Forums

In our continuing efforts to improve communications with the
SBML user community and revise the development process to
make it more transparent, accountable, timely and relevant,
we have introduced a new mailing list:

sbml-announce@caltech.edu

This is a broadcast-only mailing list for important
announcements concerning the Systems Biology Markup Language
(SBML). The release of new documents as well as errata and
revisions to old documents will be announced here.

We request that everyone who uses SBML in their software or
their work please sign up for the sbml-announce mailing
list, so that we may keep you informed about important
developments.

This is not a discussion list. It is strictly moderated by
humans to filter out any off-topic postings. Only the SBML
editors may post to the list. Only announcements of the
highest importance to SBML will be posted, including:

* Releases of specifications for new SBML Levels & Versions
* Disclosure of errata and subsequent issue of SBML revisions
* Requests for proposals for SBML technical development
* Voting topics and deadlines for SBML development issues
* Upcoming SBML community events (Forums and Hackathons)

The list membership will be kept confidential and will not
be intentionally disclosed beyond the SBML editors and their
immediate assistants. The list will not be used for
advertising.

In keeping with our normal policy, the list is opt-in
only; no one has been subscribed. You must subscribe
yourself using the following registration page:

https://utils.its.caltech.edu/mailman/listinfo/sbml-announce

The goal is to move announcement-only type postings to
sbml-announce and *not* cross-post them to sbml-discuss.
(Example: announcements of meetings and new SBML
specification documents do not need to be cross-posted.) A
very few types of postings may end up being cross-posted if
it makes sense to do so. (Example: requests for proposals
of technical development may lead to discussions, so it
makes sense to have them show up on sbml-discuss.) In
summary, the goal is to keep cross-posting to a minimum.

Consequently, everyone should subscribe to sbml-announce
regardless of whether they are on sbml-discuss or
libsbml-discuss.

Thank you,
Mike

--
Mike Hucka, Ph.D. tel +1.626.395.8128
Senior Research Fellow, Control and Dynamical Systems
Co-director, Biological Network Modeling Center
The Beckman Institute @ The California Institute of Technology

[This should have been posted to sbml-announce sooner.
Very sorry. It went to sbml-discuss but announcements of
votes are also supposed to go to sbml-announce. -- MH]

Dear SBML Community,

The discussion topic that produced the most significant
debate at the SBML Forum last October concerned the
inadequacy of the current L2V2 spec's use of the sboTerm
attribute. Specifically, the realization was that it needs
to be placed on several SBML elements where it is not
currently available. This can be done in one of two ways:
either the definitions of the individual objects where
sboTerm is missing can be redefined on a case-by-case basis,
or sboTerm can be moved to the SBase abstract class as an
optional attribute. In either case, the changes are
backward compatible in the sense that XML files containing
sboTerm attributes as currently defined in L2V2 would still
be exactly valid under either version of the fix. However,
and more seriously, either approach undeniably changes the
SBML object model.

This has put the SBML Editors in a bit of a quandary. The
guidelines under which we have been *trying* to work is that
changes to the syntax of SBML would only occur between
Versions within Levels (or else changing whole Levels). The
changes that are needed now come at the request of SBML
users, and are necessary to actually use SBO properly.
Further, some groups have begun using SBO, which is making a
fix an urgent matter. The changes *could* be done by making
them in a revision of L2V2 (i.e., in Level 2 Version 2
Revision 2), but that would violate (so soon!) the
guidelines we were trying to establish for good SBML
development. Under those guidelines, these kinds of syntax
changes *should* be done as a new Version (so, Level 2
Version 3). But if we create a Level 2 Version 3 so soon
after Level 2 Version 2 was released, will that leave a bad
impression and result in people losing confidence?

In defense of producing Level 2 Version 3, we note that (1)
it appears few people have worked on L2V2 support anyway,
apparently because most developers are waiting for a final
libSBML release with L2V2 support; (2) the SBML issue
tracker on http://sbml.org/issue-tracker now has numerous
small (albeit simple) changes on the table, including a
significant number of additional validation rules, which
suggests that producing a Level 2 Version 3 wouldn't be a
bad idea; (3) a Level 2 Version 3 specification could be
produced very quickly given the relatively simple changes on
the table; and (4) if it were done immediately, the
difference between L2V2 and a new L2V3 would be small enough
that even if someone was in the middle of implementing L2V2
support, they would probably not feel it is a difficult set
of changes to make to move to L2V3.

Either way, we believe we can produce a new document in
February, because of point #3 above.

So, here is our question for you. Assuming that either
alternative results in a release of an SBML specification
quickly, which of the following would you prefer is done?

1) Bend the guidelines and issue the changes as Revision 2
of Level 2 Version 2, or

2) Issue the changes as SBML Level 2 Version 3.

Please cast your votes by Feb. 8 using the following page:
http://www.surveymonkey.com/s.asp?u=872673185384

The SBML Level 2 Version 2 specification is at:
http://prdownloads.sourceforge.net/sbml/sbml-level-2-version-2-rev1.pdf?download

Thank you,
The SBML Editors
(Mike Hucka, Nicolas Le Novere, Sarah Keating,
Stefan Hoops, Andrew Finney)

Dear SBML-using community,

The SBML Editors are pleased to announce the release of the
SBML Level 2 Version 3 specification, now available from
http://sbml.org/documents/ as well as the SBML project
on SourceForge.net.

This new version of the SBML Level 2 specification
incorporates many corrections and clarifications. The
following is a short summary of some of the major changes;
a more detailed list is provided in Appendix G of the
document.

- Placement of the 'sboTerm' attribute on SBase instead of
only some individual object classes, and expansion of the
SBO hierarchy and the mapping of SBML objects to SBO

- Removal of 'timeUnits' from Event

- Removal of 'spatialSizeUnits' from Species

- Explanations of some differences in data type definitions
between XML Schema and MathML

- Explanation of the units assumed for literal numbers
appearing in mathematical expressions, along with
corrections to validation rules.

- Explanations of the units required by various MathML
operators and other constructs

- Corrections to the definitions of some primitive data types

- Addition of more guidelines about the content of
<annotation> elements.

- Addition of more validation rules

- Complete redrawing of all class definition diagrams to use
more proper UML

Please report issues with the SBML L2v3 specification using
the reporting facilities at

http://sbml.org/issue-tracker

We would like to thank all of the many members of the SBML
community for their current support and use of SBML.


Mike Hucka
Nicolas Le Novere
Sarah Keating
Stefan Hoops
Andrew Finney


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[Note added by moderator 2007-Jun-25: the original message had an incorrect subject line. This archived message has been edited to make the correction, thereby hopefully reducing confusion and making search easier for users of this web forum. The original message is still untouched in the sbml-announce@caltech.edu mailing list archive. -- Mike Hucka]

[Updated on: 25 Jun '07 11:42] by Moderator

Dear SBML community,

The SBML Editors are pleased to release a minor update to
the SBML Level 2 Version 3 specification, in the form of
Release 2. This release makes no SBML language changes that
were not intended to be in Release 1; rather, it makes
corrections for issues and errors that have come to light
since the announcement of Release 1. These issues are
documented in detail in the new Appendix H of the document
and can also be found online at the following URL:

http://sbml.org/specifications/sbml-level-2/version-3/errata/

There are some particularly unfortunate typographical errors
in the examples and explanations of SBML reactions in the
first release of Level 2 Version 3, so if you have been
scratching your head over some of the equations in Release
1, the Release 2 update may resolve the questions for you.

A PDF version of the SBML Level 2 Version 3 specification is
available for immediate download from SourceForge at

http://sourceforge.net/project/showfiles.php?group_id=71971

The file is called "sbml-level-2-version-3-rel-2.pdf". You
can also find a direct link at

http://sbml.org/specifications/sbml-level-2/version-3

Please report any issues you find in the new release using
the online tracker at http://sbml.org/issue-tracker

The SBML Editors.

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--------------------------------------------------------
13th Workshop on Software Platforms for Systems Biology:
The SBML Forum Meeting
--------------------------------------------------------

August 27 & 28, 2008
(as a workshop at ICSB 2008, http://icsb-2008.org)

Location:
Gothenburg Convention Centre
Gothenburg, Sweden

Workshop registration page:
http://sbml.org/Events/Workshops/The_13th_SBML_Forum_Meeting/Survey

General information page:
http://sbml.org/Events/Workshops/The_13th_SBML_Forum_Meeting

The next annual SBML Forum Meeting will be held in
Gothenburg, Sweden, as a satellite workshop of ICSB 2008.
The exact agenda has not been set and depends in part on the
wishes of the attendees; a more detailed agenda for the
meeting is forthcoming.

If you are planning on attending, please fill out the form
at the URL given above as soon as possible. We regret that
we have no travel support available for this meeting, and
hope that potential attendees can extend their ICSB 2008
stay in order to attend. We will, however, arrange for
coffee breaks and (hopefully) some meals.

As in past SBML Forum meetings, there will be a block of
time available during the meeting for people to give short
presentations (5-10 minutes) to the audience on the
following topics: SBML-enabled applications, the use of SBML
to integrate different applications, proposals for SBML
extensions, proposals for standards that compliment SBML,
announcements of software or standards or events of interest
to SBML users, and general experiences of using SBML "in the
field". The registration page provides the opportunity for
you to indicate if you would like to make a presentation.

We hope to hear from you soon.

The SBML Team

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Dear SBML-using community,

The SBML Editors are pleased to announce the release of the
SBML Level 2 Version 4 specification, now available from
http://sbml.org/Documents/Specifications as well as the SBML
project on SourceForge.net.

This new version incorporates changes requested by the SBML
community via past votes and SBML Forum meetings, as well as
numerous smaller corrections for inconsistencies. The
following is a short summary of the major changes; more
explanations of the changes are provided in Appendix G of
the document, and the textual changes (relative to L2 V3
Release 2) are marked in red throughout the document. The
details of all major issues are also logged as tracker items
in the SBML issue tracker (http://sbml.org/issue-tracker)
under the category "Level 2 Version 3".

- Unit consistency is not *required* for a valid SBML model,
following the decision made via a vote taken in late 2007.

- Removal of prohibition on forward references in
user-defined function definitions.

- Removal of prohibition on forward references in the
Compartment 'outside' attribute.

- Corrections to small syntax error in the RDF defined for
annotations.

- New flag "useValuesFromTriggerTime" on Event allows a
model to indicate when EventAssignment formulas are meant
to be evaluated.

- Clarification about the relationship of compartment sizes
when one compartment is outside of another.

- Addition of new MIRIAM qualifiers.

- Updates for SBO and values allowed for sboTerm.

- Removal of irrelevant or no longer applicable validation
rules, and addition of new rules for the changes above.

- "Built-in SBML units" are now called "predefined SBML
units", to be (hopefully) more clear.

- Other minor corrections and edits.

Please report issues with the SBML Level 2 Version 4
specification using the issue-tracker.

We would like to thank all of the many members of the SBML
community for their current support and use of SBML.

Mike Hucka
Nicolas Le Novere
Sarah Keating
Stefan Hoops
Sven Sahle
Darren Wilkinson

____________________________________________________________
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--------------------------------------------------------
14th Workshop on Software Platforms for Systems Biology:
The SBML Forum Meeting
--------------------------------------------------------

September 3 & 4, 2009
(as a workshop at ICSB 2009, http://icsb-2009.org)

Location:
Stanford University
California, USA

General information page:
http://sbml.org/Events/Workshops/The_14th_SBML_Forum_Meeting

The next annual SBML Forum Meeting will be held in
California, USA, as a satellite workshop of ICSB 2009. The
exact agenda has not yet been set and depends in part on the
wishes of the attendees; a more detailed agenda for the
meeting is forthcoming.

If you are planning on attending, please fill out the survey
form at the URL given above as soon as possible. As in past
SBML Forum meetings, there will be a block of time available
during the meeting for people to give short presentations
(5-10 minutes) to the audience on the following topics:
SBML-enabled applications, the use of SBML to integrate
different applications, proposals for SBML extensions,
proposals for standards that compliment SBML, announcements
of software or standards or events of interest to SBML
users, and general experiences of using SBML "in the field".
The survey page provides the opportunity for you to indicate
if you would like to make a presentation.

We regret that we have no travel support available for this
meeting, and hope that potential attendees can extend their
ICSB 2009 stay (for those who are going to ICSB) in order to
attend.

You are not required to attend ICSB 2009 in order to attend
the SBML Forum. However, ICSB 2009 requires that all
workshop attendees register and pay a small fee (US $45) to
defray costs of facilities and other expenses. To do that,
please visit

http://icsb-2009.org

and follow the registration link.

We hope to hear from you soon.

The SBML Team

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Dear SBML-using community,

The SBML Editors are pleased to announce the availability
of the Release 1 Candidate specification for
SBML Level 3 Version 1 Core. It is now available from

http://sbml.org/Documents/Specifications

and the SBML project on SourceForge.net. It will shortly be
available from Nature Precedings as well.

This specification is labeled "Release 1 Candidate" until
two independent software implementations are reported by the
SBML-using community. At that time, if no significant
errors are reported, the specification will be considered
final. Release 1 of SBML Level 3 Version 1 Core will not be
modified further unless errors are found.

Please report issues with this specification using the
simple, streamlined reporting form indicated on the front
page of the specification and on the sbml.org pages. (It's
a live link -- just click it to be sent to the web form.)

An explanation is warranted regarding one issue: unlike past
specification documents, there are no XML Schemas in this
one. Our plan is to create and issue the schemas as
separate companion documents, and to produce RELAX NG
schemas and probably also Schematron schemas, instead of XML
Schemas. Thus, there will be forthcoming documents titled
"The Systems Biology Markup Language (SBML): RELAX NG Schema
for Level 3 Version 1 Core", etc.

We would like to thank all of the many members of the SBML
community for their current support and use of SBML. (And a
special thanks to Nicolas Le Novere for extra feedback this
past week.)

The 2009 SBML Editors:
Mike Hucka
Frank Bergmann
Sarah M. Keating
Stefan Hoops
Sven Sahle
Darren J. Wilkinson

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I'd to draw people's attention to some recent additions to
the official list of errata in the SBML Level 2 Version 4
Release 1 specification. You can find the list at

http://sbml.org/Documents/Specifications

(click on the blue icon next to "Errata" in the Level 2
Version 4 section). At some point in the future, there will
be a Release 2 of the specification to fix the errata.

As always, we greatly welcome reports of any issues found in
the SBML specifications. You can find a link to the issue
tracking/reporting system in the same section on the page
mentioned above.

Thank you.

Mike, on behalf of the SBML Editors

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------------------------------------------------------
The SBML 10th Anniversary Symposium
http://sbml.org/Events/SBML_10th_Anniversary_Symposium
------------------------------------------------------

The first draft definition of the Systems Biology Markup Language (SBML) was produced over the summer 2000. Since that time, it has become a de facto standard in computational systems biology, supported by over 180 software tools, and a catalyst for numerous related standardization efforts.

To celebrate ten years of SBML, we are holding a special symposium on the afternoon of October 9th, 2010, in Edinburgh, UK, immediately before ICSB 2010 and after COMBINE 2010. Speakers include:

* Hiroaki Kitano
* John C. Doyle
* Hamid Bolouri
* Herbert M. Sauro
* Pedro Mendes
* Andrew M. Finney
* Michael Hucka
* Nicolas Le Novère

The event will run 13:30 to 18:00, followed by cake and refreshments. The location will be the Informatics Forum:

Informatics Forum
10 Crichton Street
Edinburgh EH8 9AB

The event is open to all. Please join us!

Nicolas Le Novère & Mike Hucka
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Announcing H A R M O N Y 2011

Dates: April 18-22, 2011
Place: New York City, USA
Website: http://www.biopax.org/harmony.php
Hosts: CBIO @ Memorial Sloan-Kettering Cancer Center

Attendance survey: http://www.surveymonkey.com/s/V2B7FZN

As most of you hopefully know, beginning this year, we are moving to making SBML Hackathons be part of a wider-scoped event named HARMONY: the HAckathon on Resources for MOdeliNg in biologY.

HARMONY 2011 will take place from April 18-22, at the Memorial Sloan-Kettering Cancer Center, New York City, USA. HARMONY events are joint meetings between the developers of formats and related standards supporting computational modeling in biology, including but not limited to SBML, SBGN, BioPAX, and others. Unlike the annual COMBINE meetings, HARMONY is not a general forum targeting the community of users at large, but rather a technical meeting aimed at bringing together developers of the standards and software implementing them.

Please help us make the best possible arrangements for this meeting by registering as soon as you can using the short form at http://www.surveymonkey.com/s/V2B7FZN

We hope to see you there!

Best regards,
Nadia Anwar and Mike Hucka, on behalf of all the organizers

[Updated on: 20 Jun '12 12:43] by Moderator

***********************************************

Announcing

H A R M O N Y 2012

May 21-25, 2012
Maastricht, The Netherlands

http://co.mbine.org/events/HARMONY_2012

***********************************************


Dear Colleagues,

We are happy to announce that the registration for HARMONY 2012 is open now.

HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There is generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. The HARMONY 2012 meeting will be hosted by the Department of Bioinformatics from Maastricht University.

The maximum number of participants is 70. Please register using the following form:

http://harmony2012.eventbrite.com

We are trying to get more funding to support the accommodation costs of the participants. We have agreed to special room rates with the Apart Hotel Randwyck and the NH hotel. The participants have to book the hotel rooms themselves. For further information please have a look at

http://www.co.mbine.org/events/HARMONY_2012#Accommodation

The conference dinner will take place on the evening of Wednesday 23rd May at Ipanema. On the first meeting day (Monday 21st May) there will be an open symposium with tutorials, talks and a reception/poster session in the evening.

A full schedule and further information will be provided on the meeting website

http://www.co.mbine.org/events/HARMONY_2012

We look forward to welcoming you all in Maastricht. For any further questions, please contact us (harmony2012@maastrichtuniversity.nl).

Best Regards,
Martina, Chris, Gary, Nicolas, Mike
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[Updated on: 08 Mar '12 11:28] by Moderator

The SBML Editors have collected and published a list of officially-recognized issues in the SBML Level 3 Version 1 Core Release 1 specification document. You can view the list by visiting

http://sbml.org/Documents/Specifications#SBML_Level_3

and clicking on the icon labeled "Errata".

As always, we greatly welcome reports of any issues found in the SBML specifications. You can find a link to the issue tracking/reporting system in the same section on the page mentioned above.

Thank you.

Mike, on behalf of the SBML Editors
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The working group for the SBML Level 3 "Flux Balance Constraints" package is pleased to announce that Version 1 of the specification is now available. You can find a link to the specification, as well as other information, from the 'fbc' package status page at

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

Special thanks to Brett Olivier and Frank Bergmann for authoring the specification and pushing the package along through the SBML Development Process.

This marks an exciting milestone in the effort to standardize model descriptions and enhance tool interoperability in the constraint-based modeling area.

Best regards,
Mike (on behalf of Brett and Frank, and the rest of the FBC working group)
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[Updated on: 14 Feb '13 09:08] by Moderator

HARMONY 2013 is kindly being organized by the Virtual Cell group at the
University of Connecticut Health Center, USA. It will take place from May
20 to 23. Registration is now open!

http://www.co.mbine.org/events/HARMONY_2013
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Hi Guys

FYI there is information here on using the SBML online validator as a
web service:

http://sbml.org/Facilities/Validator/Validator_Web_API

Sarah
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Dear all,

We played around with the SBMLWriter class in JSBML and recognized
some problems when writing notes elements.

The SBML specification 2.4 says that one can add XHTML formatted notes
in two ways. First, each element can get the in-fix "xhtml:" within
the regular HTML tag. Second, the body element may declare the XHTML
name space.

In our test, only the second form worked. Furthermore, it is a bit
unhandy if the user is required to declare the body tag. I think it
would be very convenient to check the notes for "<xhtml:" or
"</xhtml:" pre-fixes and to set the body tag as required if this is
missing.

Finally, we recognized several problems with Annotation. It is not
possible to add CVTerms without explicitly creating an Annotation
object first. To this end, we created a dummy Annotation by calling
the constructor with an empty String and then we HAD to call the
method setAbout("") for this Annotation object. Without an explicit
call of setAbout, even with an empty String, the Writer always crashed
with a NullPointerException because there is a call of getAbout()
somewhere. In my opinion, the user of JSBML shouldn't have to care
about whether or not there is already an Annotation object because the
first time, any annotation element is added, an Annotation object
should be initialized. With this trick we were able to write SBML into
a file. However, the result was that the file contained many tags such
as <none>...</none>. Maybe the result of our call to setAbout(""). In
libSBML it was not necessary to set an about element. However, I
cannot find any occurence of "<none>" in any JSBML class.

And, what confuses people when using JSBML are constructors and
model.create*() methods that do not require arguments that are
actually obligatory. For instance, it is possible to create a
Compartment without setting an ID. This leads to errors in places
where people don't expect that the missing ID is actually the reason.
What happens is, that for instance a species that refers to the
compartment without an ID causes a NullPointerException when trying to
getCompartmentInstance() because this calls getModel().getCompartment().

After writing SBML and removing the <none>...</none> elements, the
SBML validator still showed many errors, for instance, " the element
'species' is not part of the definition of SBML". The reason is that
the Writer does not insert <listOf*>... </listOf*> tags surrounding
compartments, species, etc. Furthermore, it writes "spatialDimension"
and forgets the plural "s". In case of our compartment, there was
neither a notes nor an annotation element. But still the writer
creates an opening and a closing compartment tag. The validator does
in this case, however, only accept a compartment element that ends
with "/>".
There are several other errors but I think this is enough for just one e-mail.

It would also be nice to indent the SBML output so that it becomes
better human-readable.

I think there is still a lot of work ahead of us ;-)

Cheers
Andreas

Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-70436
Fax: +49-7071-29-5091
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Dear all,

Currently, I am looking at the writing methods of JSBML. There I noticed
that currently, JSBML does not produce a nice indent as it is done in
libSBML. I just play around a little bit and try to improve this. Maybe
you have some idea about how to solve this?

Another question to this is, that Level and Version of An SBML document
can be undefined. What will happen in this case? Will we simply create
invalid SBML files? From my perspective, it would be much better to
throw an exception in such a situation. Otherwise users will have the
impression, everything is correct but then they will not be able to work
with their files.

The last thing I would like to mention is about the MathMLParser. I know
that it is not yet implemented. But, I would like to draw your attention
to the interface ASTNodeCompiler. This has already been implemented for
the TextEquation and also LaTeX export (both has to be improved but
should at least run). The ASTNodeCompiler recursively evaluates the
content of an abstract syntax tree. The same thing is necessary when
writing its content to an SBML file. Actually, what we simply have to do
is to implement the interface ASTNodeCompiler also for MathML export.
Should the class MathMLParser implement this interface? Or should we
implement another class for this purpose that is used by MathMLParser?

I am writing this e-mail just to make sure everybody knows about the
ASTNodeCompiler and to avoid that the same recursive function will be
implemented again.

Cheers
Andreas

--
Dipl.-Bioinform. Andreas Dräger
Eberhard Karls University Tübingen
Center for Bioinformatics (ZBIT)
Sand 1
72076 Tübingen
Germany

Phone: +49-7071-29-70436
Fax: +49-7071-29-5091
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Hello SBML enthusiasts and developers,

The JSBML project has been trying to choose a logo. It is
time to get more opinions and put things to a vote. Here's
a survey for this purpose:

http://www.surveymonkey.com/s/choosing-jsbml-logo

The deadline is midnight, Sep. 22 (in your timezone).

Please help the project by rating the different logo
options. You can give them values from 1 to 10, with 10
being the highest/best score. You do not have to rate every
one, and you do not have to use a rating only once. (So,
for example, if you like 2 choices equally, you can give
them the same rating.)

The winning logo will be the one that gets the highest mean
rating from among all the votes cast.

Thanks for your help,
MH (on behalf of JSBML)
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Hi Paulo,

On 11/12/2010 04:54 PM, Paulo Maia wrote:
> Hi Nicolas,
>
> I was unsure wether to submit a bug report for this or not...
>
> I was trying to create an SBML loader for OptFlux using your current
> implementation of JSBML since, to my knowledge, MathML support is now
> available.
>
Yes, it is.

> The problem I'm having is still before the actual xml parsing begins:
>
> Exception in thread "main" java.lang.NullPointerException
> at java.util.Properties.loadFromXML(Properties.java:851)
> at
> org.sbml.jsbml.xml.stax.SBMLReader.initializePackageParserNamespaces(SBMLReader.java:242)
> at
> org.sbml.jsbml.xml.stax.SBMLReader.getInitializedPackageParsers(SBMLReader.java:145)
> at
> org.sbml.jsbml.xml.stax.SBMLReader.readSBMLFromStream(SBMLReader.java:412)
> at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:329)
> at org.sbml.jsbml.xml.stax.SBMLReader.readSBMLFile(SBMLReader.java:358)
> at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:343)
> at org.sbml.jsbml.JSBML.readSBMLFromFile(JSBML.java:265)
> at
> metabolic.io.readers.OptFluxJSBMLReader.getContainer(OptFluxJSBMLReader.java:51)
> at test.OptFluxJSBMLReaderTest.main(OptFluxJSBMLReaderTest.java:16)
>
>
> When analyzing the code, I found out that the
> org.sbml.jsbml.xml.stax.SBMLReader.initializePackageParserNamespaces
> method was trying to access a
> "org/sbml/jsbml/resources/cfg/PackageParserNamespaces.xml file. This
> file does not exist in that location and the process dies immediately
> with the a nullpointer exception...
>
> public static void initializePackageParserNamespaces() {
> Properties p = new Properties();
> try {
> p.loadFromXML(Resource.getInstance()
> .getStreamFromResourceLocation("org/sbml/jsbml/resources/cfg/PackageParserNamespaces.xml"));
>
>
> I am not sure if am using the correct method to load the SBML file,
> thus this e-mail... I am using the JSBML.readSBMLFromFile() method to
> give me the SBMLDocument instance...
>
> Is this correct or am I missing something?
>
Do you used ant to create the jsbml jar file ? Or are you trying to run
it directly from a JDE ?

The problem is that you probably did not add the resources folder to
your CLASSPATH, this is there that the different configuration files are.
I guess this is one more point that we need to add in our future
documentation.

Let me know if it solve your problem,
Thanks,
Nico





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