Release Notes

From BioNetWiki

(starting with version 2.0.34)

Contents 1 2.1.5 2 2.1.4 3 2.1.3 4 2.1.2 5 2.1.1 6 2.1.0 7 2.0.48 8 2.0.46 9 2.0.45 10 2.0.44 11 2.0.41 12 2.0.40 13 2.0.39 14 2.0.38 15 2.0.37 16 2.0.36 17 2.0.35 18 2.0.34

2.1.5

• Implements all compartmental features described in the Winter Simulation Conference paper.
  • location of synthesized molecules is inferred, if not specified explicitly.
  • species location context in binding/unbinding rules is now permitted.
• Binaries are not compiled: after opening the archive file, type "make" in the root directory.
• Some output formats supported for compartments: BNGL, Matlab M-file, and XML. (Note that rule models, but not reaction networks, are supported in XML. This is true for compartmental and non-compartmental models.) SBML is not currently supported for compartmental models.
• Saturation, Michaelis-Menten, and Hill-type rate laws are implemented for non-compartmental models, but these rate laws will not work correctly in a compartmental model (fix coming soon).
• Older versions of Motivating_example_cBNGL.bngl have a slight incompatibility (please download the latest version here): abstract molecules used as sinks or sources must have a compartment location, even if it is irrelevant.
• If reactant patterns in a rule have partial overlap, the symmetry factor for reaction rates may be calculated incorrectly. E.g. R(a) + R(a,b~pY) -> R(a!1).R(a!1,b~pY) will be handled incorrectly when the first reactant also matches the second pattern. This is a legacy issue--the problem exists in all previous versions. This type of rule is not very common, so most models are unaffected.

2.1.4

• Fixed bug in symmetry handling in synthesis reactions.
• Some improvements to the NFsim interface (NFsim is not yet included in the public distributions).

2.1.3

• Added Hill rate law (usage is Hill(k,K,n), which gives a rate of k*x1^n/(K^n+x1^n)). This rate law works only with simulate_ode and simulate_ssa, and not with NFsim, Matlab, or XML output. Here is an example file the demonstrates use of the Hill function.

2.1.2

• Fixed non-elementary rate laws.

2.1.1

• Bug notice: Non-elementary rate laws are broken in this version. This bug is fixed in the next release (2.1.2). Support for these rate law types is considered legacy and users are encouraged to switch to using Function notation, which will be introduced at the time NFsim is released.

2.1.0

• Implements compartmental BNGL (cBNGL), see Wsc09.
• -log option to BNG2.pl automatically generates log file without redirect.
• Improved Matlab output.
• Outputs XML format that is compatible with NFsim and GetBonNie.
• Resolves reaction center and context to alleviate symmetry issues (some issues remain - multiple ways to satisfy rule context no longer multiples the reaction rate, but symmetries in rule context are not counted correctly).
• Doesn't include binaries, which have to be made from source (type 'make' in the root directory of the distribution).
• Default compartment location for molecule synthesis not yet implemented. At present, all synthesized molecules must have an explicit compartment location included in the product side of the rule.
• SBML output does not support compartments.
• The "$" operator and a species location prefix "@C:" cannot be used together on a reactant or product in a rule.
• Bug notice: This version does not correctly handle symmetry in the context of a rule that is not broken by application of the rule, as in the example

R(l)+L(r,r,r) -> R(l!1).L(r!1,r,r) kp1, km1. The correct multiplicity of this reaction is 3 (if R is monovalent), but BNG 2.1.0 gives the reaction a multiplicity of 3/2. This problem is fixed in version 2.1.1. For now, the fix is to manually correct the multiplicity by adding multiplicative factors in the rate law. For the example above, the correct rate constants would be 2*kp1 and 2*km1.

2.0.48

• run_network executable under Mac OS X is not optimized for performance on Intel processors. Recompile by typing 'make' in distribution directory.

2.0.46

• run_network executable under Mac OS X is not optimized for performance on Intel processors. Recompile by typing 'make' in distribution directory.
• 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)