Release of the Systems Biology Workbench 2.10.0

We are proud to finally announce a new release of the Systems Biology Workbench 2.10.0. You can download this release directly from SourceForge. This version provides updates to all components:

• Jarnac comes up with an altered front-end, that will make it easier to work with it. It features also additional script commands .
• JDesigner has been updated to work on newer Windows versions (7-8.1). It also can now load and save model parameters from / to external files. And it features a new plugin system.

Since our last official release, the SBML Level 3 Layout Package has finally been officially accepted, this release supports that final version as well. Similarly, SED-ML Level 1 Version 2 has been released, and with the Simulation Tool those files can be executed. Broken down into individual applications we have:

• Layout Viewer / SBW Auto Layout: Support for SBML Level 3 Layout Package.
• SBW Simulation Tool: Support for all SBML levels, and SED-ML Level 1 Version 2. First experiments such as Parameter Scans can also be exported. It also automatically displays targets of SBML Events / Rules in the list of selected elements, when loading models. The Simulation Tool also supports loading files from the COMBINE archive.
• SBML Support Library: SBML models using the Hierarchical Model Composition package will be automatically flattened, when possible (The file has to be valid, and all submodels have to be reachable.).
• JarnacLite / RoadRunner / SBML Support Library / JDesigner: A number of custom annotations have been added to allow the specification / simulation of distribution functions, or referencing the rate of change of a species. I've written about that before: distribution and rateOf.

As some of you know, Frank has joined the COPASI team. This made it possible to write a translator for COPASI, and now there is a new SBW import category that enables calling modules, to have a specific format converted into SBML, which can then be consumed. Current bidirectional translators are available for COPASI and JARNAC format. Practically that means that COPASI and JARNAC files can now be directly imported into: Simulation Tool, Auto Layout and others.

Of course there have been many more changes, bug fixes and improvements, so have a look at our full changelog.

SBML Validation from SBW

The SBML Online Validator, currently represents the most comprehensive validator for SBML files. While we are working on a standalone version of it, it will be some time before it will be released. In the meantime I came across a nice Web Automation Framework (see http://watin.org/). That makes it very easy to test web applications. It was easy enough to wrap it into an SBW module, so that now all SBML files can be easily validated right from your favorite SBW Application:

I’ve pushed the project over to http://fbergmann.github.io/LaunchOnlineValidator/ if you like to see how that was done. Or grab the module right from SourceForge: SetupSBMLValidator_1.0.exe.

Updated FluxBalance Tool

Today I want to announce a new version of the FluxBalance tool. New in this version is that it works better with SBW. By adding a new entry to the menu bar “Export L2”, it is now possible to export the Flux Balance problem designed to other SBW modules as SBML Level 2 Version 4 files with the FluxBalance annotation. Is the button not pressed the SBML Level 3 File with the official Flux Balance Constraints Package will be exported. The new installer is available immidiately from SourceForge under:

http://sourceforge.net/projects/sbw/files/modules/FluxBalance/

Unfortunately, we are still not quite there for the next SBW release, last changes on JDesigner are in the process. In the meantime there is a new update for SBW please feel free to download the latest version.

Applying the Scientific Method to Simulation Experiments …

I’ve just finished a one hour Rosa & Co webinar, and thought to post the slides below. You might also be interested in their other webinars, you can find the webinar archive here.

Applying the Scientific Method from Frank Bergmann

Systems Biology Workbench 2.10.0 - RC2

We are still working on the next release for SBW. Some users commented, that the last release candidate did not work for them, having issues in JDesigner. As of right now a new Windows build is available, from the Update tool or:

http://128.208.17.26/fbergman/files/latest/SetupSBW.exe

Thank you again for all the reports so far, please keep them coming.

SED-ML Level 1 Version 2–Release Candidate

The COMBINE meeting has just started, and we finally made the release candidate for the SED-ML Level 1 Version 2 specification available. SED-ML L1V2 finally extends the simulation experiments covered by SED-ML to include any kind of repeat and perturbation experiment. Apart from that it also includes the possibility to fully parameterize simulations, by specifying algorithm specific parameters like relative and absolute tolerances of integrators. The specification is available online from:

http://tinyurl.com/sed-ml-l1v2-rc

On my end I’ve updated the libSedML, and the SED-ML Script editor and of course SBW to be able to simulate L1V2. Another major change has been applied to the SED-ML Web Tools that now also support L1V2, and are now also capable of simulating the repeatedTask concept with CellML additionally to SBML.

As always any feedback is appreciated.

Systems Biology Workbench 2.10 (RC1)

As hinted at, a couple of days ago, we are shortly before the release of the next version of SBW with enhancements for all associated programs. Today I want to announce a new release candidate. On SourceForge you will find installers for Windows, OSX as well as Linux (x86 & x64). You can download them from:

http://sourceforge.net/projects/sbw/files/sbw/2.10.0/rc1/

I’ve also created virtual machines & live images with SUSE studio, that are available online:

32bit OpenSUSE 12.3,
64bit OpenSUSE 12.3

Any feedback is appreciated.

Preparing the next SBW release (2.10)

It has been some time since the last release. Of course we never stopped working, as you can tell if you look at the change log:

SBW Change log

Apart from major upgrades to JDesigner and Jarnac, there is full support for the newly released Layout package. Additionally, Level 3 models using the Hierarchical Modeling (i.e. comp) Package can be automatically flattened for use in our simulators. Also an import option has been added to many modules, so that COPASI files can be opened.

The new windows installer can be downloaded from:

Windows Installer

Or obtained from the update program.

SBML Layout Specification RC2

Finally, after a good 10 years since the first presentation of a layout extension to SBML, the specification has been sent to the SBML editors for approval. One might think it is actually quite easy to describe where something is, and it should not take all that long to agree on a bare minimum for a standard, but be that as it may, we are now in the final stretches. If you like, you could have a look at the specification:

SBML Layout Specification RC2

It is of course fully supported by libSBML. Now that the specification is in the approved format for L3 packages, including a whole number of validation rules, validation is currently added to libSBML and will be available from the Online Validator with the acceptance of the package. In the meantime you could use the

SBML RNG Online Validator

Software support is shaping up: SBW has been supporting SBML Layout since 2005, and COPASI has it enabled in publicly released builds since last year. Both software tools also import CellDesigner annotations! At last years HARMONY meeting the layout specification has received its biggest change, by adding a GeneralGlyph, that makes it possible to also layout elements, that previously where not possible. Support for that is available in the latest SBW builds,

SBML Online Layout Viewer

And within the COPASI codebase, to be released sometime soon.Here a screenshot, showing the exchange between COPASI & SBW of an SBML Level 3 model with a GeneralGlyph that represents an SBML Event, including Trigger and Event Assignment:

Flux Balance Tools

For the Friday morning here a collection of links to software applications and databases all around flux balance analysis.

Tools

• Systems Biology Workbench: While SBW does not in and of itself deal with flux balance analysis, it does make it easy to construct networks. And makes it easy to send models between applications.
  Download 
• FluxBalance; An application to add constraints and objectives to SBML models and to evaluate them using LPsolve.
  Download
• CBMPy: comprehensive python package for analyzing flux balance models. Installation instructions are here.
• OpenCOBRA: MATLAB toolbox for genome scale reconstruction. Instructions on how to use are here.

WEB

• F.A.M.E: Web based environment for Flux Analysis. With a tutorial here. 

Databases

• KEGG Pathway: KEGG PATHWAY Database (used by F.A.M.E for visualization).
• BIGG Database: Database of genome scale reconstructed networks. Among them the global reconstruction of the human metabolic network.

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.

SBW Flux Balance Analysis Tool … v2

Brett Olivier was here last week in HD, and we made quite some progress on the FBC specification. We also started with a test suite for tools implementing the FBC package. And as can be expected, these tests revealed quite some room in the original FBA Tool that from 2009.

The new version fully supports the SBML FBC package, will properly inform whether a solution was found or not, and sorts a number of problems (such as dealing with infinite bounds). The new version is still aimed as teaching tool, but now is much better suited as such. The list of changes:

• fixed issue with infinite bounds
• fixed issue accessing the results from the c library
• added display of objective value and solution quality to status bar
• added export of LP files
• added import of COPASI / Jarnac files (if latest SBW is installed)

In any case I started a github page for the project, where the first windows installer is available for download:

https://github.com/downloads/fbergmann/FluxBalance/SetupFBA-1.3.exe

Custom Annotation for using Distribution Functions in SBML Models

Drawing random numbers is a task occasionally encountered. However, there is no standard way to do that in SBML. Of course that is precisely what the SBML Level 3 package for Distributions and Ranges is for. But what to do in the meantime, or what to do when you want it working for SBML Level 2? This is precisely what I encountered a couple of weeks back, and that is why below you will find a specification for a very short custom annotation, that allows to tag an SBML function definition as distribution function. Here an example:

<functionDefinition id="normal" name="Normal distribution">
  <annotation>
    <distribution xmlns="http://sbml.org/annotations/distribution" definition="http://en.wikipedia.org/wiki/Normal_distribution" />
  </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>

The annotation (in the namespace http://sbml.org/annotations/distribution) contains one attribute definition, whose value tells us precisely which distribution we would like to draw numbers from. All software that supports it will know that we are dealing with a distribution and know what to do with it. Other software at least get the mean whenever they invoke the function.

Here the full specification of the Custom Distribution Annotation. (and here the SBML model). The annotation is so far supported by JarnacLite and RoadRunner (Windows Installer). As the same functionality is available in other software packages it would be great if they could be tagged with the annotation as well.

Systems Biology Workbench - 2.9.0

I’m pleased to announce the release of SBW 2.9.0. This release is available for the following platforms:

• Windows
• Linux x86 / x64
• OS X
• portable Apps

This release improves support for the exchange standards: SBGN-ML, SED-ML (including the nested proposal v2), and of course SBML. RoadRunner simulates a wider range of SBML models. You can get the new release from Sourceforge:

• http://sourceforge.net/projects/sbw/files/sbw/2.9.0/
• http://sourceforge.net/projects/jdesigner/files/Systems%20Biology%20Workbench/2.9.0/ 

And the portable installer from:

• http://sourceforge.net/projects/sbw/files/sbw/portable/

Screenshots

Linux

Thanks to bitrock, we are finally able to provide a new range of linux installers (as well as 32bit and 64bit RPMs and DEB packages). When installing as root, SBW will be installed into /opt/sbw-2.9.0. Otherwise it will be available in the users home directory. In these directories you will find shortcuts to all available programs.

Dependencies: most SBW applications require Mono 2.10 to be installed (we recommend to install mono-complete). If you try to run SBW on an older linux distribution that does not include mono 2.10 in its repository here are some installation scripts for fedora and ubuntu that will help you to get it running, it should be easy enough to adapt them to centos when needed. Here the example for ubuntu:

mkdir mono-2.10
cd mono-2.10
wget --no-check-certificate https://github.com/nathanb/iws-snippets/raw/master/mono-install-scripts/ubuntu/install_mono-2.10.sh
chmod 755 install_mono-2.10.sh
./install_mono-2.10.sh

If this still seems to adventurous for you, I’ve created a 32bit and a 64bit virtual machine that runs SBW 2.9.0. It includes Live CDs, Virtual Machines and hard drive images. Simply start the machine and find the SBW shortcuts in the start menu. (They simply use the SBW rpm installer!).

• 32bit: http://susestudio.com/a/gNqXM5/sbw-290-gnome-desktop-x86
• 64bit: http://susestudio.com/a/gNqXM5/sbw-gnome-desktop-x64 

OS X

We’ve listened to all your feedback about SBW being difficult to install. So this time around we don’t use any installation. Simply drag the SBW folder into your Applications folder and you are good to go.

As always, we recommend installing XQuartz and Mono prior to running SBW. The current Mono release 2.10.8 (and the 2.10.9 beta) unfortunately have a regression that causes the some application to stop working. The last known working release is 2.10.5 as available from:  http://download.mono-project.com/archive/2.10.5/download/

As for XQuartz, I’m using: http://xquartz.macosforge.org/trac/wiki/X112.7.0

Full Change Log

Feb 2012
Changes in Version 2.9.0
===========================

SBML Layout:
  - Reading Support for SBML Layout Extension (for SBML L3)
  - (at the moment the library only writes annotations though)
  - Stability and performance improvements for Layout Viewer.
  - SBGN upgrade
  - Bug Fix: Global Render Information were not correctly read
  - Stability: Now works even independently of SBW
   
SED-ML:
  - Support for Kisao Terms (full lookup and browsing of the
    hierarchy).
  - Bug Fixes for error correction facility

RoadRunner:
  - BugFix: non integral stoichiometry for L1 models
  - BugFix: model refused to load when non-L3 model used ids in speciesreferences
  - BugFix: L1 model with local parameters refused to load
  - BugFix: L1 model with non-integral stoichiometry was incorrect
  - BugFix: hasOnlySubstanceUnits was ignored in some places

NOM:
  - added methods:
    reorderRules : string reorderRules(string)
    inlineFunctionDefinitions : string inlineFunctionDefinitions(string)
  - (rules are automatically reordered by loadSBML, this will allow other modules
    to work correctly without code change)
  - fix: promote local to global parameters works for L1 models
   
Translators:
  - sort assignment rules
  - added command line option -f <sbmlfile> to translate the SBML file
    and write the file to stdout, so they can be used from the command line.
 
Portable:
  - we also have a version of SBW that you can install on a flash drive
    using portable apps.
 
All modules:
  - updated to use libSBML 5.4.0

JDesigner:
  - Fixed Chinese characters appearing when assignment rule was selected for editing.

SBW goes Portable

Portable Applications, are applications that you can easily take with you on your USB stick. This allows to use your applications on all Windows machines by simply plugging in the stick. I’m pleased to announce a first prototype that will make the Systems Biology Workbench available for the portableapps.com framework. Here the download:

http://sourceforge.net/projects/sbw/files/sbw/portable/

To install, simply launch portable apps, and then click on “Install a new App”:

It will install the following applications:

While the launcher only exposes: JDesigner,Jarnac, JarnacLite, the Simulation Tool,  SBML Translator, SBML Layout Viewer, AutoLayout and the C# Inspector, the full SBW installation is available.

If you need custom launchers for more applications, let me know (Possible candidates: BioModels Importer, Jacobian Viewer, Convert SBML, Shutdown SBW).

Please let me know whether this is working for you.

BAD NEWS:

Unfortunately we won’t be able to have SBW be part of the Portable Apps dictionary since some SBW components use .NET and portable apps do not consider .NET widely enough spread. (Even though it appears that it was on 90% of  Windows machines in 2010, and is now part of windows update, and thus *everyone* updating their machine is likely to have it installed.) But there goes me rambling …

Introducing sysbioapps/Layout

Ever since the SBW applications have been pulled from sys-bio.org and are only available via IP I am working on a new version for each of these applications. Today I’ve made the new version of my Layout web application available:

http://sysbioapps.dyndns.org/Layout 

See it live:

Features

The new application has the same basic features as the old one:

• upload of an SBML file
• displaying SBML Layout / SBML Render Format
• displaying JDesigner / JDesigner 2 / CellDesigner annotation
• generating a layout
• exporting images / SVG / PDF

New in this version:

• multiple file support
• Chrome / Firefox: upload multiple files
• Chrome / Firefox: drag and drop files onto the web site to upload
• support for SBGN-ML

Implementation

The new version has been implemented using ASP.NET MVC3  and JQuery / JQueryUI. The actual heavy lifting is performed by the SBML Layout Library. The PDF export is made possible through sbml2tikz, followed by a compilation by pdflatex.

As always any feedback is welcome.

sys-bio.org web applications down

The web site of the Saurolab was moved to a different machine the domain sys-bio.org has been transferred to that machine. As a result, all applications that previously ran on sys-bio.org are no longer available via their old URLs. The old server is still available via its IP:

http://128.208.17.26/

That web site also still hosts the web applications:

• Layout: http://128.208.17.26/Layout/
• Simulation: http://128.208.17.26/Simulation2005/
• Translation: http://128.208.17.26/SBMLTranslator/
• Web Services: http://128.208.17.26/SbwWebServiceCreatorInterface/

In the coming weeks I will update these applications and move them over to http://sysbioapps.dyndns.org.

SBW 2.8.3 Released

Just before the ICSB, here a new release of the Systems Biology Workbench. Exciting for me, lots of updates on the standard support:

• improved support for SBGN-ML
• improved support for SED-ML
• (some fixes for SBRML)

There also is a brand new JDesigner and Jarnac available, with lots of goodies. So please grab the new version from SourceForge before it gets cold:

SBW 2.8.3

Some of you might wonder what happened to the Linux and OSX release. I’m afraid it did not get done in time. Even though all modules and code has been updated to compile fine on 32 bit and 64bit Linux. So where is the holdup? As it turns out the latest distro’s don’t come with Mono 2.10, so I figured I wait a bit longer to make that release.

If someone needs those binaries sooner let me know and I upload them.

SED-ML Web Tools, SED-ML Script Editor & CellML Simulation Support

I’ve just upgraded the SED-ML Web Tools to a newer version.

http://sysbioapps.dyndns.org/SED-ML%20Web%20Tools/Home/

This version includes several bug fixes, as well as an experimental version of CellML simulation support. The CellML simulation support is thanks to an executable based on the CellML API provided by David Nickerson.

To accommodate this there have been several changes to the LibSedML API, where previously the API would have properties like .SBML or functions like GetSBMLId(), now these functions are hidden behind a native interface IModelingLanguage that will be populated based on the Model source URN as provided in the SED-ML file. This should make it easy to provide support for other languages such as NeuroML and VCellML as well.

I have also released a new version of the SED-ML Script editor. It now allows to open SBML or CellML files directly, for which then a rudimentary SED-ML file will be generated. Later it can be modified for more complex experiments. It also provides SED-ML validation capabilities. This time it is a windows only release (since I only have the CellML simulator as windows binary). It is available from SourceForge:

sf.net/projects/libsedml/files/

Introducing the SED-ML Web Tools

I’ve spend the weekend working on a new set of tools for simulating and Validating SED-ML files. They are online now under:

• http://sysbioapps.dyndns.org/SED-ML Web Tools

Let us first take a brief tour around the site:

Let me point just a couple of things.

Simulation

The current implementation will only simulate SBML files, using RoadRunner. As soon as I find time to update it I will add additional simulators. Currently 3D plots won’t work either. And of course simulation will only work if the model files are either:

• accessible via URNs
• accessible via WEB
• included in the archive.

Simulation already implements the Nested Simulation Proposal.

Validation

The new thing about the validation is that it also provides an option to fix common errors. This feature can be used to upgrade SED-ML files that were created before SED-ML L1V1 was released! Simply click on ‘Fix common errors’, and then download the file again.

Stay tuned for further updates, the next steps will be to Create and Edit simulation experiment descriptions. Also planned are web services that make it easy to create SED-ML files!