SED-ML Web Tools & COMBINE archive

A couple of days I've published the COMBINE archive project to github. Today, I'm proud to let you know, that you can now upload / download COMBINE archive also to the SED-ML web tools:

  http://sysbioapps.dyndns.org/SED-ML_Web_Tools/

If you rather try it offline on your Windows box, try the SED-ML Script editor:

  SetupSedML-win32-1.11.exe

COMBINE archive … an implementation

It has been quite some time ago, that the COMBINE archive was proposed it seemed a simple enough format. I had a library for some time, but was not yet sure where to read it. As with any format, if no files are around there will be no applications written to support them.

In any case, since the conversion is going again, I’ve decided to put all the information about the library, and an first version of a graphical frontend for it. As with any experimental frontend it is written again for Windows. The links below have the details:

• The library and all information about it,
• the source code
• the windows installer

About the User Interface

When you open an archive in the application, you will find the following layout:

On the left you find the list of files contained in the archive, separated by their type, currently only a limited number of the COMBINE standards is recognized and an even smaller number can be interacted with, but that will change in the future. When you select a file, the systems preview handler will be used to generate a preview, as you can see in the screenshot with the PDF. Also recognized are images, and websites. Can the format not be determined, the file will be displayed as plain text, which may or may not be helpful.

If an SBML file is selected, it will be displayed as plain text. But if you have SBW installed, you will see this pane on the top:

That will allow you to open the file immediately for simulation / editing with one of the defined favorite applications. Or you could choose any other installed SBW Analyzer. The next version will allow you to simulate SED-ML files, and view SBGN files … stay tunes! I’m also working on an online version for sysbioapps.

libSBML 5.8.0 Released

Just as follow up to the release of the SBML Level 3 Package for Flux Balance Constraints: we have now released a new version of libSBML, that includes the FBC package enabled in all binaries. That is not just the core library, but also all language bindings (including MATLAB). Particularly I want to highlight three features:

• the first one is full validation: all validation rules have been implemented in libSBML and will be validated automatically on a checkConsistency() call on SBMLDocuments.
• the other one are the converters: we have included converters from the COBRA annotation to the FBC package and vice versa. Examples are available online, or in the source archives including the package.
• Finally, C++ documentation of the package is available online. While package documentation is not yet available for language bindings, they do use the same function calls, so the information is transferable.

See also the full release announcement for more information.

SBML Level 3 Package for Flux Balance Constraints

It is official, the SBML Level 3 Package for Flux Balance Constraints has been released! In its first version it allows to efficiently store constraints of Flux Balance models along with objectives to be met.

You can find the full specification online under:

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

As of today the next release of libSBML (5.8.0) has gone into code freeze, that will include the FBC package, along with full validation and conversions from SBML Levels that use the COBRA annotations to SBML Level 3 models with the FBC package. This new version is bound to be released by the end of the month. In the meantime nightly windows builds can be found on our build server.

With this release I’ve also made a new version of my FluxBalance tool available. Version 1.7 now already uses the COBRA importer, and has been redesigned to efficiently compute flux balance solutions for even genome scale models (albeit the loading of these models still takes a while).

A big thanks to the SBML editors and the community to make this possible!

New SBML Test Suite Database!

As you might have noticed there is a new online service available on sbml.org, the SBML Test Suite Database. We of course had the SBML Test Suite for quite some time, with an amazing number of 1196 tests (to date), that now also include tests for the Flux Balance Package and even Hierarchical Modeling. This new application lets you browse all these tests, filter for tests (for example: Show me all tests, that test ‘RandomEventExecution’) and  download a selection of tests right there.

At the heart of course is the capability to *upload* a zipped set of test results, and analyze them for yourself in a private area, and once you are happy with them have them published publicly for the world to see. I’ve am working on a new version of SBW, that uses the 5.7.0 version of libSBML. And here is what a result for RoadRunner would look like:

As you can see in yellow, RoadRunner will still not support AlgebraicRules, FastReactions or CSymbolDelay. However, libSBML will flatten comp models for RoadRunner, and so all comp tests that do not use the above mentioned elements will work just fine.

COPASI 4.9.45 Released

Just in time for last weeks COPASI workshop we released a new version of COPASI. This has been the first release I’ve seen since joining the team in March of last year. There have been a number of changes in this release, and I thought I would call out those, that help me the most. The first one definitely has to be the changes in plots. Starting with COPASI 4.9.45 you can go ahead and define line style and widths of curves (and points). To make that even easier, you can do so for multiple curves at once. So that should make it much easier to create appealing plots. Also the plot window has changed:

It now allows to toggle between log mode of the individual axes, without the need to re-execute the task. Also prominently featured is the Window menu, that finally allows you to quickly select the plot you were looking for.

Having been re-elected for another term as SBML editor, I can’t help but mention that more of the models you define in COPASI can now be shared with other SBML capable tools. Most notably COPASI now exports rates of compartments, species and global parameters (using a custom annotations) as well as the drawing of random numbers from uniform and normal distribution (again using a custom annotation). These annotations (see below for example) follow the approach I’ve outlined before (Though I adapted it to use a reference to the UncertML definition that people liked much better for some reason). The newest snapshot of SBW can readily import these annotations already!

Apart from these, this COPASI release features a first spring layout algorithm and import for CellDesigner annotations.

There also is a new cross section task, that you could use for bifurcation plots (rather than to define events to scan over yourself), but those will be part of a future post! In any case there are a large number of additional changes that will make working with COPASI quite a lot easier, so grab your version here:

http://www.copasi.org/tiki-index.php?page=downloadnoncommercial

And as promised, here the function definitions exported.

rateOf:

<functionDefinition id="rateOf">
  <annotation>
    <symbols xmlns="http://sbml.org/annotations/symbols" 
    definition="http://en.wikipedia.org/wiki/Derivative"/>
  </annotation>
  <math xmlns="http://www.w3.org/1998/Math/MathML">
    <lambda>
      <bvar>
        <ci> a </ci>
      </bvar>
      <notanumber/>
    </lambda>
  </math>
</functionDefinition>

Uniform:

<functionDefinition id="RUNIFORM">
  <annotation>
    <distribution xmlns="http://sbml.org/annotations/distribution" 
    definition="http://www.uncertml.org/distributions/uniform"/>
  </annotation>
  <math xmlns="http://www.w3.org/1998/Math/MathML">
    <lambda>
      <bvar>
        <ci> a </ci>
      </bvar>
      <bvar>
        <ci> b </ci>
      </bvar>
      <apply>
        <divide/>
        <apply>
          <plus/>
          <ci> a </ci>
          <ci> b </ci>
        </apply>
        <cn type="integer"> 2 </cn>
      </apply>
    </lambda>
  </math>
</functionDefinition>

Normal:

  <functionDefinition id="RNORMAL">
     <annotation>
    <distribution xmlns="http://sbml.org/annotations/distribution" 
    definition="http://www.uncertml.org/distributions/normal"/>
     </annotation>
     <math xmlns="http://www.w3.org/1998/Math/MathML">
       <lambda>
         <bvar>
           <ci> m </ci>
         </bvar>
         <bvar>
           <ci> s </ci>
         </bvar>
         <ci> m </ci>
       </lambda>
     </math>
   </functionDefinition>

libSBML 5.7.0 Released

I know I’m two weeks late by now, still I wanted to let you know that we released a new version of libSBML (be sure to have a look at the full release announcement). Since the last release the hierarchical modeling composition package was approved and thus for the first time the comp package is enabled in all binaries. So no matter which one you grab, you will be able to build comp models with it, and read and write them. Much work has gone into the flattening algorithm so that even if your software does not actually make use of the comp package yet, you could automatically flatten the model into a Level 3 core model. To make this possible even from the (otherwise from comp neglected) C API, we finally wrapped the libSBML Converter API for C (including the SBMLConverterRegistry). So now you can query for converters from all languages. Example conversions are available that demonstrate how to flatten the model for all binding languages. Just as example, given an SBMLDocument ‘doc’ all it would take to convert the model are these three lines (in C#)

var props = new ConversionProperties();
props.addOption("flatten comp", true, "flatten comp");
int result = doc.convert(props);

After that, the document will be flattened. And can be treated as a regular Level 3 model. (Though you might want to check for a zero result, just to make sure no issues crept up during the conversion (which would be logged in the error log)).

Perhaps one more word about ExternalModelDefinitions. LibSBML will automatically locate files on the *local* hard drive, relative to the document opened. If you are loading documents from string, and want this feature to be working, you can set the SBMLDocuments locationURI property. More generally the comp package includes a ResolverRegistry, where you can register your own resolvers. These resolvers basically allow you to return an SBML document for a given URI. This facility also would allow you to easily extend the resolvers to resolve documents from the web, from databases and other non-local sources. To demonstrate this, I wrote an example, the SBMLHttpResolverExample, that uses libCURL to download a model from any given website (with the caveat that the comp specification does not allow the inclusion of non-level 3 models, which means that all models from the BioModels Database are rejected for the time being. If you, like me, don’t particularly like that behavior, you might want to raise that issue with the comp working group).

Please grab the new version from SourceForge:

http://sourceforge.net/projects/sbml/files/libsbml/5.7.0/

Happy coding!