sbml-multi — For those interested in the SBML L3 'multi' package

Re: [sbml-multi] rule-based modeling and sbml-multi breakout session at HARMONY 2023?

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

Thank you for those who joined session 1. We will have session 2 at the same time and the same zoom link tomorrow. I will walk through some examples and continue our discussions. Bring any questions you have to the session.

Fengkai

________________________________________
From: Zhang, Fengkai (NIH/NIAID) [E] <zha...@ni...>
Sent: Friday, April 14, 2023 3:07 PM
To: sbm...@li...
Subject: Re: rule-based modeling and sbml-multi breakout session at HARMONY 2023?

Dear all,

We are going to have breakout session(s) at HARMONY 2023. I created a google page for the information and meeting minutes related to the session(s), and here is the link:
https://docs.google.com/document/d/1cWrHW9h58THIa6NGdTCNCOs5Jw_tPjZuafoajlhlpSQ/edit?usp=sharing
Or
https://tinyurl.com/mrynwzzv

New information will be updated to this page when it is available. Please feel free to add more information to the google doc. Hope to see you in person or via zoom soon!


Fengkai


====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Immune System 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.
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________________________________________
From: Zhang, Fengkai (NIH/NIAID) [E]
Sent: Wednesday, March 8, 2023 12:57 PM
To: sbm...@li...
Subject: rule-based modeling and sbml-multi breakout session at HARMONY 2023?

Dear all,

We had some interesting discussion related to the SBML-Multi during COMBINE 2022. I am thinking to propose a breakout session at HARMONY 2023 and like to know who could be interested in joining? If interested, will you (tentatively) join in-person or virtually? We could discuss anything related to rule-based modeling and/or SBML-multi, for example, review of the current spec, new features, use cases, interaction with other packages, etc.  I would appreciate if you could respond either to this list or myself directly.

Fengkai

Re: [sbml-multi] rule-based modeling and sbml-multi breakout session at HARMONY 2023?

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

Just a reminder, we will have a breakout session tomorrow at local time 11:00am in room 403. Zoom link has been updated in the google doc page, and is also here as follows:
https://auckland.zoom.us/j/92413461326?pwd=WktwdDlmMHQyY3FyYTZzWTMrSGI3dz09
Meeting ID: 924 1346 1326
Passcode: 424005

Hope to see many of you tomorrow.

Fengkai

________________________________________
From: Zhang, Fengkai (NIH/NIAID) [E] <zha...@ni...>
Sent: Friday, April 14, 2023 3:07 PM
To: sbm...@li...
Subject: Re: rule-based modeling and sbml-multi breakout session at HARMONY 2023?

Dear all,

We are going to have breakout session(s) at HARMONY 2023. I created a google page for the information and meeting minutes related to the session(s), and here is the link:
https://docs.google.com/document/d/1cWrHW9h58THIa6NGdTCNCOs5Jw_tPjZuafoajlhlpSQ/edit?usp=sharing
Or
https://tinyurl.com/mrynwzzv

New information will be updated to this page when it is available. Please feel free to add more information to the google doc. Hope to see you in person or via zoom soon!


Fengkai


====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Immune System 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.
******************************************************************

________________________________________
From: Zhang, Fengkai (NIH/NIAID) [E]
Sent: Wednesday, March 8, 2023 12:57 PM
To: sbm...@li...
Subject: rule-based modeling and sbml-multi breakout session at HARMONY 2023?

Dear all,

We had some interesting discussion related to the SBML-Multi during COMBINE 2022. I am thinking to propose a breakout session at HARMONY 2023 and like to know who could be interested in joining? If interested, will you (tentatively) join in-person or virtually? We could discuss anything related to rule-based modeling and/or SBML-multi, for example, review of the current spec, new features, use cases, interaction with other packages, etc.  I would appreciate if you could respond either to this list or myself directly.

Fengkai

Re: [sbml-multi] rule-based modeling and sbml-multi breakout session at HARMONY 2023?

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

We are going to have breakout session(s) at HARMONY 2023. I created a google page for the information and meeting minutes related to the session(s), and here is the link:
https://docs.google.com/document/d/1cWrHW9h58THIa6NGdTCNCOs5Jw_tPjZuafoajlhlpSQ/edit?usp=sharing  
Or 
https://tinyurl.com/mrynwzzv 

New information will be updated to this page when it is available. Please feel free to add more information to the google doc. Hope to see you in person or via zoom soon!


Fengkai


====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Immune System 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.
******************************************************************

________________________________________
From: Zhang, Fengkai (NIH/NIAID) [E]
Sent: Wednesday, March 8, 2023 12:57 PM
To: sbm...@li...
Subject: rule-based modeling and sbml-multi breakout session at HARMONY 2023?

Dear all,

We had some interesting discussion related to the SBML-Multi during COMBINE 2022. I am thinking to propose a breakout session at HARMONY 2023 and like to know who could be interested in joining? If interested, will you (tentatively) join in-person or virtually? We could discuss anything related to rule-based modeling and/or SBML-multi, for example, review of the current spec, new features, use cases, interaction with other packages, etc.  I would appreciate if you could respond either to this list or myself directly.

Fengkai

[sbml-multi] rule-based modeling and sbml-multi breakout session at HARMONY 2023?

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

We had some interesting discussion related to the SBML-Multi during COMBINE 2022. I am thinking to propose a breakout session at HARMONY 2023 and like to know who could be interested in joining? If interested, will you (tentatively) join in-person or virtually? We could discuss anything related to rule-based modeling and/or SBML-multi, for example, review of the current spec, new features, use cases, interaction with other packages, etc.  I would appreciate if you could respond either to this list or myself directly.

Fengkai

Re: [sbml-multi] [sbml-discuss] A question on SBML multi

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Hi Robert,

Thank you for working to support the multi package! Thank you for the question. I include this reply to the multi list. I think we could also continue to discuss here as multi is part of sbml.

Specific to your question, you could first define mult:speciesTypes in the following way:
<multi:listOfSpeciesTypes>
    <multi:speciesType multi:id="st_SMAD1" multi:name=" SMAD1" …/>
    <multi:speciesType multi:id="st_SMAD5" multi:name=" SMAD5" …/>
    <multi:speciesType multi:id="st_SMAD8" multi:name=" SMAD8" …/>
<multi:speciesType multi:id="st_SMAD1_5_8" multi:name=" SMAD1_5_8" …>
    <multi:listOfSpecieTypeInstances>
        <multi:speciesTypeInstance multi:id=”sti_SMAD1” multi:speciesType=”st_SMAD1” … />
        <multi:speciesTypeInstance multi:id=”sti_SMAD5” multi:speciesType=”st_SMAD5” … />
        <multi:speciesTypeInstance multi:id=”sti_SMAD8” multi:speciesType=”st_SMAD8” … />
    </ multi:listOfSpecieTypeInstances >
</multi:speciesType >
…
</multi:listOfSpeciesTypes >

And in speces to reference the speciesTypes, you may have:
<listOfSpeces>
    <species id=”species_SMAD1_5_8” multi:speciesType=”st_SMAD1_5_8”… />
    <species id=”species_SMAD1” multi:speciesType=”st_SMAD1”… />
    <species id=”species_SMAD5” multi:speciesType=”st_SMAD5”… />
<species id=”species_SMAD8” multi:speciesType=”st_SMAD8”… />
…
</listOfSpeces>

Depending the purpose, annotation can be added to species, speciesType, and/or speciesTypeInstance. I consider species should be a good place to be annotated with a uniprot id.

I would be happy to answer any further questions and clarify my reply if needed.

Best,

Fengkai

====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Immune System 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.
******************************************************************

From: Robert Phair <rd...@gm...>
Reply-To: "sbm...@go..." <sbm...@go...>
Date: Thursday, March 4, 2021 at 8:54 PM
To: sbml-discuss <sbm...@go...>
Subject: [sbml-discuss] A question on SBML multi

We want to support import of at least some of the information encoded in SBML multi, but UML is not my first language and I'm having trouble discerning which multi: constructs are used for which biological scenarios. I have spent a good deal of time reading the spec.

Let me start with a basic scenario. The formation of protein complexes, by which I mean non-covalent binding of two or more proteins, is a simple and very common scenario.

When I import an SBML file, in this case, produced by the software tool, MINERVA, there is a species with a multi:speciesType="minerva_species_type_Complex". The line of SBML is:

<species boundaryCondition="false" compartment="comp_1" constant="false" hasOnlySubstanceUnits="false" id="species_45" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="SMAD1/5/8" sboTerm="SBO:0000253">

This complex is made up of three proteins, SMAD1, SMAD5, and SMAD8.

The question is: which multi: constructs should be used to specify the component proteins of this complex so that each can be annotated with an rdf:resource such as a uniprot id?

I'm not asking how MINERVA does this (I've already raised this question with them). What I'm asking is how the designers of multi: would code this information.

If this is not the correct discussion group for this question, please point me to the right place to ask it. Thanks.
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[sbml-multi] a breakout "multi" session in COMBINE?

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

I would like to seek opinions about a possible “multi” virtual breakout session in the coming COMBINE meeting. If you are interested in participating, could you reply to this list or me directly about your interest and suggestions? The deadline to suggest a breakout session to COMBINE is September 1, 2020.

Regards,

Fengkai

====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Immune System 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.
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[sbml-multi] ask feedback for multi spec version 1 release 2 release candidate 1

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

We are preparing for a new release of the multi spec version 1 release 2. Here is the link to its release candidate 1:
https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.2.rc1.pdf

The changes include:
1. Fix issues raised by the community after “Version 1 release 1”.
2. Revise part of text.
3. Add a paragraph to clarify “XML Namespace use”(see Section 3.1 on page 9).
4.Validate example models and add notes to the models for demonstration only

We would appreciate any feedback from our community. I am targeting to submit the sbml-multi spec version 1 release 2 to the SBML editors for official release approval sometime next week if possible. It would be great to get feedback at your early convenience.

For comparison, the current version 1 release 1 can be found here:
http://co.mbine.org/specifications/sbml.level-3.version-1.multi.version-1.release-1.pdf

Regards,

Fengkai

================================================
Fengkai Zhang, MD, MMath
Staff Scientist, Computational Biology Section
Laboratory of Immune System Biology (LISB)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
9000 Rockville Pike
Building 4, Room 137
MSC 0421
Bethesda MD 20892
Phone: 301.761.5442
Fax: 301.480.1660
e mail: zha...@ni...

******************************************************************
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.
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[sbml-multi] Possible breakout session for multi at HARMONY

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

I would like to ask if anyone is interested in having and joining (locally or remotely) a multi session in the coming HARMONY? The discussion could include but not limited to:

  1.  Any changes are needed to revise the current multi spec. I already received some suggestions for revision and clarification and can brief in the session.
  2.  Any changes are needed, or bugs need to fix in libsbml-multi.
  3.  Are there any issues or challenges for software tools to implement support to export/import models of multi? Solution or suggestion?

Please reply to this list or to me directly if you are interested. Thank you!

Fengkai

Re: [sbml-multi] [sbml-discuss] Manuscript describing SBML

[Sarah K. <ske...@ca...>]

Please note the current SBML Editors will continue to work on this 
publication and it will proceed as planned.

SBML Editors

Re: [sbml-multi] [sbml-discuss] Manuscript describing SBML

[Sarah K. <ske...@ca...>]

Sorry I was perhaps not completely clear.

Nicolas Le Novere has withdrawn from the paper and has handed over all 
notes/comments etc to the remaining SBML Editors.

There will be a slight hiatus in the timing, but we are close to having 
a manuscript for submission, and we will proceed with this.

Thank you to everyone who has commented so far and I hope this 
completely clarifies the situation.

Sarah
Coordinator of SBML Editors

On 18/09/2018 09:04, Sarah Keating wrote:
> Please note the current SBML Editors will continue to work on this
> publication and it will proceed as planned.
> 
> SBML Editors
> 

[sbml-multi] Manuscript describing SBML

[Nicolas Le N. <n.l...@gm...>]

Dear Colleagues,

We are in the process of submitting a manuscript describing SBML Level 3 for publication in Molecular Systems Biology as a perspective (current version attached). The manuscript has been written by past and current SBML editors and both its content and structure discussed with MSB editors.

Although the structure and the main messages of the paper have been settled, we would welcome any suggestion you would have in relation with the manuscript.

Best regards

The SBML editors.

Re: [sbml-multi] [sbml-discuss] Is the new version of SBML suitable for individual modeling / disease modeling?

[Chris M. <my...@ec...>]

Multi is likely the right approach as Lucian points out.  However, multi and arrays are related assuming multi models are encoded into sparse arrays.

I thought I would add to the discussion the status of arrays just for your information.  My student Leandro Watanabe and myself wrote the arrays specification based on input from many sources including an old proposal, Lucian, Sarah, and community discussions.  Both JSBML and libSBML support the arrays package, as does the iBioSim software package.  Unfortunately though there has not been a second software package pick it up, so its development has been stalled.  We published a simulator for the arrays package here:

https://www.ncbi.nlm.nih.gov/pubmed/26912276

This paper describes the implementation within iBioSim and its applications to cellular populations, which is perhaps related to what you are trying to accomplish.

Cheers,

Chris

> On Mar 28, 2017, at 10:23 AM, Lucian Smith <luc...@gm...> wrote:
> 
> The thing that has happened since you asked last is that Multi was released.  Multi was actually a key component of what you wanted for your disease models, so hey!
> 
> In this case, you would have a 'person' element, with one 'feature' that could be either 'male' or 'female', and another 'feature' that would be 'healthy', 'sick', or 'dead'.  Then you define your five transitions just as you described them:
> 
> (either) (healthy) -> (either) (dead)
> (male) (healthy) -> (male) (sick)
> (female) (healthy) -> (female)(sick)
> (either)(sick) -> (either)(healthy)
> (either)(sick) -> (either)(dead)
> 
> I'm copying the 'multi' package list for this, since I don't know how explicitly to encode this in multi, but I do know it can be done.
> 
> -Lucian
> 
> On Tue, Mar 28, 2017 at 8:09 AM, Jacob Barhak <jac...@gm... <mailto:jac...@gm...>> wrote:
> So Nicolas,
> 
> The Array option seems to have elements needed such as attributes and array size and can flatten a model - this is at the end of the specification document.
> 
> And I noticed that Lucian was involved with the writing of the document. Lucian was the person who helped me with the questions I initially posted. So I assume that he would have mentioned arrays when I first asked, so there must be a reason why the array package is not what I am looking for. I assume that at the time it was not implemented by a software package. Is it implemented now?
> 
> If it has an implementation, how will it solve the simple problem I called example 3. Here it is again:
> 
> There are three disease states: Healthy, Sick, Dead.
> There are two categories: Male, Female.
> The yearly transition probabilities are:
> - Healthy to Dead: 0.01.
> - Healthy to Sick: 0.2 for Male, 0.1 for Female.
> - Sick to Healthy: 0.1.
> - Sick to Dead: 0.3.
> 
> 
> The initial conditions are that there are 50 males all healthy and 50 females all healthy.
> 
> We are seeking the number of male and female at each state after 10 years.
> 
> Can the Array package solve this problem more elegantly than just flattening the model?
> 
> Hopefully this clarifies what I am asking and hopefully the new SBML spec can now formulate this.
> 
> 
>               Jacob
> 
> On Tue, Mar 28, 2017 at 2:22 AM, Nicolas Le Novere <n.l...@gm... <mailto:n.l...@gm...>> wrote:
> On 28/03/17 02:54, Jacob Barhak wrote:
> 
> However, my question was what happens after you have the initial data at hand and want to simulate a table of individuals with different characteristics such as Blood Pressure, HDL, levels, Age etc. that change during simulation and affect outcomes such as stroke or death.
> 
> Have you considered using the array package to track your population of individuals?
> 
> http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays <http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays>
> 
> -- 
> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
> Tel: +441223496433 <tel:+44%201223%20496433>   Mob:+447833147074 <tel:+44%207833%20147074>   n.l...@gm... <mailto:n.l...@gm...>
> orcid.org//0000-0002-6309-7327 <http://orcid.org//0000-0002-6309-7327>  http://lenoverelab.org/perso/lenov/ <http://lenoverelab.org/perso/lenov/>
> Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/ <http://nlenov.wordpress.com/>
> 
> 
> 
> 
> -- 
> You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
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> 
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> You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
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Re: [sbml-multi] [sbml-discuss] Is the new version of SBML suitable for individual modeling / disease modeling?

[Lucian S. <luc...@gm...>]

The thing that has happened since you asked last is that Multi was
released.  Multi was actually a key component of what you wanted for your
disease models, so hey!

In this case, you would have a 'person' element, with one 'feature' that
could be either 'male' or 'female', and another 'feature' that would be
'healthy', 'sick', or 'dead'.  Then you define your five transitions just
as you described them:

(either) (healthy) -> (either) (dead)
(male) (healthy) -> (male) (sick)
(female) (healthy) -> (female)(sick)
(either)(sick) -> (either)(healthy)
(either)(sick) -> (either)(dead)

I'm copying the 'multi' package list for this, since I don't know how
explicitly to encode this in multi, but I do know it can be done.

-Lucian

On Tue, Mar 28, 2017 at 8:09 AM, Jacob Barhak <jac...@gm...>
wrote:

> So Nicolas,
>
> The Array option seems to have elements needed such as attributes and
> array size and can flatten a model - this is at the end of the
> specification document.
>
> And I noticed that Lucian was involved with the writing of the document.
> Lucian was the person who helped me with the questions I initially posted.
> So I assume that he would have mentioned arrays when I first asked, so
> there must be a reason why the array package is not what I am looking for.
> I assume that at the time it was not implemented by a software package. Is
> it implemented now?
>
> If it has an implementation, how will it solve the simple problem I called
> example 3. Here it is again:
>
> There are three disease states: Healthy, Sick, Dead.
> There are two categories: Male, Female.
> The yearly transition probabilities are:
> - Healthy to Dead: 0.01.
> - Healthy to Sick: 0.2 for Male, 0.1 for Female.
> - Sick to Healthy: 0.1.
> - Sick to Dead: 0.3.
>
>
> The initial conditions are that there are 50 males all healthy and 50
> females all healthy.
>
> We are seeking the number of male and female at each state after 10 years.
>
> Can the Array package solve this problem more elegantly than just
> flattening the model?
>
> Hopefully this clarifies what I am asking and hopefully the new SBML spec
> can now formulate this.
>
>               Jacob
>
> On Tue, Mar 28, 2017 at 2:22 AM, Nicolas Le Novere <n.l...@gm...>
> wrote:
>
>> On 28/03/17 02:54, Jacob Barhak wrote:
>>
>> However, my question was what happens after you have the initial data at
>>> hand and want to simulate a table of individuals with different
>>> characteristics such as Blood Pressure, HDL, levels, Age etc. that change
>>> during simulation and affect outcomes such as stroke or death.
>>>
>>
>> Have you considered using the array package to track your population of
>> individuals?
>>
>> http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays
>>
>> --
>> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
>> Tel: +441223496433 <+44%201223%20496433>   Mob:+447833147074
>> <+44%207833%20147074>   n.l...@gm...
>> orcid.org//0000-0002-6309-7327  http://lenoverelab.org/perso/lenov/
>> Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/
>>
>>
>>
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[sbml-multi] Multi package accepted

[Sarah K. <ske...@ca...>]

Dear SBML community,

We are pleased to announce the availability of the final Version 1 
specification for the Multistate and Multicomponent Species package in 
SBML Level 3.  You can find the document at its resolvable URI

http://identifiers.org/combine.specifications/sbml.level-3.version-1.multi.version-1.release-1

This specification has been approved by the editors who have confirmed 
there are two working implementations.

The Multi ('multi') specification activity page is

http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/multi

The next libSBML release will include multi as part of the stable 
release, with full validation available.

Please report any errors, issues or questions to the Package Working 
Group for 'multi' (sbm...@li...).

SBML Editors

Re: [sbml-multi] Latest release candidate of the multi spec -- updated to rc5

[Michael H. <mh...@ca...>]

Just a quick note to let everyone know that the link in the SBML packages table and on sbml.org has been updated to the RC5 PDF.

MH

On Fri, 10 Mar 2017 16:25:41 +0000, Zhang, Fengkai (NIH/NIAID) [E] wrote:
> Dear all,
> 
> Thanks for Sarah's work to check the spec document and conduct stress 
> testing on the libsbml-multi library, the rc5 of the multi spec 
> release candidate is now available at:
> https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.rc5.pdf
> 
> It includes the following updates:
> • Add two validation rules multi-21213 and multi-21214 to check the 
> speciesType attribute of a species with listOfOutwardBindingSites 
> and/or listOfSpeciesFeatures╴
> • Add a constraint to the relation attribute of a 
> subListOfSpeciesFeatures having a speciesFeature child referencing a 
> speciesFeatureType with “occur > 1”. 
> • Enforce the SubListOfSpeciesFeatures class to have at least two 
> speciesFeatures and set relation as a required attribute. 
> 
> The changes have been implemented in libsbml-multi and the updated 
> library is expected to be compatible with the current supporting 
> applications. 
> 
> 
> Regards,
> 
> Fengkai
> 
> ====================
> 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.
> ******************************************************************
> 
> ------------------------------------------------------------------------------
> Announcing the Oxford Dictionaries API! The API offers world-renowned
> dictionary content that is easy and intuitive to access. Sign up for an
> account today to start using our lexical data to power your apps and
> projects. Get started today and enter our developer competition.
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[sbml-multi] Latest release candidate of the multi spec -- updated to rc5

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

Thanks for Sarah's work to check the spec document and conduct stress testing on the libsbml-multi library, the rc5 of the multi spec release candidate is now available at:
https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.rc5.pdf

It includes the following updates:
• Add two validation rules multi-21213 and multi-21214 to check the speciesType attribute of a species with listOfOutwardBindingSites and/or listOfSpeciesFeatures ̇
• Add a constraint to the relation attribute of a subListOfSpeciesFeatures having a speciesFeature child referencing a speciesFeatureType with “occur > 1”. 
• Enforce the SubListOfSpeciesFeatures class to have at least two speciesFeatures and set relation as a required attribute. 

The changes have been implemented in libsbml-multi and the updated library is expected to be compatible with the current supporting applications. 


Regards,

Fengkai

====================
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.
******************************************************************

[sbml-multi] latest release candidate of the multi spec

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

FYI, the latest version of the multi spec release candidate is available at:
https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.rc4.pdf

Thank all who contributed to the development of the multi package!

Fengkai

====================
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.
******************************************************************

[sbml-multi] Release Candidate 1 for SBML Multi v1.1

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

We are pleased to announce the 1st release candidate specification for the SBML Multi package ver 1.1, which is part of the effort towards making an official release of the SBML Multi package.

The specification is available at:

https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.1.rc1.pdf

This version contains minor wording changes from the last draft release v.1.0.7. As always, comments and feedback are welcome!

Thanks,

Fengkai + Martin

====================
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.
******************************************************************

Re: [sbml-multi] multi breakout session at COMBINE 2016

[Lucian S. <luc...@gm...>]

Updated link to the Google doc:

https://docs.google.com/document/d/11bVRo4WB_P2sXMNSffq7VrZpn_CQb5BOCUYvZ4rWvg0/edit

Link to the bluejeans meeting itself:

http://bluejeans.com/146664661

On Thu, Sep 22, 2016 at 12:01 PM, Zhang, Fengkai (NIH/NIAID) [E] <
zha...@ni...> wrote:

> Hi,
>
> For those who are interested in the breakout session in the afternoon,
> besides bluejeans, we can also use google drive for the discussion:
> https://docs.google.com/document/d/11bVRo4WB_
> P2sXMNSffq7VrZpn_CQb5BOCUYvZ4r
> Wvg0/edit
>
> Everyone can edit.
>
>
> Fengkai
>
>
>
>
> On 9/20/16, 9:26 AM, "Zhang, Fengkai (NIH/NIAID) [E]"
> <zha...@ni...> wrote:
>
> >Dear all,
> >
> >There will be a multi breakout session on Thursday afternoon 3:30 - 5:00pm
> >newcastle local time (us eastern 10:30am - 12:00pm). Thanks to Jose¹s
> >great work for the bionetgen multi exporter, we have good progress in
> >sharing models from bionetgen to multi to simmune. We may discuss the
> >current status and identify what we need to do to get multi officially
> >³released² and also for long term. I will try to have the session online
> >accessible, possibly through google hangouts. Let me know if you are
> >interested in joining the session online and also please include your
> >gmail.
> >
> >Fengkai
> >
> >====================
> >
> >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.
> >******************************************************************
> >
> >
> >-----------------------------------------------------------
> ---------------
> >----
> >_______________________________________________
> >Sbml-multi mailing list
> >Sbm...@li...
> >https://lists.sourceforge.net/lists/listinfo/sbml-multi
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Sbml-multi mailing list
> Sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-multi
>

Re: [sbml-multi] multi breakout session at COMBINE 2016

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Hi,

For those who are interested in the breakout session in the afternoon,
besides bluejeans, we can also use google drive for the discussion:
https://docs.google.com/document/d/11bVRo4WB_P2sXMNSffq7VrZpn_CQb5BOCUYvZ4r
Wvg0/edit

Everyone can edit.


Fengkai




On 9/20/16, 9:26 AM, "Zhang, Fengkai (NIH/NIAID) [E]"
<zha...@ni...> wrote:

>Dear all,
>
>There will be a multi breakout session on Thursday afternoon 3:30 - 5:00pm
>newcastle local time (us eastern 10:30am - 12:00pm). Thanks to Jose¹s
>great work for the bionetgen multi exporter, we have good progress in
>sharing models from bionetgen to multi to simmune. We may discuss the
>current status and identify what we need to do to get multi officially
>³released² and also for long term. I will try to have the session online
>accessible, possibly through google hangouts. Let me know if you are
>interested in joining the session online and also please include your
>gmail.
>
>Fengkai
>
>====================
>
>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.
>******************************************************************
>
>
>--------------------------------------------------------------------------
>----
>_______________________________________________
>Sbml-multi mailing list
>Sbm...@li...
>https://lists.sourceforge.net/lists/listinfo/sbml-multi

Re: [sbml-multi] multi breakout session at COMBINE 2016

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Thanks!

Update: 
The meeting has bluejeans for video conferencing. Feel free to join at the
time and gmail will not be required anymore.

Fengkai




On 9/20/16, 3:16 PM, "Hlavacek, William Scott" <wi...@la...> wrote:

>Hi Fengkai,
>I’ll try to join. My Gmail address is
>wsh...@gm...<mailto:wsh...@gm...>
>
>On Sep 20, 2016, at 2:26 AM, Zhang, Fengkai (NIH/NIAID) [E]
><zha...@ni...<mailto:zha...@ni...>> wrote:
>
>Dear all,
>
>There will be a multi breakout session on Thursday afternoon 3:30 - 5:00pm
>newcastle local time (us eastern 10:30am - 12:00pm). Thanks to Jose¹s
>great work for the bionetgen multi exporter, we have good progress in
>sharing models from bionetgen to multi to simmune. We may discuss the
>current status and identify what we need to do to get multi officially
>³released² and also for long term. I will try to have the session online
>accessible, possibly through google hangouts. Let me know if you are
>interested in joining the session online and also please include your
>gmail.
>
>Fengkai
>
>====================
>
>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.
>******************************************************************
>
>
>--------------------------------------------------------------------------
>----
>_______________________________________________
>Sbml-multi mailing list
>Sbm...@li...<mailto:Sbm...@li...>
>https://lists.sourceforge.net/lists/listinfo/sbml-multi
>
>--------------------------------------------------------------------------
>----
>_______________________________________________
>Sbml-multi mailing list
>Sbm...@li...
>https://lists.sourceforge.net/lists/listinfo/sbml-multi

Re: [sbml-multi] multi breakout session at COMBINE 2016

[Hlavacek, W. S. <wi...@la...>]

Hi Fengkai,
I’ll try to join. My Gmail address is wsh...@gm...<mailto:wsh...@gm...>

On Sep 20, 2016, at 2:26 AM, Zhang, Fengkai (NIH/NIAID) [E] <zha...@ni...<mailto:zha...@ni...>> wrote:

Dear all,

There will be a multi breakout session on Thursday afternoon 3:30 - 5:00pm
newcastle local time (us eastern 10:30am - 12:00pm). Thanks to Jose¹s
great work for the bionetgen multi exporter, we have good progress in
sharing models from bionetgen to multi to simmune. We may discuss the
current status and identify what we need to do to get multi officially
³released² and also for long term. I will try to have the session online
accessible, possibly through google hangouts. Let me know if you are
interested in joining the session online and also please include your
gmail.

Fengkai

====================

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.
******************************************************************


------------------------------------------------------------------------------
_______________________________________________
Sbml-multi mailing list
Sbm...@li...<mailto:Sbm...@li...>
https://lists.sourceforge.net/lists/listinfo/sbml-multi

Re: [sbml-multi] multi breakout session at COMBINE 2016

[Jose J. T. <jj...@gm...>]

Hello Fengkai,

I am interested in joining the discussion. This address is the gmail I want
to use for the hangouts.

On Tue, Sep 20, 2016 at 4:26 AM, Zhang, Fengkai (NIH/NIAID) [E] <
zha...@ni...> wrote:

> Dear all,
>
> There will be a multi breakout session on Thursday afternoon 3:30 - 5:00pm
> newcastle local time (us eastern 10:30am - 12:00pm). Thanks to Jose¹s
> great work for the bionetgen multi exporter, we have good progress in
> sharing models from bionetgen to multi to simmune. We may discuss the
> current status and identify what we need to do to get multi officially
> ³released² and also for long term. I will try to have the session online
> accessible, possibly through google hangouts. Let me know if you are
> interested in joining the session online and also please include your
> gmail.
>
> Fengkai
>
> ====================
>
> 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.
> ******************************************************************
>
>
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Sbml-multi mailing list
> Sbm...@li...
> https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2flists.
> sourceforge.net%2flists%2flistinfo%2fsbml-multi&data=
> 01%7c01%7cjjtapia%40pitt.edu%7c2873c93208fb47f48a7308d3e13491eb%
> 7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=sUruCniIz5dXX%2bXGtY6MqNn%
> 2bgUENhTCHCjh0g6P7hDs%3d
>



-- 
José Juan Tapia Valenzuela, Ph.D.
Research Associate
University of Pittsburgh
3076.1 Biological Sciences Tower 3
Pittsburgh, PA 15260

[sbml-multi] multi breakout session at COMBINE 2016

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Dear all,

There will be a multi breakout session on Thursday afternoon 3:30 - 5:00pm
newcastle local time (us eastern 10:30am - 12:00pm). Thanks to Jose¹s
great work for the bionetgen multi exporter, we have good progress in
sharing models from bionetgen to multi to simmune. We may discuss the
current status and identify what we need to do to get multi officially
³released² and also for long term. I will try to have the session online
accessible, possibly through google hangouts. Let me know if you are
interested in joining the session online and also please include your
gmail.

Fengkai

====================

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.
******************************************************************

Re: [sbml-multi] SBML Multi spec v 1.0.7

[Michael H. <mh...@ca...>]

This is now done.

Thanks,
MH


On Tue, 30 Aug 2016 13:59:01 +0000, Zhang, Fengkai (NIH/NIAID) [E] wrote:
> It will be great, thanks!
> 
> Fengkai
> 
> ________________________________________
> From: Michael Hucka [mh...@ca...]
> Sent: Tuesday, August 30, 2016 12:39 AM
> To: Discussions of the SBML Level 3 'multi' package
> Subject: Re: [sbml-multi] SBML Multi spec v 1.0.7
> 
> Hi,
> 
> The copy of the specification that is pointed to by the page
> 
>   http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/multi
> 
> is not this one (1.0.7).  Should I update the link to point to the 
> 1.0.7 version?
> 
> MH
> 
> On Wed, 24 Aug 2016 17:47:15 +0000, Zhang, Fengkai (NIH/NIAID) [E] wrote:
>> Dear All,
>> 
>> A new release of SBML Multi spec v1.0.7 is available at:
>> 
>> http://goo.gl/vzPpws
>> or
>> https://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/multi/spec/sbml-multi_spec_1.0.7.pdf?format=raw
>> 
>> This release mainly includes two changes:
>> (1) Removal of the SpeciesFeatureChange class under the
>> SpeciesTypeComponentMapInProduct class. This change helps reduce the
>> redundancy which can be inferred from the
>> SpeciesTypeComponentMapInProduct class and the speciesFeatures listed
>> in the multi extended Species class.
>> (2) Add a new validation rule "an ourwardBindingSite can not be a
>> binding site in a bond of its containing species".
>> 
>> The libsbml-multi library reflecting the changes will also be updated.
>> 
>> Your comment or questions are welcome.
>> 
>> Regards,
>> 
>> Fengkai
>> 
>> ====================
>> 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.
>> ******************************************************************
>> 
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Sbml-multi mailing list
>> Sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Sbml-multi mailing list
> Sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-multi
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Sbml-multi mailing list
> Sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-multi