BioNetGen-2.7.1

Minor updates

• Updated underlying NFsim version. Please see this NFsim release for more information.

BioNetGen-2.7.0

New Features

• Added graphml export support to visualize command. Added a new argument to visualize
  called outType. outType accepts either gml or graphml as input. The default graph output
  type is now changed to graphml.

BioNetGen-2.6.0

New Features

• We have added a new built-in function TFUN(counter, "path/to/data.dat") where counter is either an observable or another function and "path/to/data.dat" is a string pointing to a data file. The format of the data file is structured as a simple 2 column, white space separated data file (see here for an example). The first column is the value of the observable TFUN will match to and the second column is the value TFUN will return. The TFUN function can use either observables or functions as a counter value and TFUN can be used in functions like any other built-in function. TFUN is currently only supported for NFsim simulations and BNG will error out if TFUN is used in a model with network generation or ODE/SSA simulation calls.

BioNetGen-2.5.2

Bug Fixes

• Fixed a bug in the SBML export of compartmental models where the compartment of the reaction was not exported to the kinetic law of the reaction, resulting in incorrect dynamics.

BioNetGen-2.5.1

Minor changes

• NFSim XML parameters now contain the string of the original expression to allow other parsers to read the original parameter expression as well as the parameter value.

Bug Fixes

• Fixed a bug in 'RxnRule::build_reaction' so that BNG now quits if an explicit Species Compartment in a rule is not compatible with the inferred Species Compartment.

BioNetGen-2.5.0

New Features

• Due to popular demand we have added a new built-in function mratio(a,b,z) that calculates the ratio of Kummer hypergeometric functions M(a+1,b+1,z)/M(a,b,z) to within a small tolerance. The function can be used in both the parameters and functions blocks and is useful for calculating the mean and variance of the steady-state number of C molecules in the simple kinetic scheme A + B <-> C. See confluent hypergeometric function for further details.

Minor changes

• Changed the name of HAS (heterogeneous adaptive scaling) to PSA (partial scaling algorithm) and scalelevel option is now changed to poplevel

Bug Fixes

• Fixed a bug in run_network so that the code now quits if an unrecognized command line argument is encountered.
• Fixed a bug where writeMfile function did not automatically handle rateLaw parameters and functions.

BioNetGen-2.4.0+win-shared-libs

Bug Fixes

• Added two missing .dll files to Windows bundle to make NFSim.exe stand alone.

BioNetGen-2.4.0

New Features

• Heterogeneous adaptive scaling method is implemented
• Support for exporting multi state and multi component SBML files added

Minor changes

• Reworked the build process and added instructions

Bug Fixes

• Small change to Expression::getName() to not create a new local function if the rate law already starts with the _rateLaw prefix. This prevents BNG from continually making new functions every time a model is read back in.
• Fixed a bug with reactants or the products that are just "0" not being correctly written in the reactions block of output .net files.

BioNetGen-2.3.0

Merge pull request #185 from RuleWorld/release

Merge Release into Master

BioNetGen 2.2.6-stable

CHANGES to BioNetGen
updated 22 June 2015
https://github.com/RuleWorld/bionetgen/

== BioNetGen-2.2.6-stable ==
'''''2015 June 22'''''

==== New Language Conventions ====

• Whitespace is no longer allowed in rule names.
• All labels and BNG objects (except for bonds and states) must begin with a letter or underscore character.
• Labels must now be followed by a colon (':') with no intervening whitespace.
  ** Example: RuleX: A(s0) -> A(s1) k
• Leading indices in the molecule types, observables, and energy patterns blocks have been deprecated.
  ** '''Note''': These are not yet formally deprecated for the parameters, species, and functions blocks because they exist within BNG-generated NET files, which can be read in using readFile. Deprecating them completely will thus require changing the format of NET files.
• Unnamed rules are now given automatic names beginning with "_R" followed by a digit (e.g., "_R1", "_R2", etc.).
• Reverse rules are now named by prepending "reverse" to the forward rule name.

===== Actions & Arguments =====

• Added a new argument, par_scan_vals, to the parameter_scan action to allow parameter scans over unevenly spaced intervals.
  ** Example: parameter_scan({method=>"ode", t_end=>20, parameter=>"k1", par_scan_vals=>[1,5,20]})
  ** NOTE: If par_min, par_max, and n_scan_pts
  are all defined, they will take precedence over par_scan_vals if it is defined.

==== Minor Changes ====

• Both the BioNetGen version and codename (e.g., "2.2.6-stable") are now included in the headers of files written with writeBNGL (e.g., NET files).
• validate_examples.pl now ignores trailing comments in file comparisons.
• Windows executables now contain the bitness of the architecture in their names
  (e.g., run_network_MSWin32-64bit.exe).
• The run_network and sbmlTranslator executables no longer contain the architecture they are built for within the file name definition.

==== Bug Fixes ====

• An error is now thrown if an unrecognized block name is encountered.
• An error is now thrown if duplicate rule names are detected.
• Fixes a case where synthesis rules in cBNGL would fail if the product used the compartment prefix notation.