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From: Matthias K. <kon...@go...> - 2016-02-02 21:50:42
|
listOfAlgorithmParameters
maximum_bdf_order: 5
maximum_adams_order: 12
maximum_num_steps: 20000
maximum_time_step: 0
minimum_time_step: 0
initial_time_step:
On Tue, Feb 2, 2016 at 7:37 PM, Lucian Smith <luc...@gm...>
wrote:
> It's clearly important that whoever makes the diagrams use what they're
> comfortable with! I've made enough Google draw UML diagrams by now that I
> can make them pretty quickly, though of course you don't get the UML
> checking. You can export them to PDF, though, which is standard enough for
> LaTeX to include.
>
> Here's a draft UML diagram for Matthias's proposal. And clearly, great
> minds think alike, because I also had Dagmar's idea of subclassing a base
> 'TimeCourse' abstract class:
>
>
> https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing
>
> -Lucian
>
> On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath <
> dag...@un...> wrote:
>
>> Hi Lucian,
>>
>> it was me who insisted on using MagicDraw UML, because the last time I
>> drew SBML UML diagrams this was in Google draw, so no means of checking the
>> UML for consistency, and also not very automised, and not exportable to a
>> standard format ;-).
>>
>> MagicDraw UML is not a free tool though, which is why the other editors
>> didn't like it too much.
>>
>> Oh, and this is just to clarify, not an objection.
>>
>> Best, Dagmar
>>
>>
>> *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics,
>> University of Rostock, D-18051 Rostock, Germany
>> Web: http://www.sbi.uni-rostock.de/sems
>> <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/>
>> Skype: dagmar.waltemath
>> ------------------------------
>> *Von:* Lucian Smith [luc...@gm...]
>> *Gesendet:* Dienstag, 2. Februar 2016 19:16
>> *An:* sed...@li...
>> *Betreff:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>
>> Sure, I can do that. I like the idea of making a new base class which
>> UniformTimeCourse inherits from.
>>
>> As far as the new spec goes, there are a lot of issues with the current
>> UML diagrams, many of which have been filed in the sed-ml tracker. I'm
>> inclined to ditch them all and start from scratch, using UML templates from
>> SBML. Would anyone object to this? Are there features of the current
>> SED-ML UML diagrams that people like better than the ones used in the SBML
>> spec?
>>
>> -Lucian
>>
>> On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...> wrote:
>>
>>> Same with VCell, has been supported for a decade by now…
>>>
>>>
>>>
>>> It is a feature on the list of add-ons to the next SED-ML version.
>>> Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft
>>> spec?
>>>
>>>
>>>
>>> Ion
>>>
>>>
>>>
>>> *From:* Herbert Sauro [mailto:hs...@gm...]
>>> *Sent:* Tuesday, February 02, 2016 12:31 PM
>>> *To:* sed...@li...
>>> *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse
>>>
>>>
>>>
>>> libRoadRunner already support variable time step so it would be very
>>> useful to have this in sedml.
>>>
>>>
>>>
>>> Herbert
>>>
>>>
>>>
>>> On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <
>>> ped...@ma...> wrote:
>>>
>>> Matthias,
>>>
>>> > If tools like COPASI do not support variable_time_step simulation
>>>
>>> It will, the current snapshots being tested already have this feature,
>>> so it will be in the next release. It would be great if it would be
>>> supported in SED-ML.
>>>
>>> Pedro
>>> --
>>> Pedro Mendes
>>> Professor of Computational Systems Biology
>>> School of Computer Science
>>> Manchester Centre for Integrative Systems Biology
>>> University of Manchester
>>>
>>> Manchester Institute of Biotechnology
>>> 131 Princess Street
>>> Manchester, M1 7DN, U.K.
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=>
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>>> Monitor end-to-end web transactions and take corrective actions now
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>
>
> ------------------------------------------------------------------------------
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
> Monitor end-to-end web transactions and take corrective actions now
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
--
Matthias König
Email: kon...@go...
Tel: + 49 30 20938450
Tel: + 49 176 81168480
https://www.livermetabolism.com/contact.html
Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group
König
Charité Berlin, Institute of Biochemistry, Computational Systems
Biochemistry <http://www.charite.de/sysbio/people/koenig/>
|
|
From: Lucian S. <luc...@gm...> - 2016-02-02 18:37:18
|
It's clearly important that whoever makes the diagrams use what they're comfortable with! I've made enough Google draw UML diagrams by now that I can make them pretty quickly, though of course you don't get the UML checking. You can export them to PDF, though, which is standard enough for LaTeX to include. Here's a draft UML diagram for Matthias's proposal. And clearly, great minds think alike, because I also had Dagmar's idea of subclassing a base 'TimeCourse' abstract class: https://docs.google.com/drawings/d/1YqQ0h62UbEmBgrGvqGkHi9YhO1l3dUUsE3y7n83rMKw/edit?usp=sharing -Lucian On Tue, Feb 2, 2016 at 10:24 AM, Dagmar Waltemath < dag...@un...> wrote: > Hi Lucian, > > it was me who insisted on using MagicDraw UML, because the last time I > drew SBML UML diagrams this was in Google draw, so no means of checking the > UML for consistency, and also not very automised, and not exportable to a > standard format ;-). > > MagicDraw UML is not a free tool though, which is why the other editors > didn't like it too much. > > Oh, and this is just to clarify, not an objection. > > Best, Dagmar > > > *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics, > University of Rostock, D-18051 Rostock, Germany > Web: http://www.sbi.uni-rostock.de/sems > <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> > Skype: dagmar.waltemath > ------------------------------ > *Von:* Lucian Smith [luc...@gm...] > *Gesendet:* Dienstag, 2. Februar 2016 19:16 > *An:* sed...@li... > *Betreff:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse > > Sure, I can do that. I like the idea of making a new base class which > UniformTimeCourse inherits from. > > As far as the new spec goes, there are a lot of issues with the current > UML diagrams, many of which have been filed in the sed-ml tracker. I'm > inclined to ditch them all and start from scratch, using UML templates from > SBML. Would anyone object to this? Are there features of the current > SED-ML UML diagrams that people like better than the ones used in the SBML > spec? > > -Lucian > > On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...> wrote: > >> Same with VCell, has been supported for a decade by now… >> >> >> >> It is a feature on the list of add-ons to the next SED-ML version. >> Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft >> spec? >> >> >> >> Ion >> >> >> >> *From:* Herbert Sauro [mailto:hs...@gm...] >> *Sent:* Tuesday, February 02, 2016 12:31 PM >> *To:* sed...@li... >> *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse >> >> >> >> libRoadRunner already support variable time step so it would be very >> useful to have this in sedml. >> >> >> >> Herbert >> >> >> >> On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes < >> ped...@ma...> wrote: >> >> Matthias, >> >> > If tools like COPASI do not support variable_time_step simulation >> >> It will, the current snapshots being tested already have this feature, >> so it will be in the next release. It would be great if it would be >> supported in SED-ML. >> >> Pedro >> -- >> Pedro Mendes >> Professor of Computational Systems Biology >> School of Computer Science >> Manchester Centre for Integrative Systems Biology >> University of Manchester >> >> Manchester Institute of Biotechnology >> 131 Princess Street >> Manchester, M1 7DN, U.K. >> >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=> >> >> >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
|
From: Dagmar W. <dag...@un...> - 2016-02-02 18:35:13
|
Hi, regarding Matthias' idea of subclassing time courses, I would prefer to have a generic, abstract class TimeCourse which both, UniformTimeCourse and NonUniformTimeCourse inherit from. Matthias, is there any other information that you need to specify in the *non*uniform timecourse? Dagmar Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics, University of Rostock, D-18051 Rostock, Germany Web: http://www.sbi.uni-rostock.de/sems<http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> Skype: dagmar.waltemath ________________________________ Von: Matthias König [kon...@go...] Gesendet: Dienstag, 2. Februar 2016 15:04 An: SED...@li... Betreff: [SED-ML-discuss] Feature request: NonUniformTimeCourse Hi all, like mentioned during the SED-ML harmony discussion I am very interested in the support of NonUniformTimeCourse simulations. I could not find anything in the L1V3 specification about it. All my simulations are NonUniformTimeCourses, without support of these it does not make sense to integrate SED-ML in my workflows. This is very easy to add to SED-ML: Just create the additional class NonUniformTimeCourse +initialTime : double +outputStartTime : double +outputEndTime : double as additional subclass of Simulation and copy all functions/documentation for the initialTime, outputStartTime, outputEndTime from the UniformTimeCourse. Even better make UniformTimeCourse a subclass of NonUniformTimeCourse with the additional attribute numberOfPoints. If tools like COPASI do not support variable_time_step simulation they can just ignore the NonUniformTimeCourse or convert it to a UniformTimeCourse with some default step. I mentioned this request multiple times over the last few years and would be very nice if it could be part of L1V3. I wanted to submit the request via the sourceforge tracker like proposed on https://sourceforge.net/p/sed-ml/feature-requests/ but unfortunately only people authorized by the project admins are allowed to make feature requests. Matthias -- Matthias König Email: kon...@go...<mailto:kon...@go...> Tel: + 49 30 20938450 Tel: + 49 176 81168480 [https://docs.google.com/uc?export=download&id=0B5gYPV9g1eEKQmNHb3dxUWlWYmc&revid=0B5gYPV9g1eEKNW8wYVlCd3IzZmdXbitsTEJPR3VaZ3JseVU0PQ] https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry<http://www.charite.de/sysbio/people/koenig/> |
|
From: Dagmar W. <dag...@un...> - 2016-02-02 18:24:09
|
Hi Lucian, it was me who insisted on using MagicDraw UML, because the last time I drew SBML UML diagrams this was in Google draw, so no means of checking the UML for consistency, and also not very automised, and not exportable to a standard format ;-). MagicDraw UML is not a free tool though, which is why the other editors didn't like it too much. Oh, and this is just to clarify, not an objection. Best, Dagmar Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics, University of Rostock, D-18051 Rostock, Germany Web: http://www.sbi.uni-rostock.de/sems<http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> Skype: dagmar.waltemath ________________________________ Von: Lucian Smith [luc...@gm...] Gesendet: Dienstag, 2. Februar 2016 19:16 An: sed...@li... Betreff: Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse Sure, I can do that. I like the idea of making a new base class which UniformTimeCourse inherits from. As far as the new spec goes, there are a lot of issues with the current UML diagrams, many of which have been filed in the sed-ml tracker. I'm inclined to ditch them all and start from scratch, using UML templates from SBML. Would anyone object to this? Are there features of the current SED-ML UML diagrams that people like better than the ones used in the SBML spec? -Lucian On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...<mailto:mo...@uc...>> wrote: Same with VCell, has been supported for a decade by now… It is a feature on the list of add-ons to the next SED-ML version. Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft spec? Ion From: Herbert Sauro [mailto:hs...@gm...<mailto:hs...@gm...>] Sent: Tuesday, February 02, 2016 12:31 PM To: sed...@li...<mailto:sed...@li...> Subject: Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse libRoadRunner already support variable time step so it would be very useful to have this in sedml. Herbert On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <ped...@ma...<mailto:ped...@ma...>> wrote: Matthias, > If tools like COPASI do not support variable_time_step simulation It will, the current snapshots being tested already have this feature, so it will be in the next release. It would be great if it would be supported in SED-ML. Pedro -- Pedro Mendes Professor of Computational Systems Biology School of Computer Science Manchester Centre for Integrative Systems Biology University of Manchester Manchester Institute of Biotechnology 131 Princess Street Manchester, M1 7DN, U.K. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140<https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=> _______________________________________________ SED-ML-discuss mailing list SED...@li...<mailto:SED...@li...> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=> ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ SED-ML-discuss mailing list SED...@li...<mailto:SED...@li...> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
|
From: Lucian S. <luc...@gm...> - 2016-02-02 18:16:16
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Sure, I can do that. I like the idea of making a new base class which UniformTimeCourse inherits from. As far as the new spec goes, there are a lot of issues with the current UML diagrams, many of which have been filed in the sed-ml tracker. I'm inclined to ditch them all and start from scratch, using UML templates from SBML. Would anyone object to this? Are there features of the current SED-ML UML diagrams that people like better than the ones used in the SBML spec? -Lucian On Tue, Feb 2, 2016 at 9:37 AM, Moraru,Ion <mo...@uc...> wrote: > Same with VCell, has been supported for a decade by now… > > > > It is a feature on the list of add-ons to the next SED-ML version. > Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft > spec? > > > > Ion > > > > *From:* Herbert Sauro [mailto:hs...@gm...] > *Sent:* Tuesday, February 02, 2016 12:31 PM > *To:* sed...@li... > *Subject:* Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse > > > > libRoadRunner already support variable time step so it would be very > useful to have this in sedml. > > > > Herbert > > > > On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes < > ped...@ma...> wrote: > > Matthias, > > > If tools like COPASI do not support variable_time_step simulation > > It will, the current snapshots being tested already have this feature, > so it will be in the next release. It would be great if it would be > supported in SED-ML. > > Pedro > -- > Pedro Mendes > Professor of Computational Systems Biology > School of Computer Science > Manchester Centre for Integrative Systems Biology > University of Manchester > > Manchester Institute of Biotechnology > 131 Princess Street > Manchester, M1 7DN, U.K. > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > <https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=> > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=> > > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
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From: Dagmar W. <dag...@un...> - 2016-02-02 18:15:58
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Hej Matthias, comments should work now for feature requests and proposals. Thanks for spotting this. Dagmar Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics, University of Rostock, D-18051 Rostock, Germany Web: http://www.sbi.uni-rostock.de/sems<http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> Skype: dagmar.waltemath ________________________________ Von: Matthias König [kon...@go...] Gesendet: Dienstag, 2. Februar 2016 16:38 An: sed...@li... Betreff: Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse Thanks Dagmar. The feature request can be found https://sourceforge.net/p/sed-ml/feature-requests/7/ Can you also allow Dissusions/Comments on the Tickets? Currently nobody can comment on the feature requests. Matthias On Tue, Feb 2, 2016 at 3:16 PM, Dagmar Waltemath <dag...@un...<mailto:dag...@un...>> wrote: Hi Matthias, would you mind trying again? It should be possible now to submit feature requests without logging in to sourceforge. (I remember that we had this discussion before, so I just updated the permissions on SF.) Dagmar Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics, University of Rostock, D-18051 Rostock, Germany Web: http://www.sbi.uni-rostock.de/sems<http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> Skype: dagmar.waltemath ________________________________ Von: Matthias König [kon...@go...<mailto:kon...@go...>] Gesendet: Dienstag, 2. Februar 2016 15:04 An: SED...@li...<mailto:SED...@li...> Betreff: [SED-ML-discuss] Feature request: NonUniformTimeCourse Hi all, like mentioned during the SED-ML harmony discussion I am very interested in the support of NonUniformTimeCourse simulations. I could not find anything in the L1V3 specification about it. All my simulations are NonUniformTimeCourses, without support of these it does not make sense to integrate SED-ML in my workflows. This is very easy to add to SED-ML: Just create the additional class NonUniformTimeCourse +initialTime : double +outputStartTime : double +outputEndTime : double as additional subclass of Simulation and copy all functions/documentation for the initialTime, outputStartTime, outputEndTime from the UniformTimeCourse. Even better make UniformTimeCourse a subclass of NonUniformTimeCourse with the additional attribute numberOfPoints. If tools like COPASI do not support variable_time_step simulation they can just ignore the NonUniformTimeCourse or convert it to a UniformTimeCourse with some default step. I mentioned this request multiple times over the last few years and would be very nice if it could be part of L1V3. I wanted to submit the request via the sourceforge tracker like proposed on https://sourceforge.net/p/sed-ml/feature-requests/ but unfortunately only people authorized by the project admins are allowed to make feature requests. Matthias -- Matthias König Email: kon...@go...<mailto:kon...@go...> Tel: + 49 30 20938450 Tel: + 49 176 81168480<tel:%2B%2049%20176%2081168480> [https://docs.google.com/uc?export=download&id=0B5gYPV9g1eEKQmNHb3dxUWlWYmc&revid=0B5gYPV9g1eEKNW8wYVlCd3IzZmdXbitsTEJPR3VaZ3JseVU0PQ] https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry<http://www.charite.de/sysbio/people/koenig/> ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ SED-ML-discuss mailing list SED...@li...<mailto:SED...@li...> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss -- Matthias König Email: kon...@go...<mailto:kon...@go...> Tel: + 49 30 20938450 Tel: + 49 176 81168480 [https://docs.google.com/uc?export=download&id=0B5gYPV9g1eEKQmNHb3dxUWlWYmc&revid=0B5gYPV9g1eEKNW8wYVlCd3IzZmdXbitsTEJPR3VaZ3JseVU0PQ] https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry<http://www.charite.de/sysbio/people/koenig/> |
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From: Moraru,Ion <mo...@uc...> - 2016-02-02 18:07:03
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Same with VCell, has been supported for a decade by now… It is a feature on the list of add-ons to the next SED-ML version. Perhaps Lucian, as a new Editor and full of energy, can spearhead a draft spec? Ion From: Herbert Sauro [mailto:hs...@gm...] Sent: Tuesday, February 02, 2016 12:31 PM To: sed...@li... Subject: Re: [SED-ML-discuss] Feature request: NonUniformTimeCourse libRoadRunner already support variable time step so it would be very useful to have this in sedml. Herbert On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <ped...@ma...<mailto:ped...@ma...>> wrote: Matthias, > If tools like COPASI do not support variable_time_step simulation It will, the current snapshots being tested already have this feature, so it will be in the next release. It would be great if it would be supported in SED-ML. Pedro -- Pedro Mendes Professor of Computational Systems Biology School of Computer Science Manchester Centre for Integrative Systems Biology University of Manchester Manchester Institute of Biotechnology 131 Princess Street Manchester, M1 7DN, U.K. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140<https://urldefense.proofpoint.com/v2/url?u=http-3A__pubads.g.doubleclick.net_gampad_clk-3Fid-3D267308311-26iu-3D_4140&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=muXLw0tJUSLN3opHI1lcLUoTTxgHFsFf0plt_ksm3ys&e=> _______________________________________________ SED-ML-discuss mailing list SED...@li...<mailto:SED...@li...> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_sed-2Dml-2Ddiscuss&d=BQMFaQ&c=EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=Uahi_Qsm5BuafcKS0wC-iw&m=KUCPKoeskjbeTS7STo20iJGOriM1Kx-uiaLV4sJQRT4&s=_oAS5TaPkmhfMLkpK--LZvbW56Fs2TbIfvSaXkU0on0&e=> |
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From: Herbert S. <hs...@gm...> - 2016-02-02 17:31:15
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libRoadRunner already support variable time step so it would be very useful to have this in sedml. Herbert On Tue, Feb 2, 2016 at 9:12 AM, Pedro Mendes <ped...@ma...> wrote: > Matthias, > > > If tools like COPASI do not support variable_time_step simulation > > It will, the current snapshots being tested already have this feature, > so it will be in the next release. It would be great if it would be > supported in SED-ML. > > Pedro > -- > Pedro Mendes > Professor of Computational Systems Biology > School of Computer Science > Manchester Centre for Integrative Systems Biology > University of Manchester > > Manchester Institute of Biotechnology > 131 Princess Street > Manchester, M1 7DN, U.K. > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: Pedro M. <ped...@ma...> - 2016-02-02 17:12:49
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Matthias, > If tools like COPASI do not support variable_time_step simulation It will, the current snapshots being tested already have this feature, so it will be in the next release. It would be great if it would be supported in SED-ML. Pedro -- Pedro Mendes Professor of Computational Systems Biology School of Computer Science Manchester Centre for Integrative Systems Biology University of Manchester Manchester Institute of Biotechnology 131 Princess Street Manchester, M1 7DN, U.K. |
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From: Matthias K. <kon...@go...> - 2016-02-02 15:39:06
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Thanks Dagmar. The feature request can be found https://sourceforge.net/p/sed-ml/feature-requests/7/ Can you also allow Dissusions/Comments on the Tickets? Currently nobody can comment on the feature requests. Matthias On Tue, Feb 2, 2016 at 3:16 PM, Dagmar Waltemath < dag...@un...> wrote: > Hi Matthias, > > would you mind trying again? It should be possible now to submit feature > requests without logging in to sourceforge. > > (I remember that we had this discussion before, so I just updated the > permissions on SF.) > > Dagmar > > > > *Dagmar Waltemath*, Dept. of Systems Biology & Bioinformatics, > University of Rostock, D-18051 Rostock, Germany > Web: http://www.sbi.uni-rostock.de/sems > <http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> > Skype: dagmar.waltemath > ------------------------------ > *Von:* Matthias König [kon...@go...] > *Gesendet:* Dienstag, 2. Februar 2016 15:04 > *An:* SED...@li... > *Betreff:* [SED-ML-discuss] Feature request: NonUniformTimeCourse > > Hi all, > > like mentioned during the SED-ML harmony discussion I am very interested > in the support of *NonUniformTimeCourse *simulations. I could not find > anything in the L1V3 specification about it. All my simulations are > NonUniformTimeCourses, without support of these it does not make sense to > integrate SED-ML in my workflows. > > This is very easy to add to SED-ML: > Just create the additional class > > NonUniformTimeCourse > +initialTime : double > +outputStartTime : double > +outputEndTime : double > > as additional subclass of Simulation and copy all functions/documentation > for the initialTime, outputStartTime, outputEndTime from the > UniformTimeCourse. > Even better make UniformTimeCourse a subclass of NonUniformTimeCourse with > the additional attribute numberOfPoints. > If tools like COPASI do not support variable_time_step simulation they can > just ignore the NonUniformTimeCourse or convert it to a UniformTimeCourse > with some default step. > > I mentioned this request multiple times over the last few years and would > be very nice if it could be part of L1V3. > > I wanted to submit the request via the sourceforge tracker like proposed on > https://sourceforge.net/p/sed-ml/feature-requests/ > but unfortunately only people authorized by the project admins are allowed > to make feature requests. > > Matthias > > -- > Matthias König > Email: kon...@go... > Tel: + 49 30 20938450 > Tel: + 49 176 81168480 > https://www.livermetabolism.com/contact.html > Humboldt-University Berlin, Institute for Theoretical Biology, Junior > Group König > Charité Berlin, Institute of Biochemistry, Computational Systems > Biochemistry <http://www.charite.de/sysbio/people/koenig/> > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > -- Matthias König Email: kon...@go... Tel: + 49 30 20938450 Tel: + 49 176 81168480 https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry <http://www.charite.de/sysbio/people/koenig/> |
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From: Dagmar W. <dag...@un...> - 2016-02-02 14:18:30
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Hi Matthias, would you mind trying again? It should be possible now to submit feature requests without logging in to sourceforge. (I remember that we had this discussion before, so I just updated the permissions on SF.) Dagmar Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics, University of Rostock, D-18051 Rostock, Germany Web: http://www.sbi.uni-rostock.de/sems<http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/> Skype: dagmar.waltemath ________________________________ Von: Matthias König [kon...@go...] Gesendet: Dienstag, 2. Februar 2016 15:04 An: SED...@li... Betreff: [SED-ML-discuss] Feature request: NonUniformTimeCourse Hi all, like mentioned during the SED-ML harmony discussion I am very interested in the support of NonUniformTimeCourse simulations. I could not find anything in the L1V3 specification about it. All my simulations are NonUniformTimeCourses, without support of these it does not make sense to integrate SED-ML in my workflows. This is very easy to add to SED-ML: Just create the additional class NonUniformTimeCourse +initialTime : double +outputStartTime : double +outputEndTime : double as additional subclass of Simulation and copy all functions/documentation for the initialTime, outputStartTime, outputEndTime from the UniformTimeCourse. Even better make UniformTimeCourse a subclass of NonUniformTimeCourse with the additional attribute numberOfPoints. If tools like COPASI do not support variable_time_step simulation they can just ignore the NonUniformTimeCourse or convert it to a UniformTimeCourse with some default step. I mentioned this request multiple times over the last few years and would be very nice if it could be part of L1V3. I wanted to submit the request via the sourceforge tracker like proposed on https://sourceforge.net/p/sed-ml/feature-requests/ but unfortunately only people authorized by the project admins are allowed to make feature requests. Matthias -- Matthias König Email: kon...@go...<mailto:kon...@go...> Tel: + 49 30 20938450 Tel: + 49 176 81168480 [https://docs.google.com/uc?export=download&id=0B5gYPV9g1eEKQmNHb3dxUWlWYmc&revid=0B5gYPV9g1eEKNW8wYVlCd3IzZmdXbitsTEJPR3VaZ3JseVU0PQ] https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry<http://www.charite.de/sysbio/people/koenig/> |
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From: Matthias K. <kon...@go...> - 2016-02-02 14:04:20
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Hi all, like mentioned during the SED-ML harmony discussion I am very interested in the support of *NonUniformTimeCourse *simulations. I could not find anything in the L1V3 specification about it. All my simulations are NonUniformTimeCourses, without support of these it does not make sense to integrate SED-ML in my workflows. This is very easy to add to SED-ML: Just create the additional class NonUniformTimeCourse +initialTime : double +outputStartTime : double +outputEndTime : double as additional subclass of Simulation and copy all functions/documentation for the initialTime, outputStartTime, outputEndTime from the UniformTimeCourse. Even better make UniformTimeCourse a subclass of NonUniformTimeCourse with the additional attribute numberOfPoints. If tools like COPASI do not support variable_time_step simulation they can just ignore the NonUniformTimeCourse or convert it to a UniformTimeCourse with some default step. I mentioned this request multiple times over the last few years and would be very nice if it could be part of L1V3. I wanted to submit the request via the sourceforge tracker like proposed on https://sourceforge.net/p/sed-ml/feature-requests/ but unfortunately only people authorized by the project admins are allowed to make feature requests. Matthias -- Matthias König Email: kon...@go... Tel: + 49 30 20938450 Tel: + 49 176 81168480 https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry <http://www.charite.de/sysbio/people/koenig/> |
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From: Dagmar W. <dag...@un...> - 2016-02-02 13:36:50
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Hello, can someone remind me where to find information about the differences between SED-ML L1V2 and the L1V3 draft document? Also, what is the current state of L1V3? Is the latest version still: http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1.pdf ? Thanks a lot, Dagmar |
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From: Matthias K. <kon...@go...> - 2016-02-01 12:08:56
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Hi Frank, this is perfect. Works out of the box on Ubuntu 14.04LTS x64_86. Thanks so much. Matthias On Sat, Jan 30, 2016 at 12:07 PM, Frank Bergmann <fbe...@ca...> wrote: > Hello Matthias, > > I’ve spend some time and created a first pip version, please give it a try > and let me know whether that works for you: > > pip install python-libsedml > > Cheers > Frank > > P.S: the best place to make requests for libSEDML would be the libSEDML > issue tracker, then we would have one place to track the information and > don’t have to bother the list. > > > > On Jan 27, 2016, at 3:05 PM, Matthias König <kon...@go...> > wrote: > > > > Hi All, > > > > There should be an installable python pip package for libsedml and > phrasedml. Currently it is impossible to create a python `virtualenv` > virtual environment which can provide the functionality of libsedml and > phrasedml. > > > > Analogue to > > ``` > > python-libsbml > > ``` > > which allows an easy install of libsbml via > > ``` > > pip install python-libsbml > > ``` > > There should be an easy install of libsedml for python via > > ``` > > pip install python-libsedml python-phrasedml > > ``` > > I need this for creating a reproducible python virtual environment with > libsedml dependency included. It would than be sufficient to list all the > packages including python-libsedml in a requirements.txt. > > I need it for some use cases where I only can work in virtual > environments on some servers (for instance when creating docs on > readthedocs). Currently, the only way for me to provide a reproducible > install is within a docker environment (or virtual machine). > > If only pip installs within virtual environments are allowed there is no > way to get libsedml on the server because I cannot execute the make > scripts. Same for phrasedml. > > > > The best > > Matthias > > > > -- > > Matthias König > > Email: kon...@go... > > Tel: + 49 30 20938450 > > Tel: + 49 176 81168480 > > https://www.livermetabolism.com/contact.html > > Humboldt-University Berlin, Institute for Theoretical Biology, Junior > Group König > > Charité Berlin, Institute of Biochemistry, Computational Systems > Biochemistry > > > ------------------------------------------------------------------------------ > > Site24x7 APM Insight: Get Deep Visibility into Application Performance > > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > > Monitor end-to-end web transactions and take corrective actions now > > Troubleshoot faster and improve end-user experience. Signup Now! > > > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > -- Matthias König Email: kon...@go... Tel: + 49 30 20938450 Tel: + 49 176 81168480 https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry <http://www.charite.de/sysbio/people/koenig/> |
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From: Frank B. <fbe...@ca...> - 2016-01-30 11:08:04
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Hello Matthias, I’ve spend some time and created a first pip version, please give it a try and let me know whether that works for you: pip install python-libsedml Cheers Frank P.S: the best place to make requests for libSEDML would be the libSEDML issue tracker, then we would have one place to track the information and don’t have to bother the list. > On Jan 27, 2016, at 3:05 PM, Matthias König <kon...@go...> wrote: > > Hi All, > > There should be an installable python pip package for libsedml and phrasedml. Currently it is impossible to create a python `virtualenv` virtual environment which can provide the functionality of libsedml and phrasedml. > > Analogue to > ``` > python-libsbml > ``` > which allows an easy install of libsbml via > ``` > pip install python-libsbml > ``` > There should be an easy install of libsedml for python via > ``` > pip install python-libsedml python-phrasedml > ``` > I need this for creating a reproducible python virtual environment with libsedml dependency included. It would than be sufficient to list all the packages including python-libsedml in a requirements.txt. > I need it for some use cases where I only can work in virtual environments on some servers (for instance when creating docs on readthedocs). Currently, the only way for me to provide a reproducible install is within a docker environment (or virtual machine). > If only pip installs within virtual environments are allowed there is no way to get libsedml on the server because I cannot execute the make scripts. Same for phrasedml. > > The best > Matthias > > -- > Matthias König > Email: kon...@go... > Tel: + 49 30 20938450 > Tel: + 49 176 81168480 > https://www.livermetabolism.com/contact.html > Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König > Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Matthias K. <kon...@go...> - 2016-01-27 14:06:06
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Hi All, There should be an installable python pip package for libsedml and phrasedml. Currently it is impossible to create a python `virtualenv` virtual environment which can provide the functionality of libsedml and phrasedml. Analogue to ``` python-libsbml ``` which allows an easy install of libsbml via ``` pip install python-libsbml ``` There should be an easy install of libsedml for python via ``` pip install python-libsedml python-phrasedml ``` I need this for creating a reproducible python virtual environment with libsedml dependency included. It would than be sufficient to list all the packages including python-libsedml in a requirements.txt. I need it for some use cases where I only can work in virtual environments on some servers (for instance when creating docs on readthedocs). Currently, the only way for me to provide a reproducible install is within a docker environment (or virtual machine). If only pip installs within virtual environments are allowed there is no way to get libsedml on the server because I cannot execute the make scripts. Same for phrasedml. The best Matthias -- Matthias König Email: kon...@go... Tel: + 49 30 20938450 Tel: + 49 176 81168480 https://www.livermetabolism.com/contact.html Humboldt-University Berlin, Institute for Theoretical Biology, Junior Group König Charité Berlin, Institute of Biochemistry, Computational Systems Biochemistry <http://www.charite.de/sysbio/people/koenig/> |
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From: Jonathan C. <jon...@cs...> - 2016-01-22 09:56:09
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Hi Lucian, A few thoughts from me. I'd agree about using a single 'maximum order' parameter than can be applied to any integrator (or at least, any that makes sense). "Multiple steps" I'm less clear on, as I don't know the context for this - does it only apply to one kind of integrator? The rest look sensible and useful. "Maximum iterations" can certainly apply to numerical algorithms beyond finding steady states, so might want to be generalised (CVODE for instance has 'maximum steps' as the limit on number of internal steps before an output point; iterative linear algebra solvers have 'maximum iterations', etc.). Best wishes, Jonathan On 20/01/2016 23:27, Lucian Smith wrote: > [Note: cross-posted to biomodels-net-discuss, sed-m-discuss, and the > roadrunner list. I don't think there's a ton of overlap between those > lists, but if you're getting multiple copies of this message, I > apologize.] > > Before filling out a formal request for new KiSAO terms, I thought I'd > discuss them here to make sure that the terms were a) actually needed > (i.e. not covered by a term I didn't find), and b) well described (so > they can be as broadly applied as necessary). > > In implementing SED-ML support for libroadrunner, I came up with a > list of parameters that can be set in roadrunner that do not seem to > have KiSAO equivalents. If I've missed something in KiSAO, or if one > of these parameters could apply to other algorithms if slightly > re-worded, I'd appreciate your input: > > * Maximum BDF order: Specifies the maximum order for Backward > Differentiation Formula integration. > * Maximum Adams order: Specifies the maximum order for Adams-Moulton > intergration. > * Minimum time step: The minimum absolute value of step size allowed. > * Multiple steps (boolean): Perform a multiple time step simulation. > * Maximum iterations: for steady state algorithms, the maximum number > of times the algorithm should iterate before stopping. Used when the > steady state is hard to find, or exhibits oscillation, to avoid > fruitless searching. > * Minimum dampening: for steady state algorithms, the minimum damping > factor > * Seed: for any stochastic algorithm, sets the seed for the random > number generator. This lets you reproduce the same results if run > again (on the same computer using the same algorithm). > > It seems likely that a single 'maximum order' parameter might be used, > and whether (for roadrunner) it applied to the BDF vs. the > Adams-Moulton integrator depended on what simulation algorithm was > being used. > > It also may be that the 'multiple steps' setting might be more cleanly > translated to KiSAO by using a sub-type of a particular algorithm, but > I'm less sure about this. > > Thanks in advance for your thoughts! > > -Lucian > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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From: Lucian S. <luc...@gm...> - 2016-01-20 23:27:44
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[Note: cross-posted to biomodels-net-discuss, sed-m-discuss, and the roadrunner list. I don't think there's a ton of overlap between those lists, but if you're getting multiple copies of this message, I apologize.] Before filling out a formal request for new KiSAO terms, I thought I'd discuss them here to make sure that the terms were a) actually needed (i.e. not covered by a term I didn't find), and b) well described (so they can be as broadly applied as necessary). In implementing SED-ML support for libroadrunner, I came up with a list of parameters that can be set in roadrunner that do not seem to have KiSAO equivalents. If I've missed something in KiSAO, or if one of these parameters could apply to other algorithms if slightly re-worded, I'd appreciate your input: * Maximum BDF order: Specifies the maximum order for Backward Differentiation Formula integration. * Maximum Adams order: Specifies the maximum order for Adams-Moulton intergration. * Minimum time step: The minimum absolute value of step size allowed. * Multiple steps (boolean): Perform a multiple time step simulation. * Maximum iterations: for steady state algorithms, the maximum number of times the algorithm should iterate before stopping. Used when the steady state is hard to find, or exhibits oscillation, to avoid fruitless searching. * Minimum dampening: for steady state algorithms, the minimum damping factor * Seed: for any stochastic algorithm, sets the seed for the random number generator. This lets you reproduce the same results if run again (on the same computer using the same algorithm). It seems likely that a single 'maximum order' parameter might be used, and whether (for roadrunner) it applied to the BDF vs. the Adams-Moulton integrator depended on what simulation algorithm was being used. It also may be that the 'multiple steps' setting might be more cleanly translated to KiSAO by using a sub-type of a particular algorithm, but I'm less sure about this. Thanks in advance for your thoughts! -Lucian |
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From: Ilya K. <ax...@de...> - 2016-01-14 07:41:18
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Congratulations! -- Best regards, Ilya. |
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From: Lucian S. <luc...@gm...> - 2016-01-14 00:07:13
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Thanks, Dagmar and everyone! I'm looking forward to it. -Lucian On Wed, Jan 13, 2016 at 3:31 PM, Dagmar Waltemath < dag...@un...> wrote: > Congratulations, Lucian. And thank you for accepting the editorship. > *clap hands* > > Dagmar :) > > > > On 01/13/2016 10:26 PM, David Nickerson wrote: > >> Hi all, >> >> The vote for one new SED-ML editor for 2016-2018 has closed and the >> election results are now available. The new editor starting in 2016 >> will be Lucian Smith. >> >> Lucian will replace outgoing editor Jonathan Cooper, whose term ended >> in 2015. Please join the current SED-ML editors in congratulating >> Lucian and thanking him for accepting the new position! >> >> The results of the vote are attached as an image showing the total >> number of unique votes received by each candidate. A total of 20 >> unique and valid votes were received. >> >> >> Cheers, >> David. >> >> >> >> >> ------------------------------------------------------------------------------ >> Site24x7 APM Insight: Get Deep Visibility into Application Performance >> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >> Monitor end-to-end web transactions and take corrective actions now >> Troubleshoot faster and improve end-user experience. Signup Now! >> http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 >> >> >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > |
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From: Dagmar W. <dag...@un...> - 2016-01-13 23:43:49
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Congratulations, Lucian. And thank you for accepting the editorship. *clap hands* Dagmar :) On 01/13/2016 10:26 PM, David Nickerson wrote: > Hi all, > > The vote for one new SED-ML editor for 2016-2018 has closed and the > election results are now available. The new editor starting in 2016 > will be Lucian Smith. > > Lucian will replace outgoing editor Jonathan Cooper, whose term ended > in 2015. Please join the current SED-ML editors in congratulating > Lucian and thanking him for accepting the new position! > > The results of the vote are attached as an image showing the total > number of unique votes received by each candidate. A total of 20 > unique and valid votes were received. > > > Cheers, > David. > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > > > > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > |
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From: David N. <dav...@gm...> - 2016-01-13 21:27:14
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Hi all, The vote for one new SED-ML editor for 2016-2018 has closed and the election results are now available. The new editor starting in 2016 will be Lucian Smith. Lucian will replace outgoing editor Jonathan Cooper, whose term ended in 2015. Please join the current SED-ML editors in congratulating Lucian and thanking him for accepting the new position! The results of the vote are attached as an image showing the total number of unique votes received by each candidate. A total of 20 unique and valid votes were received. Cheers, David. -- David Nickerson about.me/david.nickerson |
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From: David N. <dav...@gm...> - 2016-01-05 20:45:21
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Hi all, Just a reminder that voting in the election of a new SED-ML editor will close in a couple of days on January 8. Please be sure to have your say! The voting form is available at: http://goo.gl/forms/pwdwIjDhTz Cheers, David. On Fri, Dec 18, 2015 at 1:41 PM, David Nickerson <dav...@gm...> wrote: > This is a call for votes for electing one new SED-ML Editor to replace > Jonathan Cooper, whose current three year term ends at the end of this > year. Every member of the SED-ML forum (as determined by membership of > the sed...@li... mailing list) is entitled to vote. > Please vote for one candidate using the voting form at: > > http://goo.gl/forms/pwdwIjDhTz > > Voting will end on January 8, 2016. > > Thank you in advance for your participation in this important process! > > David, on behalf of the SED-ML editors. > > > -- > > > David Nickerson > about.me/david.nickerson -- David Nickerson about.me/david.nickerson |
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From: Pedro M. <ped...@ma...> - 2015-12-21 23:46:20
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SBML knows about species and reactions, which is some biology/biochemistry already. But not if you use rate rules, of course... Obviously, with MIRIAM annotations we can tell what is everything (or nearly everything) that is in an SBML model. See for example our yeast reconstructions at yeast.sf.net Pedro On 12/21/2015 09:22 PM, Herbert Sauro wrote: > I've got a feeling the same goes for SBML. > > Herbert > > On Mon, Dec 21, 2015 at 1:13 PM, David Nickerson > <dav...@gm... <mailto:dav...@gm...>> wrote: > > > I think in CellML there is no way to determine what kind of ODE it is > > without some kind of annotation. > > yep - there is nothing in CellML itself to inform you anything about > the biology, just the math. (There is a "reaction" construct, but that > is deprecated and not supported by the CellML API.) > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > <mailto: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 > -- Pedro Mendes Professor of Computational Systems Biology School of Computer Science Manchester Centre for Integrative Systems Biology University of Manchester Manchester Institute of Biotechnology 131 Princess Street Manchester, M1 7DN, U.K. |
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From: Chris J. M. <my...@ec...> - 2015-12-21 22:35:48
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We reviewed the paper in a group meeting. It was not so difficult as I recall. I don’t remember Jacobian being needed, but it was awhile ago. As for rate rules, you are free to make any variable the target of a rate rule. So, if you want to just have an ODE model that has nothing to do with biology where you use just parameters and rate rules, no problem. Indeed, I do this with my analog circuit modeling research. You are correct though that the method in Fages paper does assume that everything changing is a species, so it cannot know that certain things are simply dynamic variables. Again, you would need annotations if you want to have for example a rate parameter that changes over time. Chris > On Dec 20, 2015, at 9:41 PM, Herbert Sauro <hs...@gm...> wrote: > > I was thinking of the situation where the differential equations have nothing to do with reactions and species, for example someone might encode the lorenz attractor as three rate rules. It doesn't make much sense to decompose these into a set of reactions and species even though one could - I have just to see what they looked like . I've not kept up with SBML but can one have rate rules that are associated with general state variables and NOT species, or must all variables be species? This was something I wanted to be able to distinguish when SBML 1 was developed but it never became part of the standard. Is it possible now to distinguish species variables from generic state variables? > > I think in CellML there is no way to determine what kind of ODE it is without some kind of annotation. > > I had a look at that paper a while ago but wasn't able to spend long enough to decipher the theory. Doesn't any one have the paper explained in more simpler terms? I think I might have understood it has something to do with determining the Jacobian but not sure? > > Herbert > > On Sun, Dec 20, 2015 at 6:03 PM, Chris J. Myers <my...@ec... <mailto:my...@ec...>> wrote: > I don’t think so. The BioCham method I believe assumes that values that are targets of ODEs are species and other values are constants. You really should take a look: > > http://www.sciencedirect.com/science/article/pii/S0304397514006197 <http://www.sciencedirect.com/science/article/pii/S0304397514006197> > > Chris > >> On Dec 20, 2015, at 3:53 PM, Herbert Sauro <hs...@gm... <mailto:hs...@gm...>> wrote: >> >> Wouldn't you need CellML annotation to identify the differential equations that correspond to rate of change of species, assuming they in turn have been constructed such that they can be separated? >> >> Herbert >> >> On Sun, Dec 20, 2015 at 2:50 PM, Chris J. Myers <my...@ec... <mailto:my...@ec...>> wrote: >> One could use the BioCham approach to extract the reactions from the math like Mike does with the matlab to sbml converter. >> >> Chris >> >> Sent from my iPhone >> >> On Dec 20, 2015, at 2:29 PM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: >> >>> That was actually going to be the next part of my question: stochastic Reactions are a 'standard thing' in SBML, but I believe nobody ever tries to interpret the 'rate rules' in a stochastic manner. If they did, that could presumably be applied to the CellML side of things. Conversely, if CellML *did* have some sort of stochastic interpretation, the reverse could be true. >>> >>> For now, it sounds like I should just not try to generate stochastic tests for CellML at all, and stick to reactions for SBML models. Although if we want to explicitly claim that the SBML RateRule construct is 'immune' to stochastic simulations, I should include that, too. >>> >>> -Lucian >>> >>> On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson <dav...@gm... <mailto:dav...@gm...>> wrote: >>> Hi Lucian, >>> >>> Short answer - I'm not aware of any simulator that would know what to >>> do with a CellML model and a Monte Carlo simulation. >>> >>> Long answer - something intelligent sounding about the math being >>> directly encoded in CellML vs the process description of SBML being >>> used to generate the math depending on your simulation algorithm (I >>> don't know if you can do a stochastic simulation of an SBML model that >>> only consists of math, no reactions?). Andrew Miller did have a >>> proposal for something along these lines with SED-ML, but requires >>> extra information provided for the CellML (or SBML) model >>> (distributions, ranges, etc.). >>> >>> >>> Cheers, >>> Andre. >>> >>> >>> On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm... <mailto:luc...@gm...>> wrote: >>> > So, SBML has a tradition of allowing the user to encode a single model, and >>> > allows you to simulate it deterministically or stochastically. Does CellML >>> > have the same capability? I'm obviously asking from the perspective of >>> > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean anything to >>> > a CellML simulator. >>> > >>> > -Lucian >>> > >>> > ------------------------------------------------------------------------------ >>> > >>> > _______________________________________________ >>> > 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> >>> > >>> >>> >>> >>> -- >>> >>> >>> 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 <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss> >>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> 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> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> 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> >> >> >> ------------------------------------------------------------------------------ >> _______________________________________________ >> 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> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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> > > > ------------------------------------------------------------------------------ > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
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