SBW (Systems Biology Workbench)

File Release Notes and Changelog

Release Name: 2.5.0

Notes:
Welcome to the Systems Biology Workbench – Release 2.5.0

This project was initiated by the Japan Science and Technology
Agency under the ERATO umbrella and led by Hiroaki Kitano, Hamid
Bolouri and John Doyle at Caltech, Pasadena. Further funding was
received from the DARPA BioComp program and more recently by the
Department of Energy GTL program. We are very grateful for all the
support we have received. The current workbench is still
undergoing development but now includes simulation tools, model
editors, translators and analysis software. Its key characteristic
is its modular architecture allowing third-party developers to
easily add new functionality. Software development was provided by
a number of individuals, including Frank Bergmann, Ben Bornstein,
Vijay Chickarmane, Andrew Finney, Mike Hucka, Ben Kovitz, Sri
Paladugu, Herbert Sauro, and Cameron Wellock All Software is
licensed under LGPL Copyright © 1999-2005

07 Nov 2005

Changes:
17 Oct 2005

Change in Version 2.5.0
=======================

SBW C# core:
- native C# version
SBW C++ core:
- fixed bug in category treatment
- fixed bug in auto-registration
- several optimizations
.NET SimDriver
- new version supporting steady state and continuous timecourse simulations
JDesigner
- Splash screen now centered on one screen when used with dual monitors
- Fix a number of bugs in the slider controller and define sliders dialog
- Installation now stores models in user My Documents
Jarnac
- SBW API Modified to conform to Simulation API
- Installation now stores models in user My Documents
NOM
- New methods added to NOM to conform to SBML Level 2
- Model validation carried out by the NOM, exception in the event of error
General bug fixes to Inspector and Frequency tool

Change in Version 2.4.1
-----------------------

Inspector
- Added 'Run and Close' Button
JDesigner
- Changed Save and Save As to be more consistent (Thanks to Jason for spotting this)

Changes in Version 2.4.0
-----------------------

JDesigner
- Removed MDI Interface, JDesigner API now compatible with SBW stimulation API
- Better error reporting when SBW method cannot be located.

Jarnac
- Changed aim API to be in line with SBW simulation API

SBW CPP Core & Broker:
- bugfix DataBlockWriter ... adding of empty 2d arrays of type **
  now throws proper exception
- optimized internal message calls

JDesigner
- Fixed a bug when users tried to export a model but the translator crashes.
- Experimental Version 2.0 of JDesigner available at www.jdesigner.org
Jarnac
- No changes
Inspector
- Internal changes to reduce message traffic

New Modules with this Release

CLAPACK
- SBW wrapper for some functions in LAPACK
StructAnalysis
- SBW Module that computes structure metrics for reaction networks, including
  stoichiometry matrix, conservation attributes, flux attributes.
XPPTranslator
- SBML to XPPTranslator. Generates reduced model according to the number of conservation laws. Critical
  for any analysis that requires a non-singular Jacobian.
- Used by Oscill8 Bifurcation tool from Emery Conrad.


Changes in Version 2.3.1a
-------------------------

SimDriver Module:
- minor visual changes,

SBW C# interface:
- bugfix in Exception propagation
- bugfix in Memory Management in PInvoke to SBW Dlls
- bugfix of CallingConventions

Changes in Version 2.3.1
----------------------

SimDriver Module:
- added checkboxes to add all or remove all species from the
  list of variables to plot

SBW Matlab Translator:
- added support for pow(x,y) functions

JDesigner
- Added new splash screens and about box
- Increased font size on model summary window

Jarnac (2.16g)
- Updated integrator to latest CVODE 2.3 (Thanks to Christophe Chassagnole for his help)
- Added new integrator options in the sim object (maxsteps and maxorder)
- Made CVODE the default integrator
- Changed slash and about screens


Changes in Version 2.3.0
----------------------

Python SBW bindings
- the installer will now install the python bindings iff
  - python 2.4.x with numpy (http://www.sf.net/projects/numpy)
  - python 2.3.x with numpy (http://www.sf.net/projects/numpy) or
  - python 2.2.x with numpy (http://www.sf.net/projects/numpy)
  is installed
- the python bindings have been rewritten to be more stable


Broker/SBWCore:
- now working with Windows Server 2003

Jarnac:
- changed to Sundials default CVode integrator (lsoda still available)

JDesigner:
- modified SBML export to make the files fully compliant with validating
  applications.
- lot of small changes that improve usability

SimDriver Module:
- since the existing Java SimDriver module (used as Jarnac frontend in CD)
  was written a long time ago, it seems to fall over after a couple of runs.
- this installation includes a C# Version that contains the same functionality
- the .NET Framework 1.1 has to be installed for this to work it can be
  downloaded at:
  	http://www.microsoft.com/downloads/details.aspx?FamilyID=262d25e3-f589-4842-8157-034d1e7cf3a3&DisplayLang=en



Changes in Version 2.1.0
----------------------

Broker:

- interoperability with other Brokers on the same host possible
- changed linkBroker() handling so that it is possible to specify
  the port to connect to. e.g.: localhost:10301
- registry now uses the same code for all platforms
- XML is properly formated

- modules are now allowed to run on a remote broker. (use ModuleImpl::runOnHost(char* host));
- modules can connect to remote brokers (use SBW::connect(char* host))

Jarnac:

Fixed a problem with the eigenvalue determination when matrix contained NAN values

Added better error messages when parsing ill-formed rate laws

Fixed a rare parse error, would issue an error message for things like a+-b, a++b etc., it was
necessary to correctly this because libSBML tends to generate this kind of infix.


Changes in Version 2.0.1
--------------------------

JDesigner:

- added GDIPLUS.DLL for Win2k

Broker:

- small fixes on multi-threading issues

NOM

- changed problems with edu.caltech.NOM so that the following methods work again:

   string[] getBuiltinFunctions()
   string[] getBuiltinFunctionInfo(string)

  in the previous versions these functions just returned integers and thus would
  not work correctly

re-added java modules from 1.0.5:

- SimDriver (with fix from Stephen Ramsey)
- plot (plot module needed by SimDriver)
- edu.caltech.MatlabTranslator (to convert models to Matlab/Simulink)


Changes in Version 2.0.0
--------------------------

Broker

1. bug fix in module startup
2. bug fix of several threading issues
3. bug fix in remote negotiation
4. support for Mac OSX 10.3 / Linux (gcc 3.3)

Binding Libraries:

1. support for complex numbers added to all binding libraries
2. new c# binding library (usable for all .NET languages)
3. Java: startup of broker via JAVA modules possible again
4. Reintroduced Python support in C++ Broker (Python 2.2 and Numerical Python (numpy) must be installed).

JDesigner

1. Mouse Wheel support added to JDesigner
2. Some cosmetic changes to the export dialog window
3. Changes to SBML support to improve compatibility
4. Pictograms are now properly resizable, can have arbitrary colors
5. Fixed bug in stoichiometry setting edit box
6. Straight lines as well as bezier curves added.

Jarnac

1. The previous version of Jarnac was not shutting down correctly when instructed to by SBW.
2. Changes to the core integrator to improve performance on stiff systems
3. Fixed local/global parameter issue in some SBML files

matlabTranslator

1. Fixed error in generation of stoichiometries in C++ version of translator
2. Write out full precision numbers ot Matlab file

FORTRANTranslator

1. Fixed some syntax errors in the generated FORTRAN

Inspector

1. Improvements to the Interface
2. Support for distributed SBW
3. Support for Complex number entry


Changes in Release 3d
----------------------------------

1. Matlab translator was badly mangled in the last release, it is now
fixed (Sri Paladugu).

2. SBML L2 broken in release 3c, now fixed in 3d (Herbert Sauro)

3. General bug fixes, small updates to Inspector, JDesigner and Jarnac.(Herbert Sauro)


Changes in Release 3c
----------------------------------

1. Fixed bug in SBML output from Jarnac, failed to write out global
parameters to SBML (user reported bug).

25 August 2004

Changes in Release 3b
----------------------------------

	JDesigner

1. Fixed a bug in SBML export window where repeated clicks of the copy
to clipboard button would result in multiple copies being concatenated
to the clipboard.

2. The lastest version of JDesigner supports Level 1 Version 2 of SBML
(User request)

Jarnac has a number of important fixes.

1. The Jacobian for networks containing conserved cycles was not In the
correct reduced form, it was instead just a section taken from the full
Jacobian.

2. The Gillespie method had a bug when reaction networks contained
bimolecular reactions.

3. A variety of cosmetic changes to the output formats.

Release 3a includes some fixes to the NOM module and the Inspector.
-------------------------------------------------------------------------------------------------------

1. The inspector would paste twice into the input edit boxes when a
user hit Ctrl-V. (Herbert Sauro)

2. The MathML conversion routines in the NOM did not test for invalid
MathML before attempting the conversion (Sri Paladugu).

Release 3 includes:
-----------------------------

1. New versions of JDesigner to fix some issues with Metatool
integration (Herbert Sauro).

2. New Metatool module to fix problem with empty reaction
blocks (Sri Paladugu).

3. New inspector (Herbert Sauro).

Release 2 includes:
-----------------------------

1. A new cross-platform (C++) version of Metatool (Sri Paladugu).
2. New update libSBML from Ben Bornstein.
3. Separation of the NOM and libSBML (Sri Paladugu)
4. Updates to JDesigner, Inspector and Jarnac (Herbert Sauro)
5. New SBML to FORTRAN translator (available as a plugin to JDesigner – Herbert Sauro)
6. Broker remote capabilities are now operational in this version (Frank Bergmann)
7. Command line based Module Tester (Sri Paladugu).