Release Notes

From BioNetWiki

(starting with version 2.0.34)

Contents 1 2.0.46 2 2.0.45 3 2.0.44 4 2.0.41 5 2.0.40 6 2.0.39 7 2.0.38 8 2.0.37 9 2.0.36 10 2.0.35 11 2.0.34

2.0.46

• Stable version that allows component state mapping but retains checks for incomplete molecule specifications.

--Faeder 00:16, 6 July 2007 (MDT)

2.0.45

• This is an ALPHA release. It provides a temporary fix for an issue that prevents use of rules that map component states from reactant onto product molecules, which are required for metabolic label tracing.

--Faeder 09:28, 6 June 2007 (MDT)

2.0.44

• Optional syntax changes
  • Enclose model block in begin/end model
  • Omit rate constants in reaction rules – automatically generated.
  • Use arbitrary math expressions for initial concentrations and rate constants (not rate laws).
• Define observables based on stoichiometry of a single component.
• Ability to use HNauty for graph isomorphism checking using setOption command.

--Faeder 09:55, 28 March 2007 (MDT)

2.0.41

• Improved recognition of OS specific binaries using the $Config{myarch} variable in Perl.
• Fixed model naming in SBML files (path header is removed).

--Faeder 10:36, 8 November 2006 (MST)

2.0.40

• Now includes RuleBuilder GUI interface to BioNetGen.
• Back end executables for Linux, Mac, and Windows also provided in the default distribution.

2.0.39

• Fixes small bugs in reading of Expressions from parameter block.

2.0.38

• Fixes bug that appeared starting in 2.0.36 that reading of Reactions from a .NET file was broken. It also marks the first version to use the new Expression.pm module, which allows the use of simple math expressions in the parameter block. This version may be somewhat unstable due to incomplete testing of the Expression.pm and other related changes. --Faeder 21:31, 27 September 2006 (MDT)

2.0.37

• Fixes deleteMolecules bug. Also introduces stricter Molecule Type checking. If the Molecule types block is used, only molecules matching defined types will be allowed as seed species, in observables, or in reaction rules. You will also note that Compartments are now defined in the .net file. There is now a partial implementation of Compartments, but the next release will fully implement these capabilities, and will be accompanied by documentation of the new syntax.

--Faeder 11:13, 13 September 2006 (MDT)

2.0.36

• Fixes Sat/MM bug involving reactions that use MM and Sat RateLaws in which reactant order was not preserved in the generated reactions.

2.0.35

• Fixed the Dimer dissociation bug, which resulted from improper checking of product connectivity when molecules were deleted in a reaction. The bug could only arise in a rule in which a molecule is deleted, but it is otherwise difficult to anticipate. Updating to this version is therefore strongly recommended.

--Faeder 00:53, 27 July 2006 (MDT)

2.0.34

• Fixed bug in handling of include/exclude directives that allowed reactions that should have been excluded. A test input file that demonstrates the bug is here.
• Added a java plotting utility called PhiBPlot for plotting CDAT and GDAT files.

--Faeder 12:11, 11 July 2006 (MDT)