[[public.kgi.edu/~fbergman]]

News

It was quite troublesome to post information here, so I'm going to try for now to update a new blog, and have those changes reflected here.

Wave

Ok ... i've jumped the wave ... here a first try of embedding it.

Previous News entries

• 2009-01-29:
  MIASE might be the best way to exchange simulation recipes. After the initial prototype from last year, which only read the MIASE descrition, i've fnally updated it to read / write / create MIASE files. The prototype currently consists of: a C# library for reading MIASE files, a C# library running MIASE files, a command line version to view MIASE files and a Web Application to view / create simple MIASE files from SBML models.
• 2009-01-11:
  Apparently SBW 2.7.8 did not work quite as well on some linux systems. So here a set of binaries generated for openSUSE 11 and Centos 4.6. In order to install, just unpack the file, change to the directory created and call register.sh with the full path as argument.
• 2009-01-09:
  I have a new application that de-codes the networks of our Network Enumeration crusade. You may try the web application or the web service. It will be on sys-bio as soon as it is approved.
• 2008-08-05:
  The new SBW release is almost ready, here the release candidate for the OSX Installer, supporting Universal Binaries. Update 2008-08-08: And here the next Linux Installer.
• 2008-07-09:
  We are working on a new structural library, more information here.
• 2008-07-05:
  A short update, since Visual Studio 2008 has been available for some time here a SBW plugin for it. (I have not actually modified the plugin, but just updated the registration file and thus it works fine). You can download it here.
• 2008-05-23:

  Just a short update, I'm still working on the Simulator Comparison and have a new preliminary version on my development machine

• 2007-11-04:

  I won't even start trying to come up with a story for not updating this page as frequently anymore. Anyway SBW 2.7.6 was just released, now mono is doing rather well under OS X have a look
• 2007-06-25:
  A short update, a Visual Studio 2005 Version for our SBW plugin was requested frequently, thus I tried to compile one. I would consider it an early beta, download it here
• 2007-04-21:

  Finally I'm in Seattle, and things are looking better. The SBW main server is finally online, and the web applications there are working again. Have a look: http://sys-bio.org.

  This week I've had a look at CompuCell3D (http://compucell3d.org). You definitely should have a look. It's a modeling environment and PDE solver, nicely hooked up to VTK for great visualizations. With help a proof-of-concept connection of CompuCell3D and SBW was created.

  Here are three videos that demonstrate the progress. As always you need the Divx codec (http://divx.com). I also recommend the VLC media player, which will allow you to speed up the playback as necessary. Here we go:

  1. 109 cells sharing one Simulator
  2. 109 cells, each getting a simulator, initial conditions are modified, by performing a short simulation, to put the model into a different parameter region.
  3. 109 cells, each getting a simulator and having same initial conditions.

• 2007-03-26:
  This week SBW will be moving to Seattle, WA. Hence the web applications on this page will go offline tomorrow. As soon as i get them up and running again I will announce it here. For the time being, please use the contact options on the JDesigner SourceForge Page.
• 2007-03-10:
  Sorry for the sporadic updates to this site. Development is as high as ever, as you will see the current SBW Installer now uses libSBML3, for better or worse. I'm aware of the problems with the current installer with regards to level1 SBML documents and hope to have them resolved soon. The 3D Tool sees major updates all the time, but i'm aware that it's still not quite as usable as it should be.
  For now though upon request, I finally put what Java-documentation we have online. Let me know if there is trouble with it.
• 2007-02-07:
  Since last month I am experimenting with a new threading approach to SBW ... if you feel brave enough, you could try the experimental installer. In case something bad happens, just send me some feedback, uninstall and reinstall the stable version.
• 2007-01-23:
  I just can't believe I haven't updated this page in so long. So first of all a happy 2007 for us all. I've been spending most of these days working again on the 3D Tool and am making progress. Right now parameters and species concentrations can be changed interactively while the Simulation is performed. Though there are still a lot of changes to be made.
• 2006-11-16:
  Ok, we are alrmost ready for the next release of SBW. Thus there are a couple of release candidates of 2.6.0 for Linux (tested with Ubuntu 6.06 and 6.10), OSX (ppc & intel) and of course the WIN32 Version. Note as always that Jarnac and JDesigner are currently not available on non-Windows platforms. *BUT* whith this next release we are finally able to release a first batch of C# modules that have ben exhaustily tested to run with MONO ... with them you get in a first Version, JarnacLite (script based model editor), SimDriver(Simulation Interface), roadRunner (simulator), Auto Layout and StructAnalysisGUI. All modules being equipped with a SBW - menu and fascilitate jumping from one application to the next without hickups. Please look at the readme files, or mail me in case of problems ...
• 2006-07-05:
  Updated a Online Services on my development machine (and on sys-bio.org).
• 2006-06-25:
  I finally managed to update the Simulate 3D site. It now closely resembles the actual current version. Have a look :)
• 2006-06-22:
  We are getting closer to the next big release of SBW ... here is a new windows installer that solves many problems. It also includes roadRunner, the SBML Layout and AutoLayout modules.
  There also is a new version of the Bifurcation Discovery Tool. Now it uses roadRunner and this results in a unbelievable speedup. It also features a SBW menu and can save parameter changes into an SBML file.
• 2006-04-27:
  • Ok I admit, I've been slow updating this page. Of course I haven't stopped working on SBW so here some updates:
    • A new version of the SBW Visual Studio Add-in. Now SBW Module Wrapper can be automatically restarted. Which will lead to much more stable applications. Also some minor bugfixes have been made.
    • Obviously a new Version of the SBW Windows installer with lot's of changes regarding JD2, Jarnac, SimDriver and StructAnalysis Tool.
    • New version of the Bifurcation Discovery Tool, GUI changes include a fix in selecting/deselecting species, fix to number format issues and more.
• 2006-03-20:
  • Finaly I've taken some time to fix some loose ends with the Linux & OSX SBW installers. After things are done it will be possible to have SBW start up automatically on Linux and OSX just like it works on WIn32. The installers have been created with the Bitrock InstallBuilder 3.5.1 ... if you have trouble installing have a look at the installation instructions.
  • Download OSX Installer (verified to work with OS X 10.3 & OS X 10.4.5)
  • Download Linux Installer (verified to run with Suse 9.2, Suse 10, Fedora Core 4)
•  2006-03-03:
  • Redesign of this website
•  2006-03-02:
  • Update of the SBW Win32 Installer ...
  • This new version finally contains the long awaited JDesigner2 with lots of other changes.
•  2006-02-26:
  • Update of the SBW OSX Installer ...
  • This version brings all the recent Win32 changes to SBW to OS X.
•  2006-02-21:
  • Update of the SBW OSX Installer ...
  • bug fix release ... works with OSX 10.4.5 and OSX 10.3.x
•  2006-02-02:
  • Update of the 3D concentration viewer ...
  • new help system, updated auto layout tool
•  2006-01-27:
  • Update of the 3D concentration viewer ... .
•  2006-01-20:
  • Update of the  SBW Windows Installer
  • this includes the fix for the leaking NOM.