sbml-qual Mailing List for Systems Biology Markup Language (SBML)

Hi Cole,

thanks Sarah for forwarding this question!

I don't see anything wrong with this model. The function to reach level 1
is "IFNgR OR IFNbR", which is encoded in GINsim (for technical reasons) as
"(IFNgR=0 AND IFNbR=1) OR IFNgR=1"

In this function, IFNbR does appear in the root apply, but not in all
sub-branches, which should be fine. Maybe the validator is being a bit too
picky here?

Best


On Mon, Sep 7, 2020 at 11:10 AM Sarah Keating <ske...@ca...> wrote:

>
> Hi Cole
>
> Best place for this question is the sbml qual list (included in forward).
>
> Sarah
>
>
> -------- Forwarded Message --------
> Subject: [sbml:sbml-specifications] #368 qual: Input Species not in
> FunctionTerm
> Date: Fri, 04 Sep 2020 17:04:50 -0000
> From: Cole Lyman <col...@us...>
> Reply-To: Ticket #368: qual: Input Species not in FunctionTerm
> <36...@sb...>
> To: Ticket #368: qual: Input Species not in FunctionTerm
> <36...@sb...>
>
>
>
>
> ---
>
> ** [sbml-specifications:#368] qual: Input Species not in FunctionTerm**
>
> **Status:** open
> **Group:** Reported-Proposed
> **Created:** Fri Sep 04, 2020 05:04 PM UTC by Cole Lyman
> **Last Updated:** Fri Sep 04, 2020 05:04 PM UTC
> **Owner:** nobody
> **Attachments:**
>
> -
> [Th17.sbml](
> https://sourceforge.net/p/sbml/sbml-specifications/368/attachment/Th17.sbml)
>
> (34.1 kB; application/octet-stream)
>
>
> I'm not sure if this is the best place to ask this question, I apologize
> if this question isn't relevant here and would appreciate any
> suggestions for a better place to ask it.
>
> I have encountered a model (originally found here
> http://ginsim.org/node/41 and converted to SBML using GINSIM, the
> converted SBML file, Level 3 Version 1 Qual Version 1 is attached) that
> appears to be valid (according to libsbml and
> http://sbml.org/Facilities/Validator/. In this model, there are a number
> of Transitions that have a Species listed in the ListOfInputs, but then
> not appear in the corresponding FunctionTerm. I'm curious if this is
> documented behavior, or if this is an error in this model.
>
> Here is an example from this model:
>
> ~~~
>        <qual:transition qual:id="tr_STAT1">
>          <qual:listOfInputs>
>            <qual:input qual:qualitativeSpecies="IFNgR"
> qual:transitionEffect="none" qual:sign="positive" qual:id="tr_STAT1_in_1"/>
>            <qual:input qual:qualitativeSpecies="IFNbR"
> qual:transitionEffect="none" qual:sign="positive" qual:id="tr_STAT1_in_6"/>
>          </qual:listOfInputs>
>          <qual:listOfOutputs>
>            <qual:output qual:qualitativeSpecies="STAT1"
> qual:transitionEffect="assignmentLevel" qual:id="tr_STAT1_out"/>
>          </qual:listOfOutputs>
>          <qual:listOfFunctionTerms>
>            <qual:defaultTerm qual:resultLevel="0">
>            </qual:defaultTerm>
>            <qual:functionTerm qual:resultLevel="1">
>              <math xmlns="http://www.w3.org/1998/Math/MathML">
>                 <apply>
>                  <or/>
>                  <apply>
>                    <and/>
>                    <apply>
>                      <eq/>
>                      <ci> IFNgR </ci>
>                      <cn type="integer"> 0 </cn>
>                    </apply>
>                    <apply>
>                      <eq/>
>                      <ci> IFNbR </ci>
>                      <cn type="integer"> 1 </cn>
>                    </apply>
>                  </apply>
>                  <apply>
>                    <eq/>
>                    <ci> IFNgR </ci>
>                    <cn type="integer"> 1 </cn>
>                    <!--Should there be a value for IFNbR in this apply
> group?-->
>                  </apply>
>                </apply>
>              </math>
>                      </qual:functionTerm>
>            <qual:functionTerm qual:resultLevel="2">
>              <math xmlns="http://www.w3.org/1998/Math/MathML">
>                 <apply>
>                  <eq/>
>                  <ci> IFNgR </ci>
>                  <cn type="integer"> 2 </cn>
>                </apply>
>              </math>
>                      </qual:functionTerm>
>          </qual:listOfFunctionTerms>
>        </qual:transition>
> ~~~
>
> Perhaps if an input isn't listed then it applies to any value of that
> Species? I wasn't able to find this in the specification, so I don't
> want to jump to that conclusion unless this is accepted behavior.
>
> Any input would be helpful! Thank you in advance.
>
>
> ---
>
> Sent from sourceforge.net because you indicated interest in
> <https://sourceforge.net/p/sbml/sbml-specifications/368/>
>
>
>
> To unsubscribe from further messages, please visit
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>
>
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>


-- 
Aurélien Naldi

Hi Cole

Best place for this question is the sbml qual list (included in forward).

Sarah


-------- Forwarded Message --------
Subject: [sbml:sbml-specifications] #368 qual: Input Species not in 
FunctionTerm
Date: Fri, 04 Sep 2020 17:04:50 -0000
From: Cole Lyman <col...@us...>
Reply-To: Ticket #368: qual: Input Species not in FunctionTerm 
<36...@sb...>
To: Ticket #368: qual: Input Species not in FunctionTerm 
<36...@sb...>




---

** [sbml-specifications:#368] qual: Input Species not in FunctionTerm**

**Status:** open
**Group:** Reported-Proposed
**Created:** Fri Sep 04, 2020 05:04 PM UTC by Cole Lyman
**Last Updated:** Fri Sep 04, 2020 05:04 PM UTC
**Owner:** nobody
**Attachments:**

- 
[Th17.sbml](https://sourceforge.net/p/sbml/sbml-specifications/368/attachment/Th17.sbml) 
(34.1 kB; application/octet-stream)


I'm not sure if this is the best place to ask this question, I apologize 
if this question isn't relevant here and would appreciate any 
suggestions for a better place to ask it.

I have encountered a model (originally found here 
http://ginsim.org/node/41 and converted to SBML using GINSIM, the 
converted SBML file, Level 3 Version 1 Qual Version 1 is attached) that 
appears to be valid (according to libsbml and 
http://sbml.org/Facilities/Validator/. In this model, there are a number 
of Transitions that have a Species listed in the ListOfInputs, but then 
not appear in the corresponding FunctionTerm. I'm curious if this is 
documented behavior, or if this is an error in this model.

Here is an example from this model:

~~~
       <qual:transition qual:id="tr_STAT1">
         <qual:listOfInputs>
           <qual:input qual:qualitativeSpecies="IFNgR" 
qual:transitionEffect="none" qual:sign="positive" qual:id="tr_STAT1_in_1"/>
           <qual:input qual:qualitativeSpecies="IFNbR" 
qual:transitionEffect="none" qual:sign="positive" qual:id="tr_STAT1_in_6"/>
         </qual:listOfInputs>
         <qual:listOfOutputs>
           <qual:output qual:qualitativeSpecies="STAT1" 
qual:transitionEffect="assignmentLevel" qual:id="tr_STAT1_out"/>
         </qual:listOfOutputs>
         <qual:listOfFunctionTerms>
           <qual:defaultTerm qual:resultLevel="0">
           </qual:defaultTerm>
           <qual:functionTerm qual:resultLevel="1">
             <math xmlns="http://www.w3.org/1998/Math/MathML"> 
                <apply>
                 <or/>
                 <apply>
                   <and/>
                   <apply>
                     <eq/>
                     <ci> IFNgR </ci>
                     <cn type="integer"> 0 </cn>
                   </apply>
                   <apply>
                     <eq/>
                     <ci> IFNbR </ci>
                     <cn type="integer"> 1 </cn>
                   </apply>
                 </apply>
                 <apply>
                   <eq/>
                   <ci> IFNgR </ci>
                   <cn type="integer"> 1 </cn>
                   <!--Should there be a value for IFNbR in this apply 
group?-->
                 </apply>
               </apply>
             </math>
                     </qual:functionTerm>
           <qual:functionTerm qual:resultLevel="2">
             <math xmlns="http://www.w3.org/1998/Math/MathML"> 
                <apply>
                 <eq/>
                 <ci> IFNgR </ci>
                 <cn type="integer"> 2 </cn>
               </apply>
             </math>
                     </qual:functionTerm>
         </qual:listOfFunctionTerms>
       </qual:transition>
~~~

Perhaps if an input isn't listed then it applies to any value of that 
Species? I wasn't able to find this in the specification, so I don't 
want to jump to that conclusion unless this is accepted behavior.

Any input would be helpful! Thank you in advance.


---

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Dear Valeria

We chose to use RNG schemas for SBML Level 3 and packages such as qual. 
Information is available here

http://sbml.org/Documents/Specifications/RELAX_NG_schemas_and_validation_for_SBML_Level_3


It is exciting to hear that you are extending qual; rather than 
reinventing something. It would be interesting to hear more about it.

Thank you

Sarah



On 19/11/2018 13:51, Valeria Boscaino wrote:
> Dear Development Team,
> we are currently working on a possible extension package of sbml-qual
> language. We are searching for a xsd schema of sbml-qual in order to
> validate our instances.
> Could you please provide us this schema?
> I'm looking forward to hearing from you.
> Best regards,
> Valeria Boscaino
> 
> 
> 
> 
> 
> _______________________________________________
> sbml-qual mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-qual
> 

Dear Development Team,
we are currently working on a possible extension package of sbml-qual
language. We are searching for a xsd schema of sbml-qual in order to
validate our instances.
Could you please provide us this schema?
I'm looking forward to hearing from you.
Best regards,
Valeria Boscaino

Hi there,

Could someone let us know the best solution for conversion of .sif file
into sbml qual.

Thanks
Sam

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

SBML Editors

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
> 

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.

Hi Pedro,

This seems like something that would be worth sending to all of sbm...@go... -- please feel free to post it there.

MH

On Sat, 21 Apr 2018 03:15:25 +0100, Pedro T. Monteiro wrote:
> Dear colleagues,
> 
> As you know the use of model checkers for the verification of biological
> models comes with a few strings attached.
> 
> I'm finishing tailoring NuSMV to facilitate its usage for logical models,
> and to provide a single model checker bringing together a few existing
> NuSMV extensions.
> 
> To better assess the real needs of modelers verifying models through NuSMV,
> I kindly ask you to answer a small Google Forms (5 min estimated response
> time).
> https://docs.google.com/forms/d/e/1FAIpQLSdlsmTheBwz7Z_oVZuPDzGboQSnVExP2d1Gu_jahI6_Vb3Cng/viewform?usp=sf_link
> 
> PS: feel free to distribute the Form to your students or anyone that
> directly encodes NuSMV properties for the verification of qualitative
> biological models.
> 
> Thank you in advance for your precious time and feedback,
> Pedro
> 
> -- 
> INESC-ID / IST - Universidade de Lisboa, PT
> http://pedromonteiro.org
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! 
> http://sdm.link/slashdot_______________________________________________
> sbml-qual mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-qual

​​Dear colleagues,

As you know the use of model checkers for the verification of biological
models comes with a few strings attached.

I'm finishing tailoring NuSMV to facilitate its usage for logical models,
and to provide a single model checker bringing together a few existing
NuSMV extensions.

To better assess the real needs of modelers verifying models through NuSMV,
I kindly ask you to answer a small Google Forms (5 min estimated response
time).
https://docs.google.com/forms/d/e/1FAIpQLSdlsmTheBwz7Z_oVZuPDzGboQSnVExP2d1Gu_jahI6_Vb3Cng/viewform?usp=sf_link

PS: feel free to distribute the Form to your students or anyone that
directly encodes NuSMV properties for the verification of qualitative
biological models.

Thank you in advance for your precious time and feedback,
Pedro

-- 
INESC-ID / IST - Universidade de Lisboa, PT
http://pedromonteiro.org

March 2018 :-)

Sarah

On 02/02/2018 09:43, Justin McManus wrote:
> Fantastic. I'm not relying on that change (since it's trivial for me to 
> make myself in the meantime). But, out of curiosity, when is the next 
> release planned?
> 
> Justin
> 
> On Fri, Feb 2, 2018 at 4:15 AM, Sarah Keating <ske...@ca... 
> <mailto:ske...@ca...>> wrote:
> 
>     Thanks
> 
>     This will be fixed in the next libSBML release.
> 
>     Sarah
> 
> 
>     On 31/01/2018 15:24, Justin McManus wrote:
> 
>         Thanks very much, Claudine.
> 
>         On Wed, Jan 31, 2018 at 10:12 AM, Claudine Chaouiya
>         <cha...@ig... <mailto:cha...@ig...>
>         <mailto:cha...@ig...
>         <mailto:cha...@ig...>>> wrote:
> 
>              Hi Sarah,
> 
>              Thank you Justin for rising this issue...
>              Indeed, for logical models this rule should be respected
>         because
>              their should not be several transitions defining the
>         regulation of a
>              component… we kept this as a recommendation because for
>         Petri net
>              models, it would be possible to have distinct transitions
>         sharing
>              the same output.
>              I would thus keep it as a recommendation…
>              Best regards
>              Claudine
> 
> 
>               > On 29 Jan 2018, at 09:17, Sarah Keating
>         <ske...@ca... <mailto:ske...@ca...>
>              <mailto:ske...@ca...
>         <mailto:ske...@ca...>>> wrote:
>               >
>               > Hi Qual people
>               >
>               > We received a query (see below) from a libsbml user (Justin
>              McManus cc'ed) about an anomaly between the qual
>         specification and
>              the libsbml implementation:
>               >
>               > We have rule qual-20311:
>               >
>               > A QualitativeSpecies that is referenced by an Output
>         with the
>              qual:transitionEffect at-tribute set to “assignmentLevel”
>         cannot be
>              referenced by any other Output with the same transitionEffect
>              throughout the set of transitions for the containing model.
>               >
>               > In the spec it is marked as 'recommendation' but libSBML
>         flags it
>              as an 'error' - i.e. must not be violated.
>               >
>               > A recommendation would suggest that it is a good idea to
>         stick to
>              this rule but it should not cause problems if you violate it.
>               >
>               > Before changing libSBML code I wanted to check with
>         people more
>              familiar with these models as to whether the rule is fine as a
>              recommendation :-)
>               >
>               > i.e. which is right -  the specification or libSBML
>              implementation ?? :-)
>               >
>               > Thanks
>               >
>               > Sarah
>               >
>               > -------- Forwarded Message --------
>               > Subject: Re: [libsbml-team] Incorrect entry in
>              QualSBMLErrorTable.h version 5.16.0
>               > Date: Fri, 26 Jan 2018 09:01:05 +0000
>               > From: Sarah Keating <ske...@ca...
>         <mailto:ske...@ca...>
>              <mailto:ske...@ca... <mailto:ske...@ca...>>>
>               > To: Justin McManus <ju...@ka...
>         <mailto:ju...@ka...>
>              <mailto:ju...@ka... <mailto:ju...@ka...>>>,
>         lib...@go... <mailto:lib...@go...>
>              <mailto:lib...@go...
>         <mailto:lib...@go...>>
>               >
>               > On 25/01/2018 15:07, Justin McManus wrote:
>               >> To the SBML developer team,
>               >> First, thank you so much for the profoundly important
>         software
>              you maintain.
>               >> I noticed one issue that I'd like to report. In what I
>         believe
>              is the latest specification of the qual package for SBML, Rule
>              qual-20311 is listed as a /recommendation/, not a
>         /requirement/.
>              However, the source code (libsbml v 5.16.0) treats this
>         rule as a
>              requirement, and will result in an error (rather than a
>         warning)
>              when the recommendation is violated.
>               >> In src/sbml/packages/qual/validator, please see
>              QualSBMLErrorTable.h. Specifically, please see the entry for
>              QualQSAssignedOnlyOnce, which corresponds to this rule (Rule
>              qual-20311) and error code 3020311. This entry treats the
>         occurrence
>              of this flag as a LIBSBML_SEV_ERROR rather than
>         LIBSBML_SEV_WARNING.
>               >> I first noticed the issue while using the R package
>         rsbml, which
>              relies on the libSBML, and which throws the error encoded
>         in the
>              libsbml when it reads an SBML containing multiple transition
>              assignments for the same qualitative species.
>               >> Please note that I did /not/ run the library through a
>         debugger
>              to confirm that the issue in QualSBMLErrorTable.h is the
>         cause of
>              the misspecified behavior I describe above. That's merely
>         my guess
>              based on a cursory look at the source code.
>               >> Warm regards, and thank you for considering my comments
>         here,
>               >> Justin
>               >> --
>               >> Justin McManus, Ph.D.
>               >> Senior Scientist
>               >> Lead Computational Biologist
>               >> Kallyope, Inc.
>               >> 430 East 29th Street, Suite 1050
>               >> New York, NY 10016
>               >> (646) 596-3471 <tel:%28646%29%20596-3471>
>               >> --
>               >> You received this message because you are subscribed to the
>              Google Groups "libsbml-team" group.
>               >> To unsubscribe from this group and stop receiving
>         emails from
>              it, send an email to
>         lib...@go...
>         <mailto:libsbml-team%2Bu...@go...>
>              <mailto:libsbml-team%2Bu...@go...
>         <mailto:libsbml-team%252...@go...>>
>              <mailto:lib...@go...
>         <mailto:libsbml-team%2Bu...@go...>
>              <mailto:libsbml-team%2Bu...@go...
>         <mailto:libsbml-team%252...@go...>>>.
>               >> For more options, visit
>         https://groups.google.com/d/optout
>         <https://groups.google.com/d/optout>
>              <https://groups.google.com/d/optout
>         <https://groups.google.com/d/optout>>.
>               >
>               >
>               >
>             
>         ------------------------------------------------------------------------------
>               > Check out the vibrant tech community on one of the
>         world's most
>               > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>               > _______________________________________________
>               > sbml-qual mailing list
>               > sbm...@li...
>         <mailto:sbm...@li...>
>              <mailto:sbm...@li...
>         <mailto:sbm...@li...>>
>               > https://lists.sourceforge.net/lists/listinfo/sbml-qual
>         <https://lists.sourceforge.net/lists/listinfo/sbml-qual>
>              <https://lists.sourceforge.net/lists/listinfo/sbml-qual
>         <https://lists.sourceforge.net/lists/listinfo/sbml-qual>>
> 
> 
> 
> 
>         -- 
>         Justin McManus, Ph.D.
>         Senior Scientist
>         Lead Computational Biologist
>         Kallyope, Inc.
>         430 East 29th Street, Suite 1050
>         New York, NY 10016
>         (646) 596-3471 <tel:%28646%29%20596-3471>
> 
> 
>         ------------------------------------------------------------------------------
>         Check out the vibrant tech community on one of the world's most
>         engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> 
> 
> 
>         _______________________________________________
>         sbml-qual mailing list
>         sbm...@li...
>         <mailto:sbm...@li...>
>         https://lists.sourceforge.net/lists/listinfo/sbml-qual
>         <https://lists.sourceforge.net/lists/listinfo/sbml-qual>
> 
> 
> 
> 
> 
> -- 
> Justin McManus, Ph.D.
> Senior Scientist
> Lead Computational Biologist
> Kallyope, Inc.
> 430 East 29th Street, Suite 1050
> New York, NY 10016
> (646) 596-3471

Thanks

This will be fixed in the next libSBML release.

Sarah


On 31/01/2018 15:24, Justin McManus wrote:
> Thanks very much, Claudine.
> 
> On Wed, Jan 31, 2018 at 10:12 AM, Claudine Chaouiya 
> <cha...@ig... <mailto:cha...@ig...>> wrote:
> 
>     Hi Sarah,
> 
>     Thank you Justin for rising this issue...
>     Indeed, for logical models this rule should be respected because
>     their should not be several transitions defining the regulation of a
>     component… we kept this as a recommendation because for Petri net
>     models, it would be possible to have distinct transitions sharing
>     the same output.
>     I would thus keep it as a recommendation…
>     Best regards
>     Claudine
> 
> 
>      > On 29 Jan 2018, at 09:17, Sarah Keating <ske...@ca...
>     <mailto:ske...@ca...>> wrote:
>      >
>      > Hi Qual people
>      >
>      > We received a query (see below) from a libsbml user (Justin
>     McManus cc'ed) about an anomaly between the qual specification and
>     the libsbml implementation:
>      >
>      > We have rule qual-20311:
>      >
>      > A QualitativeSpecies that is referenced by an Output with the
>     qual:transitionEffect at-tribute set to “assignmentLevel” cannot be
>     referenced by any other Output with the same transitionEffect
>     throughout the set of transitions for the containing model.
>      >
>      > In the spec it is marked as 'recommendation' but libSBML flags it
>     as an 'error' - i.e. must not be violated.
>      >
>      > A recommendation would suggest that it is a good idea to stick to
>     this rule but it should not cause problems if you violate it.
>      >
>      > Before changing libSBML code I wanted to check with people more
>     familiar with these models as to whether the rule is fine as a
>     recommendation :-)
>      >
>      > i.e. which is right -  the specification or libSBML
>     implementation ?? :-)
>      >
>      > Thanks
>      >
>      > Sarah
>      >
>      > -------- Forwarded Message --------
>      > Subject: Re: [libsbml-team] Incorrect entry in
>     QualSBMLErrorTable.h version 5.16.0
>      > Date: Fri, 26 Jan 2018 09:01:05 +0000
>      > From: Sarah Keating <ske...@ca...
>     <mailto:ske...@ca...>>
>      > To: Justin McManus <ju...@ka...
>     <mailto:ju...@ka...>>, lib...@go...
>     <mailto:lib...@go...>
>      >
>      > On 25/01/2018 15:07, Justin McManus wrote:
>      >> To the SBML developer team,
>      >> First, thank you so much for the profoundly important software
>     you maintain.
>      >> I noticed one issue that I'd like to report. In what I believe
>     is the latest specification of the qual package for SBML, Rule
>     qual-20311 is listed as a /recommendation/, not a /requirement/.
>     However, the source code (libsbml v 5.16.0) treats this rule as a
>     requirement, and will result in an error (rather than a warning)
>     when the recommendation is violated.
>      >> In src/sbml/packages/qual/validator, please see
>     QualSBMLErrorTable.h. Specifically, please see the entry for
>     QualQSAssignedOnlyOnce, which corresponds to this rule (Rule
>     qual-20311) and error code 3020311. This entry treats the occurrence
>     of this flag as a LIBSBML_SEV_ERROR rather than LIBSBML_SEV_WARNING.
>      >> I first noticed the issue while using the R package rsbml, which
>     relies on the libSBML, and which throws the error encoded in the
>     libsbml when it reads an SBML containing multiple transition
>     assignments for the same qualitative species.
>      >> Please note that I did /not/ run the library through a debugger
>     to confirm that the issue in QualSBMLErrorTable.h is the cause of
>     the misspecified behavior I describe above. That's merely my guess
>     based on a cursory look at the source code.
>      >> Warm regards, and thank you for considering my comments here,
>      >> Justin
>      >> --
>      >> Justin McManus, Ph.D.
>      >> Senior Scientist
>      >> Lead Computational Biologist
>      >> Kallyope, Inc.
>      >> 430 East 29th Street, Suite 1050
>      >> New York, NY 10016
>      >> (646) 596-3471
>      >> --
>      >> You received this message because you are subscribed to the
>     Google Groups "libsbml-team" group.
>      >> To unsubscribe from this group and stop receiving emails from
>     it, send an email to lib...@go...
>     <mailto:libsbml-team%2Bu...@go...>
>     <mailto:lib...@go...
>     <mailto:libsbml-team%2Bu...@go...>>.
>      >> For more options, visit https://groups.google.com/d/optout
>     <https://groups.google.com/d/optout>.
>      >
>      >
>      >
>     ------------------------------------------------------------------------------
>      > Check out the vibrant tech community on one of the world's most
>      > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>      > _______________________________________________
>      > sbml-qual mailing list
>      > sbm...@li...
>     <mailto:sbm...@li...>
>      > https://lists.sourceforge.net/lists/listinfo/sbml-qual
>     <https://lists.sourceforge.net/lists/listinfo/sbml-qual>
> 
> 
> 
> 
> -- 
> Justin McManus, Ph.D.
> Senior Scientist
> Lead Computational Biologist
> Kallyope, Inc.
> 430 East 29th Street, Suite 1050
> New York, NY 10016
> (646) 596-3471
> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> 
> 
> 
> _______________________________________________
> sbml-qual mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-qual
> 

Fantastic. I'm not relying on that change (since it's trivial for me to
make myself in the meantime). But, out of curiosity, when is the next
release planned?

Justin

On Fri, Feb 2, 2018 at 4:15 AM, Sarah Keating <ske...@ca...> wrote:

> Thanks
>
> This will be fixed in the next libSBML release.
>
> Sarah
>
>
> On 31/01/2018 15:24, Justin McManus wrote:
>
>> Thanks very much, Claudine.
>>
>> On Wed, Jan 31, 2018 at 10:12 AM, Claudine Chaouiya <
>> cha...@ig... <mailto:cha...@ig...>> wrote:
>>
>>     Hi Sarah,
>>
>>     Thank you Justin for rising this issue...
>>     Indeed, for logical models this rule should be respected because
>>     their should not be several transitions defining the regulation of a
>>     component… we kept this as a recommendation because for Petri net
>>     models, it would be possible to have distinct transitions sharing
>>     the same output.
>>     I would thus keep it as a recommendation…
>>     Best regards
>>     Claudine
>>
>>
>>      > On 29 Jan 2018, at 09:17, Sarah Keating <ske...@ca...
>>     <mailto:ske...@ca...>> wrote:
>>      >
>>      > Hi Qual people
>>      >
>>      > We received a query (see below) from a libsbml user (Justin
>>     McManus cc'ed) about an anomaly between the qual specification and
>>     the libsbml implementation:
>>      >
>>      > We have rule qual-20311:
>>      >
>>      > A QualitativeSpecies that is referenced by an Output with the
>>     qual:transitionEffect at-tribute set to “assignmentLevel” cannot be
>>     referenced by any other Output with the same transitionEffect
>>     throughout the set of transitions for the containing model.
>>      >
>>      > In the spec it is marked as 'recommendation' but libSBML flags it
>>     as an 'error' - i.e. must not be violated.
>>      >
>>      > A recommendation would suggest that it is a good idea to stick to
>>     this rule but it should not cause problems if you violate it.
>>      >
>>      > Before changing libSBML code I wanted to check with people more
>>     familiar with these models as to whether the rule is fine as a
>>     recommendation :-)
>>      >
>>      > i.e. which is right -  the specification or libSBML
>>     implementation ?? :-)
>>      >
>>      > Thanks
>>      >
>>      > Sarah
>>      >
>>      > -------- Forwarded Message --------
>>      > Subject: Re: [libsbml-team] Incorrect entry in
>>     QualSBMLErrorTable.h version 5.16.0
>>      > Date: Fri, 26 Jan 2018 09:01:05 +0000
>>      > From: Sarah Keating <ske...@ca...
>>     <mailto:ske...@ca...>>
>>      > To: Justin McManus <ju...@ka...
>>     <mailto:ju...@ka...>>, lib...@go...
>>     <mailto:lib...@go...>
>>      >
>>      > On 25/01/2018 15:07, Justin McManus wrote:
>>      >> To the SBML developer team,
>>      >> First, thank you so much for the profoundly important software
>>     you maintain.
>>      >> I noticed one issue that I'd like to report. In what I believe
>>     is the latest specification of the qual package for SBML, Rule
>>     qual-20311 is listed as a /recommendation/, not a /requirement/.
>>     However, the source code (libsbml v 5.16.0) treats this rule as a
>>     requirement, and will result in an error (rather than a warning)
>>     when the recommendation is violated.
>>      >> In src/sbml/packages/qual/validator, please see
>>     QualSBMLErrorTable.h. Specifically, please see the entry for
>>     QualQSAssignedOnlyOnce, which corresponds to this rule (Rule
>>     qual-20311) and error code 3020311. This entry treats the occurrence
>>     of this flag as a LIBSBML_SEV_ERROR rather than LIBSBML_SEV_WARNING.
>>      >> I first noticed the issue while using the R package rsbml, which
>>     relies on the libSBML, and which throws the error encoded in the
>>     libsbml when it reads an SBML containing multiple transition
>>     assignments for the same qualitative species.
>>      >> Please note that I did /not/ run the library through a debugger
>>     to confirm that the issue in QualSBMLErrorTable.h is the cause of
>>     the misspecified behavior I describe above. That's merely my guess
>>     based on a cursory look at the source code.
>>      >> Warm regards, and thank you for considering my comments here,
>>      >> Justin
>>      >> --
>>      >> Justin McManus, Ph.D.
>>      >> Senior Scientist
>>      >> Lead Computational Biologist
>>      >> Kallyope, Inc.
>>      >> 430 East 29th Street, Suite 1050
>>      >> New York, NY 10016
>>      >> (646) 596-3471
>>      >> --
>>      >> You received this message because you are subscribed to the
>>     Google Groups "libsbml-team" group.
>>      >> To unsubscribe from this group and stop receiving emails from
>>     it, send an email to lib...@go...
>>     <mailto:libsbml-team%2Bu...@go...>
>>     <mailto:lib...@go...
>>     <mailto:libsbml-team%2Bu...@go...>>.
>>      >> For more options, visit https://groups.google.com/d/optout
>>     <https://groups.google.com/d/optout>.
>>      >
>>      >
>>      >
>>     ------------------------------------------------------------
>> ------------------
>>      > Check out the vibrant tech community on one of the world's most
>>      > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>      > _______________________________________________
>>      > sbml-qual mailing list
>>      > sbm...@li...
>>     <mailto:sbm...@li...>
>>      > https://lists.sourceforge.net/lists/listinfo/sbml-qual
>>     <https://lists.sourceforge.net/lists/listinfo/sbml-qual>
>>
>>
>>
>>
>> --
>> Justin McManus, Ph.D.
>> Senior Scientist
>> Lead Computational Biologist
>> Kallyope, Inc.
>> 430 East 29th Street, Suite 1050
>> New York, NY 10016
>> (646) 596-3471
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> _______________________________________________
>> sbml-qual mailing list
>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbml-qual
>>
>>
>


-- 
Justin McManus, Ph.D.
Senior Scientist
Lead Computational Biologist
Kallyope, Inc.
430 East 29th Street, Suite 1050
New York, NY 10016
(646) 596-3471

Thanks very much, Claudine.

On Wed, Jan 31, 2018 at 10:12 AM, Claudine Chaouiya <
cha...@ig...> wrote:

> Hi Sarah,
>
> Thank you Justin for rising this issue...
> Indeed, for logical models this rule should be respected because their
> should not be several transitions defining the regulation of a component…
> we kept this as a recommendation because for Petri net models, it would be
> possible to have distinct transitions sharing the same output.
> I would thus keep it as a recommendation…
> Best regards
> Claudine
>
>
> > On 29 Jan 2018, at 09:17, Sarah Keating <ske...@ca...> wrote:
> >
> > Hi Qual people
> >
> > We received a query (see below) from a libsbml user (Justin McManus
> cc'ed) about an anomaly between the qual specification and the libsbml
> implementation:
> >
> > We have rule qual-20311:
> >
> > A QualitativeSpecies that is referenced by an Output with the
> qual:transitionEffect at-tribute set to “assignmentLevel” cannot be
> referenced by any other Output with the same transitionEffect throughout
> the set of transitions for the containing model.
> >
> > In the spec it is marked as 'recommendation' but libSBML flags it as an
> 'error' - i.e. must not be violated.
> >
> > A recommendation would suggest that it is a good idea to stick to this
> rule but it should not cause problems if you violate it.
> >
> > Before changing libSBML code I wanted to check with people more familiar
> with these models as to whether the rule is fine as a recommendation :-)
> >
> > i.e. which is right -  the specification or libSBML implementation ?? :-)
> >
> > Thanks
> >
> > Sarah
> >
> > -------- Forwarded Message --------
> > Subject: Re: [libsbml-team] Incorrect entry in QualSBMLErrorTable.h
> version 5.16.0
> > Date: Fri, 26 Jan 2018 09:01:05 +0000
> > From: Sarah Keating <ske...@ca...>
> > To: Justin McManus <ju...@ka...>, lib...@go...
> >
> > On 25/01/2018 15:07, Justin McManus wrote:
> >> To the SBML developer team,
> >> First, thank you so much for the profoundly important software you
> maintain.
> >> I noticed one issue that I'd like to report. In what I believe is the
> latest specification of the qual package for SBML, Rule qual-20311 is
> listed as a /recommendation/, not a /requirement/. However, the source code
> (libsbml v 5.16.0) treats this rule as a requirement, and will result in an
> error (rather than a warning) when the recommendation is violated.
> >> In src/sbml/packages/qual/validator, please see QualSBMLErrorTable.h.
> Specifically, please see the entry for QualQSAssignedOnlyOnce, which
> corresponds to this rule (Rule qual-20311) and error code 3020311. This
> entry treats the occurrence of this flag as a LIBSBML_SEV_ERROR rather than
> LIBSBML_SEV_WARNING.
> >> I first noticed the issue while using the R package rsbml, which relies
> on the libSBML, and which throws the error encoded in the libsbml when it
> reads an SBML containing multiple transition assignments for the same
> qualitative species.
> >> Please note that I did /not/ run the library through a debugger to
> confirm that the issue in QualSBMLErrorTable.h is the cause of the
> misspecified behavior I describe above. That's merely my guess based on a
> cursory look at the source code.
> >> Warm regards, and thank you for considering my comments here,
> >> Justin
> >> --
> >> Justin McManus, Ph.D.
> >> Senior Scientist
> >> Lead Computational Biologist
> >> Kallyope, Inc.
> >> 430 East 29th Street, Suite 1050
> >> New York, NY 10016
> >> (646) 596-3471
> >> --
> >> You received this message because you are subscribed to the Google
> Groups "libsbml-team" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an email to lib...@go... <mailto:
> lib...@go...>.
> >> For more options, visit https://groups.google.com/d/optout.
> >
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > _______________________________________________
> > sbml-qual mailing list
> > sbm...@li...
> > https://lists.sourceforge.net/lists/listinfo/sbml-qual
>
>


-- 
Justin McManus, Ph.D.
Senior Scientist
Lead Computational Biologist
Kallyope, Inc.
430 East 29th Street, Suite 1050
New York, NY 10016
(646) 596-3471

Hi Sarah,

Thank you Justin for rising this issue...
Indeed, for logical models this rule should be respected because their should not be several transitions defining the regulation of a component… we kept this as a recommendation because for Petri net models, it would be possible to have distinct transitions sharing the same output. 
I would thus keep it as a recommendation…
Best regards
Claudine

 
> On 29 Jan 2018, at 09:17, Sarah Keating <ske...@ca...> wrote:
> 
> Hi Qual people
> 
> We received a query (see below) from a libsbml user (Justin McManus cc'ed) about an anomaly between the qual specification and the libsbml implementation:
> 
> We have rule qual-20311:
> 
> A QualitativeSpecies that is referenced by an Output with the qual:transitionEffect at-tribute set to “assignmentLevel” cannot be referenced by any other Output with the same transitionEffect throughout the set of transitions for the containing model.
> 
> In the spec it is marked as 'recommendation' but libSBML flags it as an 'error' - i.e. must not be violated.
> 
> A recommendation would suggest that it is a good idea to stick to this rule but it should not cause problems if you violate it.
> 
> Before changing libSBML code I wanted to check with people more familiar with these models as to whether the rule is fine as a recommendation :-)
> 
> i.e. which is right -  the specification or libSBML implementation ?? :-)
> 
> Thanks
> 
> Sarah
> 
> -------- Forwarded Message --------
> Subject: Re: [libsbml-team] Incorrect entry in QualSBMLErrorTable.h version 5.16.0
> Date: Fri, 26 Jan 2018 09:01:05 +0000
> From: Sarah Keating <ske...@ca...>
> To: Justin McManus <ju...@ka...>, lib...@go...
> 
> On 25/01/2018 15:07, Justin McManus wrote:
>> To the SBML developer team,
>> First, thank you so much for the profoundly important software you maintain.
>> I noticed one issue that I'd like to report. In what I believe is the latest specification of the qual package for SBML, Rule qual-20311 is listed as a /recommendation/, not a /requirement/. However, the source code (libsbml v 5.16.0) treats this rule as a requirement, and will result in an error (rather than a warning) when the recommendation is violated.
>> In src/sbml/packages/qual/validator, please see QualSBMLErrorTable.h. Specifically, please see the entry for QualQSAssignedOnlyOnce, which corresponds to this rule (Rule qual-20311) and error code 3020311. This entry treats the occurrence of this flag as a LIBSBML_SEV_ERROR rather than LIBSBML_SEV_WARNING.
>> I first noticed the issue while using the R package rsbml, which relies on the libSBML, and which throws the error encoded in the libsbml when it reads an SBML containing multiple transition assignments for the same qualitative species.
>> Please note that I did /not/ run the library through a debugger to confirm that the issue in QualSBMLErrorTable.h is the cause of the misspecified behavior I describe above. That's merely my guess based on a cursory look at the source code.
>> Warm regards, and thank you for considering my comments here,
>> Justin
>> -- 
>> Justin McManus, Ph.D.
>> Senior Scientist
>> Lead Computational Biologist
>> Kallyope, Inc.
>> 430 East 29th Street, Suite 1050
>> New York, NY 10016
>> (646) 596-3471
>> -- 
>> You received this message because you are subscribed to the Google Groups "libsbml-team" group.
>> To unsubscribe from this group and stop receiving emails from it, send an email to lib...@go... <mailto:lib...@go...>.
>> For more options, visit https://groups.google.com/d/optout.
> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> sbml-qual mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-qual

Hi Qual people

We received a query (see below) from a libsbml user (Justin McManus 
cc'ed) about an anomaly between the qual specification and the libsbml 
implementation:

We have rule qual-20311:

A QualitativeSpecies that is referenced by an Output with the 
qual:transitionEffect at-tribute set to “assignmentLevel” cannot be 
referenced by any other Output with the same transitionEffect throughout 
the set of transitions for the containing model.

In the spec it is marked as 'recommendation' but libSBML flags it as an 
'error' - i.e. must not be violated.

A recommendation would suggest that it is a good idea to stick to this 
rule but it should not cause problems if you violate it.

Before changing libSBML code I wanted to check with people more familiar 
with these models as to whether the rule is fine as a recommendation :-)

i.e. which is right -  the specification or libSBML implementation ?? :-)

Thanks

Sarah

-------- Forwarded Message --------
Subject: Re: [libsbml-team] Incorrect entry in QualSBMLErrorTable.h 
version 5.16.0
Date: Fri, 26 Jan 2018 09:01:05 +0000
From: Sarah Keating <ske...@ca...>
To: Justin McManus <ju...@ka...>, lib...@go...

On 25/01/2018 15:07, Justin McManus wrote:
> To the SBML developer team,
> 
> First, thank you so much for the profoundly important software you 
> maintain.
> 
> I noticed one issue that I'd like to report. In what I believe is the 
> latest specification of the qual package for SBML, Rule qual-20311 is 
> listed as a /recommendation/, not a /requirement/. However, the source 
> code (libsbml v 5.16.0) treats this rule as a requirement, and will 
> result in an error (rather than a warning) when the recommendation is 
> violated.
> 
> In src/sbml/packages/qual/validator, please see QualSBMLErrorTable.h. 
> Specifically, please see the entry for QualQSAssignedOnlyOnce, which 
> corresponds to this rule (Rule qual-20311) and error code 3020311. This 
> entry treats the occurrence of this flag as a LIBSBML_SEV_ERROR rather 
> than LIBSBML_SEV_WARNING.
> 
> I first noticed the issue while using the R package rsbml, which relies 
> on the libSBML, and which throws the error encoded in the libsbml when 
> it reads an SBML containing multiple transition assignments for the same 
> qualitative species.
> 
> Please note that I did /not/ run the library through a debugger to 
> confirm that the issue in QualSBMLErrorTable.h is the cause of the 
> misspecified behavior I describe above. That's merely my guess based on 
> a cursory look at the source code.
> 
> Warm regards, and thank you for considering my comments here,
> 
> Justin
> 
> -- 
> Justin McManus, Ph.D.
> Senior Scientist
> Lead Computational Biologist
> Kallyope, Inc.
> 430 East 29th Street, Suite 1050
> New York, NY 10016
> (646) 596-3471
> 
> -- 
> You received this message because you are subscribed to the Google 
> Groups "libsbml-team" group.
> To unsubscribe from this group and stop receiving emails from it, send 
> an email to lib...@go... 
> <mailto:lib...@go...>.
> For more options, visit https://groups.google.com/d/optout.

Thank you Claudine! The .sbml file is very helpful!

Haoran

On Fri, Jul 14, 2017 at 5:30 AM, Claudine Chaouiya <
cha...@ig...> wrote:

> Dear Haoran,
>
> I am briefly commenting on your question 2. I would suggest that you post
> your questions also on the SBML-discuss mailing list.
> It seems to me that the best way to map your logical glyph would be onto
> Math element of a FunctionTerm
> A Transition may have multiple QualitativeSpecies as Inputs and one
> QualitativeSpecies as Output. Inputs would converge on the logical operator
> (encode in a FunctionTerms). When a Transition has several FunctionTerms,
> these are connected through a disjunction (OR).
> I am attaching the SBML qual file for your example, with a co-activator
> AND a co-repressor affecting a gene_transcription, hope this will help.
> I will bring the discussion to our CoLoMoTo meeting next week, and
> hopefully will come with more complete answers then!
>
> Finally, SBML qual supports Multi-valued logical models (i.e.
> QualitativeSpecies can take values from 0 to a mex greater than 1, e.g.
> qual:maxLevel=“2”)
>
> Best wishes
> Claudine
>
>
>
>
> On 14 Jul 2017, at 07:55, Haoran Yu <hal...@gm...> wrote:
>
> Hi all,
>
> I have a couple of questions regarding how to design Logic Models when
> writing SBML from scratch. The questions might not be specifically for SBML
> 'qual', but I thought it might be convenient to have all my questions in
> one place rather than across different mailing lists.
>
> I'm currently implementing the following bidirectional converters between
> SBML and SBGN-ML:
>
> (1) SBML 'core'+'layout'+'render' <-> SBGN-ML PD
> (2) SBML 'core'+'qual' <-> SBGN-ML AF
>
> I have made some progress in both converters (1) and (2). All the
> questions I have is for the SBGN - > SBML conversion. The questions were
> posted on my blog over the last 2 weeks, Week 10
> <http://haleyyew-gsoc.blogspot.ca/2017/07/week-10.html> (section 2) and Week
> 11 <http://haleyyew-gsoc.blogspot.ca/2017/07/week-11.html> (section 1.1).
>
> The SBGN examples that motivated the questions are
> libsbgn/test-files/PD/or.sbgn
> <https://github.com/sbgn/libsbgn/blob/master/test-files/PD/or-simple.png>
> and libsbgn/test-files/AF/compartment.sbgn
> <https://github.com/sbgn/libsbgn/blob/master/test-files/AF/compartment.png>
>
> *Question 1:*
> There are 2 alternative mappings for SBGN PD->SBML for the example
> "or.sbgn" that involves choosing between 'layout' SpeciesGlyphs,
> ReactionGlyphs and GeneralGlyphs.
> I included a color coded diagram to illustrate the 2 mapping alternatives, Blue
> is SpeciesGlyphs, Green is ReactionGlyphs and Red is GeneralGlyphs.
> [Figure 1]
>
>
>
> [Figure 2]
>
>
>
>
> In Figure 1, I mapped the 'OR' SBGN Glyph to a ReactionGlyph ,and
> therefore all Arcs connecting the 'OR' glyph should become
> SpeciesReferences. But I found this mapping to be inadequate. Arc [1] is a
> ModifierSpeciesReference, and by *Rule 21111* in the
> *sbml-level-3-version-1-core-release-2* specification, the *species *attribute
> must refer to an existing Species. Which means Arc [1] refers to the 'OR'
> glyph and 'OR' must be a Species, otherwise Arc [1] can't be a
> ModifierSpeciesReference of the green reaction. That is why I had to make
> Arc [1] a GeneralGlyph instead without associating with any core Model
> components.
>
> In Figure 2, the reason that the 'OR' SBGN Glyph is changed from a
> ReactionGlyph to a SpeciesGlyph is to fix the problem with the Arc [1] in
> Figure 1. The 2 Logic Arcs below *Enzyme1 *and *Enzyme2 *become
> GeneralGlyphs, and the 'OR' SBGN Glyph becomes a Species. Then Arc [1] can
> be a ModifierSpeciesReference in the green reaction below, and associate
> with the 'OR' Species. The 2 Logic Arcs should be GeneralGlyphs because
> they are not real Model components anyway.
>
> I have implemented the mapping in Figure 1, but later changed the
> implementation to the mapping in Figure 2. *Since neither of the 2
> alternatives are perfect, I'm wondering if there is a third alternative
> that might be a better mapping? Or any suggestions that improve the
> mappings in either Figure 1 or Figure 2? *
>
>
> *Question 2:*
> While working on converter (2), the "compartment.sbgn" example in SBGN AF
> is more complex than I thought, and I have trouble mapping it to SBML
> 'qual'. I can map an SBGN Logic Arc to a SBML 'qual' Transition, where the
> Input and Output QualitativeSpecies could be anything connected to the
> Logic Arc.
> [Figure 3]
>
>
>
> ​
> But in the more complex case where many Logic Arcs meet with a Logic
> Operator, and then output an Arc to connect to the target Glyph. All of
> these Arcs and Glyphs would belong to a single Transition in 'qual'. Each
> Logic Arc has an Input. Then each of them would have a separate
> FunctionTerm. But each FunctionTerm must have a resultLevel. The problem is
> that in Logic Models, the possible Input and Ouput values could only be 0
> or 1. *Are there are only 2 possible FunctionTerms in all Transitions
> (resultLevel 0 or 1)?*
>
> Due to my current choice mapping: the 'AND' glyph would be mapped to a
> QualitativeSpecies, and for each SBGN Glyph that is connected to a Logic
> Arc, I map the Glyph to a QualitativeSpecies. Then I create SpeciesGlyphs
> that correspond to the QualitativeSpecies. But the 'AND' Logic Operator is
> part of a Transition, and the Arc that acts as the Output must connect to
> only one QualitativeSpecies. Therefore the 'AND' glyph does not have a
> mapping, i.e. it is lost in the mapped SBML Model.
>
> *Is there a better mapping that is able to preserve the 'AND' glyph? *
> I have thought about storing the 'AND' as part of the Math element in a
> FunctionTerm. But I have trouble coming up with a good algorithm to map the
> SBGN Glyph+Arcs to a Transition containing multiple FunctionTerms. It would
> be great if someone could help me trace an algorithm for mapping of the
> "compartment.sbgn" example.
>
>
> Thank you for all your help!
> Haoran
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org>!
> http://sdm.link/slashdot_______________________________________________
> sbml-qual mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbml-qual
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
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>
>

Dear Haoran,

I am briefly commenting on your question 2. I would suggest that you post your questions also on the SBML-discuss mailing list. 
It seems to me that the best way to map your logical glyph would be onto Math element of a FunctionTerm
A Transition may have multiple QualitativeSpecies as Inputs and one QualitativeSpecies as Output. Inputs would converge on the logical operator (encode in a FunctionTerms). When a Transition has several FunctionTerms, these are connected through a disjunction (OR). 
I am attaching the SBML qual file for your example, with a co-activator AND a co-repressor affecting a gene_transcription, hope this will help. 
I will bring the discussion to our CoLoMoTo meeting next week, and hopefully will come with more complete answers then!

Finally, SBML qual supports Multi-valued logical models (i.e. QualitativeSpecies can take values from 0 to a mex greater than 1, e.g. qual:maxLevel=“2”)

Best wishes
Claudine




> On 14 Jul 2017, at 07:55, Haoran Yu <hal...@gm... <mailto:hal...@gm...>> wrote:
> 
> Hi all,
> 
> I have a couple of questions regarding how to design Logic Models when writing SBML from scratch. The questions might not be specifically for SBML 'qual', but I thought it might be convenient to have all my questions in one place rather than across different mailing lists.
> 
> I'm currently implementing the following bidirectional converters between SBML and SBGN-ML:
> 
> (1) SBML 'core'+'layout'+'render' <-> SBGN-ML PD
> (2) SBML 'core'+'qual' <-> SBGN-ML AF
> 
> I have made some progress in both converters (1) and (2). All the questions I have is for the SBGN - > SBML conversion. The questions were posted on my blog over the last 2 weeks, Week 10 <http://haleyyew-gsoc.blogspot.ca/2017/07/week-10.html> (section 2) and Week 11 <http://haleyyew-gsoc.blogspot.ca/2017/07/week-11.html> (section 1.1). 
> 
> The SBGN examples that motivated the questions are libsbgn/test-files/PD/or.sbgn <https://github.com/sbgn/libsbgn/blob/master/test-files/PD/or-simple.png> and libsbgn/test-files/AF/compartment.sbgn <https://github.com/sbgn/libsbgn/blob/master/test-files/AF/compartment.png>
> 
> Question 1:
> There are 2 alternative mappings for SBGN PD->SBML for the example "or.sbgn" that involves choosing between 'layout' SpeciesGlyphs, ReactionGlyphs and GeneralGlyphs.
> I included a color coded diagram to illustrate the 2 mapping alternatives, Blue is SpeciesGlyphs, Green is ReactionGlyphs and Red is GeneralGlyphs.
> [Figure 1]

> 
> [Figure 2]

> 
> 
> In Figure 1, I mapped the 'OR' SBGN Glyph to a ReactionGlyph ,and therefore all Arcs connecting the 'OR' glyph should become SpeciesReferences. But I found this mapping to be inadequate. Arc [1] is a ModifierSpeciesReference, and by Rule 21111 in the sbml-level-3-version-1-core-release-2 specification, the species attribute must refer to an existing Species. Which means Arc [1] refers to the 'OR' glyph and 'OR' must be a Species, otherwise Arc [1] can't be a ModifierSpeciesReference of the green reaction. That is why I had to make Arc [1] a GeneralGlyph instead without associating with any core Model components.
> 
> In Figure 2, the reason that the 'OR' SBGN Glyph is changed from a ReactionGlyph to a SpeciesGlyph is to fix the problem with the Arc [1] in Figure 1. The 2 Logic Arcs below Enzyme1 and Enzyme2 become GeneralGlyphs, and the 'OR' SBGN Glyph becomes a Species. Then Arc [1] can be a ModifierSpeciesReference in the green reaction below, and associate with the 'OR' Species. The 2 Logic Arcs should be GeneralGlyphs because they are not real Model components anyway. 
> 
> I have implemented the mapping in Figure 1, but later changed the implementation to the mapping in Figure 2. Since neither of the 2 alternatives are perfect, I'm wondering if there is a third alternative that might be a better mapping? Or any suggestions that improve the mappings in either Figure 1 or Figure 2? 
> 
> 
> Question 2:
> While working on converter (2), the "compartment.sbgn" example in SBGN AF is more complex than I thought, and I have trouble mapping it to SBML 'qual'. I can map an SBGN Logic Arc to a SBML 'qual' Transition, where the Input and Output QualitativeSpecies could be anything connected to the Logic Arc. 
> [Figure 3]

> 
> ​
> But in the more complex case where many Logic Arcs meet with a Logic Operator, and then output an Arc to connect to the target Glyph. All of these Arcs and Glyphs would belong to a single Transition in 'qual'. Each Logic Arc has an Input. Then each of them would have a separate FunctionTerm. But each FunctionTerm must have a resultLevel. The problem is that in Logic Models, the possible Input and Ouput values could only be 0 or 1. Are there are only 2 possible FunctionTerms in all Transitions (resultLevel 0 or 1)?
> 
> Due to my current choice mapping: the 'AND' glyph would be mapped to a QualitativeSpecies, and for each SBGN Glyph that is connected to a Logic Arc, I map the Glyph to a QualitativeSpecies. Then I create SpeciesGlyphs that correspond to the QualitativeSpecies. But the 'AND' Logic Operator is part of a Transition, and the Arc that acts as the Output must connect to only one QualitativeSpecies. Therefore the 'AND' glyph does not have a mapping, i.e. it is lost in the mapped SBML Model. Is there a better mapping that is able to preserve the 'AND' glyph? 
> 
> I have thought about storing the 'AND' as part of the Math element in a FunctionTerm. But I have trouble coming up with a good algorithm to map the SBGN Glyph+Arcs to a Transition containing multiple FunctionTerms. It would be great if someone could help me trace an algorithm for mapping of the "compartment.sbgn" example.
> 
> 
> Thank you for all your help!
> Haoran
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________>
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Sorry for not attaching the links to the Figures, here are the links in
case the Figures don't shown up in the previous email.
Figure 1
<https://1.bp.blogspot.com/-fs90lVuf2xw/WVypEN9zJGI/AAAAAAAAGfY/gsEbiGH228w9ocY1hgg0v7cDlwxpkllQgCLcBGAs/s320/or-simple.png>
Figure 2
<https://2.bp.blogspot.com/-u_5AitRQqfw/WVypIP5Rz0I/AAAAAAAAGfc/CeQGeo3Ua6gOmDqT8KJeuvbj_-ze3_ddQCLcBGAs/s1600/or-simple-new.png>
Figure 3
<https://4.bp.blogspot.com/-gmKV5sxzvbs/WWhtqdAzU_I/AAAAAAAAGiY/Rx1m2l5Z9Gw5aXIUmJn9tdg75udVW-R_wCLcBGAs/s1600/compartment.png>

Thank you again!
Haoran

On Fri, Jul 14, 2017 at 2:55 AM, Haoran Yu <hal...@gm...> wrote:

> Hi all,
>
> I have a couple of questions regarding how to design Logic Models when
> writing SBML from scratch. The questions might not be specifically for SBML
> 'qual', but I thought it might be convenient to have all my questions in
> one place rather than across different mailing lists.
>
> I'm currently implementing the following bidirectional converters between
> SBML and SBGN-ML:
>
> (1) SBML 'core'+'layout'+'render' <-> SBGN-ML PD
> (2) SBML 'core'+'qual' <-> SBGN-ML AF
>
> I have made some progress in both converters (1) and (2). All the
> questions I have is for the SBGN - > SBML conversion. The questions were
> posted on my blog over the last 2 weeks, Week 10
> <http://haleyyew-gsoc.blogspot.ca/2017/07/week-10.html> (section 2) and Week
> 11 <http://haleyyew-gsoc.blogspot.ca/2017/07/week-11.html> (section 1.1).
>
> The SBGN examples that motivated the questions are
> libsbgn/test-files/PD/or.sbgn
> <https://github.com/sbgn/libsbgn/blob/master/test-files/PD/or-simple.png>
> and libsbgn/test-files/AF/compartment.sbgn
> <https://github.com/sbgn/libsbgn/blob/master/test-files/AF/compartment.png>
>
> *Question 1:*
> There are 2 alternative mappings for SBGN PD->SBML for the example
> "or.sbgn" that involves choosing between 'layout' SpeciesGlyphs,
> ReactionGlyphs and GeneralGlyphs.
> I included a color coded diagram to illustrate the 2 mapping alternatives, Blue
> is SpeciesGlyphs, Green is ReactionGlyphs and Red is GeneralGlyphs.
> [Figure 1]
> [Figure 2]
>
> In Figure 1, I mapped the 'OR' SBGN Glyph to a ReactionGlyph ,and
> therefore all Arcs connecting the 'OR' glyph should become
> SpeciesReferences. But I found this mapping to be inadequate. Arc [1] is a
> ModifierSpeciesReference, and by *Rule 21111* in the
> *sbml-level-3-version-1-core-release-2* specification, the *species *attribute
> must refer to an existing Species. Which means Arc [1] refers to the 'OR'
> glyph and 'OR' must be a Species, otherwise Arc [1] can't be a
> ModifierSpeciesReference of the green reaction. That is why I had to make
> Arc [1] a GeneralGlyph instead without associating with any core Model
> components.
>
> In Figure 2, the reason that the 'OR' SBGN Glyph is changed from a
> ReactionGlyph to a SpeciesGlyph is to fix the problem with the Arc [1] in
> Figure 1. The 2 Logic Arcs below *Enzyme1 *and *Enzyme2 *become
> GeneralGlyphs, and the 'OR' SBGN Glyph becomes a Species. Then Arc [1] can
> be a ModifierSpeciesReference in the green reaction below, and associate
> with the 'OR' Species. The 2 Logic Arcs should be GeneralGlyphs because
> they are not real Model components anyway.
>
> I have implemented the mapping in Figure 1, but later changed the
> implementation to the mapping in Figure 2. *Since neither of the 2
> alternatives are perfect, I'm wondering if there is a third alternative
> that might be a better mapping? Or any suggestions that improve the
> mappings in either Figure 1 or Figure 2? *
>
>
> *Question 2:*
> While working on converter (2), the "compartment.sbgn" example in SBGN AF
> is more complex than I thought, and I have trouble mapping it to SBML
> 'qual'. I can map an SBGN Logic Arc to a SBML 'qual' Transition, where the
> Input and Output QualitativeSpecies could be anything connected to the
> Logic Arc.
> [Figure 3]
> ​
> But in the more complex case where many Logic Arcs meet with a Logic
> Operator, and then output an Arc to connect to the target Glyph. All of
> these Arcs and Glyphs would belong to a single Transition in 'qual'. Each
> Logic Arc has an Input. Then each of them would have a separate
> FunctionTerm. But each FunctionTerm must have a resultLevel. The problem is
> that in Logic Models, the possible Input and Ouput values could only be 0
> or 1. *Are there are only 2 possible FunctionTerms in all Transitions
> (resultLevel 0 or 1)?*
>
> Due to my current choice mapping: the 'AND' glyph would be mapped to a
> QualitativeSpecies, and for each SBGN Glyph that is connected to a Logic
> Arc, I map the Glyph to a QualitativeSpecies. Then I create SpeciesGlyphs
> that correspond to the QualitativeSpecies. But the 'AND' Logic Operator is
> part of a Transition, and the Arc that acts as the Output must connect to
> only one QualitativeSpecies. Therefore the 'AND' glyph does not have a
> mapping, i.e. it is lost in the mapped SBML Model.
>
> *Is there a better mapping that is able to preserve the 'AND' glyph? *
> I have thought about storing the 'AND' as part of the Math element in a
> FunctionTerm. But I have trouble coming up with a good algorithm to map the
> SBGN Glyph+Arcs to a Transition containing multiple FunctionTerms. It would
> be great if someone could help me trace an algorithm for mapping of the
> "compartment.sbgn" example.
>
>
> Thank you for all your help!
> Haoran
>
>

Hi all,

I have a couple of questions regarding how to design Logic Models when
writing SBML from scratch. The questions might not be specifically for SBML
'qual', but I thought it might be convenient to have all my questions in
one place rather than across different mailing lists.

I'm currently implementing the following bidirectional converters between
SBML and SBGN-ML:

(1) SBML 'core'+'layout'+'render' <-> SBGN-ML PD
(2) SBML 'core'+'qual' <-> SBGN-ML AF

I have made some progress in both converters (1) and (2). All the questions
I have is for the SBGN - > SBML conversion. The questions were posted on my
blog over the last 2 weeks, Week 10
<http://haleyyew-gsoc.blogspot.ca/2017/07/week-10.html> (section 2) and Week
11 <http://haleyyew-gsoc.blogspot.ca/2017/07/week-11.html> (section 1.1).

The SBGN examples that motivated the questions are
libsbgn/test-files/PD/or.sbgn
<https://github.com/sbgn/libsbgn/blob/master/test-files/PD/or-simple.png>
and libsbgn/test-files/AF/compartment.sbgn
<https://github.com/sbgn/libsbgn/blob/master/test-files/AF/compartment.png>

*Question 1:*
There are 2 alternative mappings for SBGN PD->SBML for the example
"or.sbgn" that involves choosing between 'layout' SpeciesGlyphs,
ReactionGlyphs and GeneralGlyphs.
I included a color coded diagram to illustrate the 2 mapping alternatives, Blue
is SpeciesGlyphs, Green is ReactionGlyphs and Red is GeneralGlyphs.
[Figure 1]
[Figure 2]

In Figure 1, I mapped the 'OR' SBGN Glyph to a ReactionGlyph ,and therefore
all Arcs connecting the 'OR' glyph should become SpeciesReferences. But I
found this mapping to be inadequate. Arc [1] is a ModifierSpeciesReference,
and by *Rule 21111* in the *sbml-level-3-version-1-core-release-2*
specification, the *species *attribute must refer to an existing Species.
Which means Arc [1] refers to the 'OR' glyph and 'OR' must be a Species,
otherwise Arc [1] can't be a ModifierSpeciesReference of the green
reaction. That is why I had to make Arc [1] a GeneralGlyph instead without
associating with any core Model components.

In Figure 2, the reason that the 'OR' SBGN Glyph is changed from a
ReactionGlyph to a SpeciesGlyph is to fix the problem with the Arc [1] in
Figure 1. The 2 Logic Arcs below *Enzyme1 *and *Enzyme2 *become
GeneralGlyphs, and the 'OR' SBGN Glyph becomes a Species. Then Arc [1] can
be a ModifierSpeciesReference in the green reaction below, and associate
with the 'OR' Species. The 2 Logic Arcs should be GeneralGlyphs because
they are not real Model components anyway.

I have implemented the mapping in Figure 1, but later changed the
implementation to the mapping in Figure 2. *Since neither of the 2
alternatives are perfect, I'm wondering if there is a third alternative
that might be a better mapping? Or any suggestions that improve the
mappings in either Figure 1 or Figure 2? *


*Question 2:*
While working on converter (2), the "compartment.sbgn" example in SBGN AF
is more complex than I thought, and I have trouble mapping it to SBML
'qual'. I can map an SBGN Logic Arc to a SBML 'qual' Transition, where the
Input and Output QualitativeSpecies could be anything connected to the
Logic Arc.
[Figure 3]
​
But in the more complex case where many Logic Arcs meet with a Logic
Operator, and then output an Arc to connect to the target Glyph. All of
these Arcs and Glyphs would belong to a single Transition in 'qual'. Each
Logic Arc has an Input. Then each of them would have a separate
FunctionTerm. But each FunctionTerm must have a resultLevel. The problem is
that in Logic Models, the possible Input and Ouput values could only be 0
or 1. *Are there are only 2 possible FunctionTerms in all Transitions
(resultLevel 0 or 1)?*

Due to my current choice mapping: the 'AND' glyph would be mapped to a
QualitativeSpecies, and for each SBGN Glyph that is connected to a Logic
Arc, I map the Glyph to a QualitativeSpecies. Then I create SpeciesGlyphs
that correspond to the QualitativeSpecies. But the 'AND' Logic Operator is
part of a Transition, and the Arc that acts as the Output must connect to
only one QualitativeSpecies. Therefore the 'AND' glyph does not have a
mapping, i.e. it is lost in the mapped SBML Model.

*Is there a better mapping that is able to preserve the 'AND' glyph? *
I have thought about storing the 'AND' as part of the Math element in a
FunctionTerm. But I have trouble coming up with a good algorithm to map the
SBGN Glyph+Arcs to a Transition containing multiple FunctionTerms. It would
be great if someone could help me trace an algorithm for mapping of the
"compartment.sbgn" example.


Thank you for all your help!
Haoran

Dear all,

The Consortium for Logical Models and Tools (http://www.colomoto.org)
reunites researchers interested in logical modelling, from modelers to
curators and developers of methods and tools.
CoLoMoTo essentially focuses on the comparison and integration of  logical
models, analysis methods and tools, as well as on the definition of
standards for model representation and interchange (especially the SBML
qual format).

The next CoLoMoTo meeting will take place in Paris on July 17-19, at the
Ecole Normale Supérieure. The first day (afternoon) will be dedicated to
scientific presentations (from methodological and software developments to
biological applications) and open to the public. The following days are
devoted to more technical working groups.

The programme  of the meeting is available at the url:
http://colomoto.org/meetings/2017

Registration is free but mandatory (through the web page form).


Best regards


-- 
Aurélien Naldi
Claudine Chaouiya
Denis Thieffry
Gautier Stoll
Laurence Calzone

Dear all,

We have worked out a draft proposal for SED-ML extension to support qualitative models (as specified in the SBML qual package). 

With this extension, we aim to encode simulation experiments on qualitative models. The current SED-ML does already provide the frame for the encoding of simulation experiments in computational biology. However, the nature of qualitative models is different to ODE-based models, which have been in the focus so far: Qualitative models are a class of discrete event systems, whose dynamics are represented by means of state transition graphs (STGs). These STGs represent, in the form of a graph, which nodes are the reachable states; the edges represent the state transitions.
The proposal at hand is the result of discussions at Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, February 2016. 

This is a first draft and we need feedback from you, the community, to turn it into a an official proposal to the SED-ML editors.

The PDF of the Draft Version 1 is kept at 10.6084/m9.figshare.2075143 for later reference. 

Please feel free to edit the following google doc to improve the proposal: 
https://docs.google.com/document/d/1WrLiOSxK58sxJwRDe-rXyCSpuvtiSQWjJd43WaBw_wE/edit?usp=sharing

We suggest to keep discussions on specific concepts on the SED-ML mailing list (please use the SED-ML list sed...@li...).


Greetings from the sunny side of Europe (edit from Dagmar!),
Claudine, Pedro, Aurélien & Dagmar

Am 27.09.13 12:59, schrieb Chris J. Myers:
> SBML L3V2 will likely remove some of the barriers to this in that it will allow qualitative species to appear in math expressions as well as on the left-hand side of initial assignments, event assignments, rules, etc.

Dear all,

First, I would like to thank Claudine and Sarah for bringing this topic 
up at this mailing list because I believe having test cases for qual in 
the SBML test suite would be of great benefit for this standard.

To the topic above: I am very much infavor of defining an 
AbstractSpecies class in the SBML core, which could be the parent SBML 
element for QualitativeSpecies and also the regular core Species. In my 
opinion this would make the relationship between both types of species 
more obvious and easier to interpret.

Thanks
Andreas

-- 
Dr. Andreas Draeger
University of California, San Diego, La Jolla, CA 92093-0412, USA
Bioengineering Dept., Systems Biology Research Group, Office #2506
Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae

Hi Claudine and Sarah,

Sorry that I missed your presentation at COMBINE.  I think the future directions that you describe below are important ones, and I have some comments on them.
> 
> It became clear whilst working on the recent qual paper that having a common description of the model was not sufficient to guarantee identical simulation results. It is also necessary to precisely establish such things as update mechanism, initial condition(s), input nodes behaviours or even perturbations (LOF, GOF, or subtler ones).
> Thus the ability to produce a SED-ML file to describe what should be done with a qual model would be advantageous in standardising our use of logical models.
> 
Some of this may be good for SED-ML such as update synchronous or asynchronous update mechanism, but I think some things will require a tighter definition of the semantics is some of the places that I highlighted in early comments.
> 
> 1. identify aspects of logical models that are possibly not yet expressed in qual and thus highlight the way forward for the specification
> 
There are two issues with qual which limit my ability to use it.

1) The inability for qual and core to easily interact. 

I would like to be able to use qual to represent the logical portion of the model, but have it capable of interacting with the quantitive portion expressed using core.  SBML L3V2 will likely remove some of the barriers to this in that it will allow qualitative species to appear in math expressions as well as on the left-hand side of initial assignments, event assignments, rules, etc.  As for appearing in math, the interpretation is pretty straightforward as it is just the value of the species current level.  Assignments are trickier as what should be done when an expression assigns a value outside the allowed levels?

One special case where qual could be very helpful are Boolean variables (i.e., one with only two levels).  It would be nice to special case these so they can appear for example as operands to logical operators.  I'm currently faking Boolean variables using parameters, but it requires awkward conversions (added automatically) such as X==1 to convert the variable to a Boolean and piecewise to convert an assignment from a Boolean expression into a real result.  If qual could add real Boolean variables to SBML modeling, I believe this would be a nice benefit.  

2) The inability to express quantitative values such as delay or probability of a transition.

Right now I model this by using events rather than transitions.  I'm not sure the best way to deal with this as we would likely not want to simply extend transitions to include all the components of events which would be a bit redundant.  Maybe the best solution is once qualitative species can occur in event assignments then events can be used in the place of transitions when quantitative information is needed.  This is definitely though something worth experimenting with and discussing further.

> 2. establish a common means of outputting results to allow easy comparison
> 
I think this can be accomplished by simply outputting traces in CSV format where time is simply given as an integer representing the simulation step rather than absolute time.  

> 3. establish what information a simulation needs to ensure the results of a simulation are identical.
> 
This is a challenging problem since even if one agrees to synchronous or asynchronous simulation as the update scheme, qual allows for non-determinism.  Indeed, this is a critical and important aspect of qual.  Therefore, for testing one likely needs to store a state graph in which the nodes are the states with the levels of the QS and the transitions are the possible next states.  To do comparison then to a simulation, one would need to walk the graph starting in the initial state to show that the simulation produced is one that is allowed by the state graph.

> The last two points would involve creating SED-ML files and thus establish how SED-ML needs to be adjusted to accommodate description of logical model simulation. For now, it seems that most requirements may be covered by specifying relevant terms in KISAO. In the coming weeks, we will make a proposal, to be discussed.
> 
You are correct that at a minimum a KISAO term is need to express what type of update to use (synchronous or asynchronous).  I don't think there are other things that you want to express in SED-ML.  One could perhaps indicate how to resolve non-determinisim but I think that is a pretty odd thing to put into SED-ML.  It would be like telling an SSA simulator what random numbers to draw.  It would make it reproducible but it is very artificial.  Better to work out a scheme of comparison like the state graph one that I described above.

Cheers,

Chris

Dear all,

It became clear whilst working on the recent qual paper that having a common description of the model was not sufficient to guarantee identical simulation results. It is also necessary to precisely establish such things as update mechanism, initial condition(s), input nodes behaviours or even perturbations (LOF, GOF, or subtler ones).
Thus the ability to produce a SED-ML file to describe what should be done with a qual model would be advantageous in standardising our use of logical models.

There were a couple of sessions at COMBINE regarding the qual package and how logical modelling may interact with SED-ML.

No real conclusions were drawn, other than the fact that the issue of simulation description (SED-ML) needs to be addressed. Nobody present had any major requests for extension of the features currently covered by Version 1 of the qual specification.

It was proposed that a way forward would be to start to develop a test-suite of toy models with expected simulation results to allow compliance of different software to be tested. This test-suite would also need to include the necessary SED-ML files for each case. Since some people already have test models this Defining elementary models
for this test-suite and specifying simulation parameters would enable the following:

1. identify aspects of logical models that are possibly not yet expressed in qual and thus highlight the way forward for the specification

2. establish a common means of outputting results to allow easy comparison

3. establish what information a simulation needs to ensure the results of a simulation are identical.

The last two points would involve creating SED-ML files and thus establish how SED-ML needs to be adjusted to accommodate description of logical model simulation. For now, it seems that most requirements may be covered by specifying relevant terms in KISAO. In the coming weeks, we will make a proposal, to be discussed.

Best
Claudine & Sarah

----------------------------------------------
Claudine Chaouiya
Instituto Gulbenkian de Ciência - IGC
Rua da Quinta Grande, 6
P-2780-156 Oeiras - PORTUGAL

http://compbio.igc.gulbenkian.pt/nmd/
Phone:	(351) 214 46 45 01 
Email: cha...@ig...