB comes across 'notes' and 'annotation' defined in both sbml-mathml and sedml schemas. When generating classes from the schema, it gets confused as it attempts to create classes of the same name twice. To prevent this happening, you can add a processing instruction in the notes element declaration in the sedml schema, saying 'don't create another notes class for this notes element, create a class called 'SedmlNotes instead'. Just looking through the JAXB docs, there doesn't seem to be an obvious solution readily available, e.g., to make the classes in two different packages, which would prevent the need for these annotations. Basically, there are a quite a lot of processing instructions which could be included, for example, specifying java collection classes, method names, class names, javadoc. Some of these, but not all, can be put in an external file, called a binding file, so I'm just thinking that these schema annotations could pollute the schema definition somewhat. Cheers Richard > I'm sorry, i don't quite see the issue ... the schema right now says > that you are free to put under the annotation element pretty much > anything, and as far as MIASE goes, it will be ignored. The same goes > for the notes section. > i've never used jaxb so I'm not sure what the issues are. Could you > explain further? best Frank On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: > > Hi all, > Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> > elements > into a schema for tool-specific customization of schema processing. > Is this tolerable in the sed-ml schema, or would it clutter up the > schema too much? > > Just wondered as Dagmar's last change ( to add the notes/annotation > elements) causes a namespace conflict to the JAXB schema parser with > the elements of the same name defined in sbml-mathml. One way round > this is to add this jaxb specific annotations in the .xsd file to > produce classes with different names. An alternative is to specify > instructions in a separate 'binding' file, this would be ideal but > I've not got it to work yet. > > Basically it would add: > > <xs:annotation> > <xs:appinfo> > <jxb:class name="SedMLNotes"> > </jxb:class> > </xs:appinfo> -- Dr Richard Adams Senior Software Developer, Computational Systems Biology Group, University of Edinburgh Tel: 0131 650 8281/8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Frank B. <fbergman@u.washington.edu> - 2009-02-15 02:33:56
|
I'm sorry, i don't quite see the issue ... the schema right now says that you are free to put under the annotation element pretty much anything, and as far as MIASE goes, it will be ignored. The same goes for the notes section. i've never used jaxb so I'm not sure what the issues are. Could you explain further? best Frank On Feb 14, 2009, at 2:28 PM, Richard Adams wrote: > > Hi all, > Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> > elements > into a schema for tool-specific customization of schema processing. > Is this tolerable in the sed-ml schema, or would it clutter up the > schema too much? > > Just wondered as Dagmar's last change ( to add the notes/annotation > elements) causes a namespace conflict to the JAXB schema parser with > the elements of the same name defined in sbml-mathml. One way round > this is to add this jaxb specific annotations in the .xsd file to > produce classes with different names. An alternative is to specify > instructions in a separate 'binding' file, this would be ideal but > I've not got it to work yet. > > Basically it would add: > > <xs:annotation> > <xs:appinfo> > <jxb:class name="SedMLNotes"> > </jxb:class> > </xs:appinfo> > </xs:annotation> > into the 'notes' definition and similarly into the 'annotation' > definition. > > I have a feeling that this will be frowned upon but I just wanted to > make sure before ruling it out :) > > Thanks > Richard > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San > Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the > Enterprise > -Strategies to boost innovation and cut costs with open source > participation > -Receive a $600 discount off the registration fee with the source > code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
From: Richard A. <ra...@st...> - 2009-02-14 23:04:01
|
Hi all, Just wondering, it is possible to add <xsd:annotation><xsd:appinfo> elements into a schema for tool-specific customization of schema processing. Is this tolerable in the sed-ml schema, or would it clutter up the schema too much? Just wondered as Dagmar's last change ( to add the notes/annotation elements) causes a namespace conflict to the JAXB schema parser with the elements of the same name defined in sbml-mathml. One way round this is to add this jaxb specific annotations in the .xsd file to produce classes with different names. An alternative is to specify instructions in a separate 'binding' file, this would be ideal but I've not got it to work yet. Basically it would add: <xs:annotation> <xs:appinfo> <jxb:class name="SedMLNotes"> </jxb:class> </xs:appinfo> </xs:annotation> into the 'notes' definition and similarly into the 'annotation' definition. I have a feeling that this will be frowned upon but I just wanted to make sure before ruling it out :) Thanks Richard -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Dagmar K. <da...@eb...> - 2009-02-09 15:07:59
|
Hello everybody, " we miss a logo ..." Would anyone be interested in proposing something? I am myself not very talented with those design things. And as we all would have to live with the outcome ... Suggestions (drafts or professional) are very welcome and could be posted on the list or send to me personally, as you wish :-) Thanks in advance, Dagmar |
From: Dagmar K. <da...@eb...> - 2009-02-03 13:39:33
|
Frank Bergmann wrote: > > > - Inheritances differ in OM and schema, see for example curve and > surface. > - for notes and annotations, which are currently strings, it might be > nice to use more than simple strings. If I were to use annotations, > I'd rather use a block of xml ... good news, mike has gone through the > trouble before and the sbml schema has the needed specification: > > <xsd:sequence> > <xsd:element name="notes" minOccurs="0"> > <xsd:complexType> > <xsd:sequence> > <xsd:any namespace="http://www.w3.org/1999/xhtml" > processContents="skip" > minOccurs="0" maxOccurs="unbounded"/> > </xsd:sequence> > </xsd:complexType> > </xsd:element> > <xsd:element name="annotation" minOccurs="0"> > <xsd:complexType> > <xsd:sequence> > <xsd:any processContents="skip" > minOccurs="0" maxOccurs="unbounded"/> > </xsd:sequence> > </xsd:complexType> > </xsd:element> > </xsd:sequence> Changed according to Franks suggestion - in the sedml-tmp.xsd on SF /Dagmar |
From: <da...@eb...> - 2009-01-31 04:42:43
|
added dagmar >> >> I set up a Wiki page to collect all the open questions/issues for the >> workshop day in April: >> http://miase.wiki.sourceforge.net/OpenIssues >> Remind me if I forget things, please. >> > > Do you want us to contribute to it? Otherwise here my list of open issues: > > - storage format > - what math is allowed in the math for datagenerators (or ChangeMath) > - how to refer to the time symbol > > > And then of course for later: > - 'AnySimulation' > - how to refer to measurement data > - K I S A O and what it means for the specified Simulations > - > > Cheers > Frank > >> Have a nice weekend everybody, >> Dagmar >> >> ----------------------------------------------------------------------- >> ------- >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf-spreadtheword >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss > |
From: <da...@eb...> - 2009-01-30 23:53:26
|
>> they are optional - one of the references is for use of the variable >> element in ChangeMath, the other one is for use of the variable element >> in Task and DataGenerator... > > Except they are not both optional, they are mutual exclusive ... Yes, but being attributes in the schema you could not specify it... neither in the UML actually (at least I would not see how). Well, the problem will be non-existent as soon as we solved the other one ... > >> ... or we could check whether we want to go back to using >> modelReferences in the DataGenerator class instead of using the >> taskReference - which I would prefer. > > As Nicolas was describing, (and I should have remembered from the > discussions), the taskReference is vital for DataGenerators, so that we > can > refer to the transient values, with the model reference we would only > record > the initial value. So we will have to fork them ... but again, this can > wait > until concrete examples about ChangeMath have been put into play ... Sorry, I didn't get that before. Should have looked at the UML... So forget what I said :-) Problem solved. (Although I still think it is weird to have 2 different entities/classes for the same thing. Well...) > >> >> Dagmar >> >> ----------------------------------------------------------------------- >> ------- >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf-spreadtheword >> _______________________________________________ >> Miase-discuss mailing list >> Mia...@li... >> https://lists.sourceforge.net/lists/listinfo/miase-discuss > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss > |