Dear Jacob,
Indeed, Multi can bring some of the features you need. If the purpose is to generate populations of patients from the same model but with initial conditions and parameters sampled from distributions (as is done in pharmacometrics), you might want to test the package "distrib" currently in development. And of course contribute to its development and support :-)
http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/distrib
Best regards
On 28/03/17 00:32, Jacob Barhak wrote:
> Greetings,
>
> Some of you may recall a discussion that took place over the last two years about suitability of SBML for disease modeling. Here is a link to the discussion thread:
> https://groups.google.com/forum/#!searchin/sbml-discuss/barhak%7Csort:relevance/sbml-discuss/PB_nMzqswIQ/T-OO1neGBwAJ
> _
> _
> In a nutshell it was concluded that SBML has potential, yet was not year ready for disease modeling that involves individual modeling such as micro-simulation where each individual has a set of characteristics and each individual is simulated independently using the same model.
>
> At that time it seemed that the library called SBMLMulti has potential to solve this problem.
>
> I just met Herbert Sauro last week at the NIH and he told me that new SBML specs have been released including SBML Multi. I decided to revisit this thread to see if SBML multi can now model more complicated disease models such as examples 4 and 5 in the thread I quote above that use individual modeling?
>
> Hopefully there was progress.
>
> Jacob
>
> --
> Jacob Barhak Ph.D.
> http://sites.google.com/site/jacobbarhak/
>
> --
> You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com <mailto:sbml-discuss+unsub...@googlegroups.com>.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3TMCMDszFr1mTd-tdTbcnS%3DOc4XD3xbBwnGU9UnXhzJBg%40mail.gmail.com.
Hi Jacob,
Thanks for bringing this up! Right, the sbml-multi spec was just
accepted and released. The library of libsbml-multi is currently
available at the experimental branch of the libsbml svn repository
and will be included in the next release of libsbml stable version
in April.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3RSV9z%2BC5-TkfrEiu1wW3UNnOTncz64OJAN6CD%2B0e3YYw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
-- ==================== Fengkai Zhang, MD, MMath Staff Scientist Laboratory of Systems Biology, DIR, NIAID 9000 Rockville Pike Building 4, Room 137 MSC 0421 Bethesda MD 20892 Phone: 301.761.5442 Fax: 301.480.1660 NIAID, National Institutes of Health, DHHS ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAHLmBr0Xp%3DKSLd0EWOvpM6RPCbYAo-0pJQyfruzO%3DWB%3Di%2B10uw%40mail.gmail.com.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3RSV9z%2BC5-TkfrEiu1wW3UNnOTncz64OJAN6CD%2B0e3YYw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
-- ==================== Fengkai Zhang, MD, MMath Staff Scientist Laboratory of Systems Biology, DIR, NIAID 9000 Rockville Pike Building 4, Room 137 MSC 0421 Bethesda MD 20892 Phone: 301.761.5442 Fax: 301.480.1660 NIAID, National Institutes of Health, DHHS ****************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/65201338-5d4f-9157-499c-4ba9a0f3b55d%40niaid.nih.gov.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAHLmBr0Xp%3DKSLd0EWOvpM6RPCbYAo-0pJQyfruzO%3DWB%3Di%2B10uw%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/9C5A10B0-2E5C-41DF-9212-AC8AB3617383%40ece.utah.edu.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3R%3DGzKVZ-NXjKV1UUVtJ9Lu4%2BML8d4RAG5ng0pTzDHOcw%40mail.gmail.com.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu.
For more options, visit https://groups.google.com/d/optout.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAN1fttCwTh%3DNOasa6vw40awiHrJXRditxvrTZ4qiHm1m3aQk%3Dw%40mail.gmail.com.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu.
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu <https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit
https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe <https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe>.
To unsubscribe from this group and all its topics, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu <https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit
https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe <https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe>.
To unsubscribe from this group and all its topics, send an email to
To post to this group, send email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3TMCMDszFr1mTd-tdTbcnS%3DOc4XD3xbBwnGU9UnXhzJBg%40mail.gmail.com <https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3TMCMDszFr1mTd-tdTbcnS%3DOc4XD3xbBwnGU9UnXhzJBg%40mail.gmail.com?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/CAHLmBr0Xp%3DKSLd0EWOvpM6RPCbYAo-0pJQyfruzO%3DWB%3Di%2B10uw%40mail.gmail.com <https://groups.google.com/d/msgid/sbml-discuss/CAHLmBr0Xp%3DKSLd0EWOvpM6RPCbYAo-0pJQyfruzO%3DWB%3Di%2B10uw%40mail.gmail.com?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit
https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe <https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe>.
To unsubscribe from this group and all its topics, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/9C5A10B0-2E5C-41DF-9212-AC8AB3617383%40ece.utah.edu <https://groups.google.com/d/msgid/sbml-discuss/9C5A10B0-2E5C-41DF-9212-AC8AB3617383%40ece.utah.edu?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3R%3DGzKVZ-NXjKV1UUVtJ9Lu4%2BML8d4RAG5ng0pTzDHOcw%40mail.gmail.com <https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3R%3DGzKVZ-NXjKV1UUVtJ9Lu4%2BML8d4RAG5ng0pTzDHOcw%40mail.gmail.com?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/CAN1fttCwTh%3DNOasa6vw40awiHrJXRditxvrTZ4qiHm1m3aQk%3Dw%40mail.gmail.com <https://groups.google.com/d/msgid/sbml-discuss/CAN1fttCwTh%3DNOasa6vw40awiHrJXRditxvrTZ4qiHm1m3aQk%3Dw%40mail.gmail.com?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit
https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe <https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe>.
To unsubscribe from this group and all its topics, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu <https://groups.google.com/d/msgid/sbml-discuss/E72BE147-01E0-4A86-A527-B43EFEBAEB78%40ece.utah.edu?utm_medium=email&utm_source=footer>.
For more options, visit
https://groups.google.com/d/optout <https://groups.google.com/d/optout>.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3RPzsf0Dw-bk3um_5ULrnZ9kNREYFfnDnW_aM2KcJmLvQ%40mail.gmail.com <https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3RPzsf0Dw-bk3um_5ULrnZ9kNREYFfnDnW_aM2KcJmLvQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/7625FD6C-8B74-4473-864C-4270E2EACAA8%40niaid.nih.gov.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3RPzsf0Dw-bk3um_5ULrnZ9kNREYFfnDnW_aM2KcJmLvQ%40mail.gmail.com.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3RPzsf0Dw-bk3um_5ULrnZ9kNREYFfnDnW_aM2KcJmLvQ%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/7F21327E-5B22-4791-904D-3D1156557CA2%40ece.utah.edu.
However, before I make any commitment, allow me to explain my constraints.1. MIST was designed with its own language and many features geared towards disease modeling - some of them like population generation seem to be out of scope for SBML. Also SBML may have features that MIST does not support. Even without going to details, I am pretty sure MIST will not be able to import any SBML file unless a large portion of it is rewritten which I have no intention of doing. However, I can explore the possibility of exporting SBML output from MIST - will this be sufficient for SBML array to be accepted formally? If so, I can start diving deeper into the topic.
2. My knowledge with SBML is limited and without the experts on this list, it would be too difficult to accomplish and as you have seen, my questions are quite demanding, after all I am new to SBML. If I can rely on your support, I will be happy to explore further. For example, pointing out correct literature and testing SBML outputs can be easier if someone else helps - and I do ask a lot of questions.
3. My time and resources for doing this are quite limited, I can dedicate a month or perhaps a couple of months at most towards an attempt to generate SBML output, and that is, if all the pieces are in place now with SBML array and perhaps other libraries.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3QLhx%2BqhiNm%3Dc%2BWEMq-9c4Z%3DB-bAygf2DqDb-UQ%2Bpv23g%40mail.gmail.com.
Hi Jacob,
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3QLhx%2BqhiNm%3Dc%2BWEMq-9c4Z%3DB-bAygf2DqDb-UQ%2Bpv23g%40mail.gmail.com.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/37569131-ADC8-4FDD-AF82-B7397298DE21%40ece.utah.edu.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/58E0FDBF.5030909%40niaid.nih.gov.
Good to know.Thanks,Chris
On Apr 2, 2017, at 2:33 PM, Zhang, Fengkai (NIH/NIAID) [E] <zhan...@niaid.nih.gov> wrote:
Hi Chris and Jacob,
Regarding the requirement of two software implementations, Multi has the similar situation. At the time of acceptance, Simmune supports both export and import, and BioNetGen supports export. An example (export a BioNetGen model to multi, and import the multi model to Simmune) was provided in the release request to demonstrate model exchange. The model simulation results by Simmune and BioNetGen were provided to demonstrate the consistency and also to show two applications interpret the model in the same way. (The request to release Multi was submitted before I joined the editor board and then I was excused from the approving process.)
The current SBML editors discussed the array package and consider it is reasonable to accept two software implementations in the same way as Multi. The mathematics of the model package implementation should show consistent results, and the interpretations of a model by the supporting applications should be consistent.
Fengkai
(On behalf of the SBML editors)
On 3/31/17 4:46 AM, Chris Myers wrote:
Hi Jacob,
However, before I make any commitment, allow me to explain my constraints.
1. MIST was designed with its own language and many features geared towards disease modeling - some of them like population generation seem to be out of scope for SBML. Also SBML may have features that MIST does not support. Even without going to details, I am pretty sure MIST will not be able to import any SBML file unless a large portion of it is rewritten which I have no intention of doing. However, I can explore the possibility of exporting SBML output from MIST - will this be sufficient for SBML array to be accepted formally? If so, I can start diving deeper into the topic.
I’ll let the current editors comment on this one, but my feeling is two tools that support a package either import or export, should be sufficient. However, I would certainly understand if two tools only support export OR only support import would not demonstrate exchange. In our case, we could certainly validate exchange by importing your generated files.
--
You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/58E0FDBF.5030909%40niaid.nih.gov.
For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to a topic in the Google Groups "sbml-discuss" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/sbml-discuss/gQsLHmP5i9U/unsubscribe.
To unsubscribe from this group and all its topics, send an email to sbml-discuss+unsubscribe@googlegroups.com.
To post to this group, send email to sbml-d...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/sbml-discuss/6050FDA8-4ABC-44E7-95E6-B9AB1024BCC6%40ece.utah.edu.