@ASinanSaglam ASinanSaglam released this Oct 17, 2018 · 1 commit to master since this release

Assets 5

CHANGES to BioNetGen
updated 23 October 2018

== BioNetGen-2.4.0 ==
'''''2018 October 25'''''

==== 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.
Oct 17, 2018
Update atomizer version
Aug 3, 2017
Fix up documentation.

@rhclark rhclark released this Apr 28, 2017 · 414 commits to master since this release

Assets 2
Merge pull request #185 from RuleWorld/release

Merge Release into Master
Assets 2

CHANGES to BioNetGen
updated 22 June 2015

== 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.
Jun 22, 2015
Update CHANGES.txt

@lh64 lh64 released this Jul 1, 2015 · 1060 commits to master since this release

Assets 2

== BioNetGen-2.2.6-testing ==
'''''2015 March 3'''''

==== New Features ====

===== SBML-to-BNGL Translator =====

  • The SBML-to-BNGL translator can perform both a flat (one-to-one) translation
    of an SBML model in terms of unstructured species and an "atomized" translation
    that recovers the implicit molecular structure (binding sites and states) of the
    species within the model. The translator can be accessed in the following three ways:

    Using the readFile() BioNetGen action: The 'atomize' argument specifies whether a

    flat or atomized translation is to be performed (default is flat, i.e.,
    atomize). The translated model is written to [sbml_filename].bngl,
    which is then read and loaded into memory. This allows additional actions [e.g., simulate(),
    parameter_scan()] to be performed on the model if desired. See the
    [[BioNetGen_Actions_and_Arguments | BioNetGen Actions & Arguments Guide]] for a comprehensive
    listing of all actions and arguments, including readFile().

    Running the [BNGPATH]/bin/sbmlTranslator executable directly:

    This provides the functionality described above along with additional customization flags.
    Run ./sbmlTranslator --help> for a complete list of options with descriptions.

    As a standalone web application at [http://ratomizer.appspot.com/translate http://ratomizer.appspot.com/translate].

For further information, see the SBML-to-BNGL documentation.

===== Visualization Tools =====

  • Visualization tools can be accessed by calling the visualize() action in a BNGL model file
    or running the visualize.pl script included in
    [BNGPATH]/Perl2/Visualization. The output is generated in Graph Modeling
    Language (GML) format, which can be processed by graph editors such as yEd
    ([http://www.yworks.com/yed www.yworks.com/yed]) and Cytoscape
    ([http://www.cytoscape.org www.cytoscape.org]). Currently supported visualizations are:
    ** Model visualization as a contact map: >visualize({type=>"contactmap"})
    ** Model visualization as a regulatory graph: visualize({type=>"regulatory"})
    ** Rule visualization as a Petri net: visualize({type=>"ruleviz_pattern"})
    ** Rule visualization using graph operations: visualize({type=>"ruleviz_operation"})

For further information, call visualize({help=>1}) or run ./visualize.pl --help.

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

  • Added a 'reset_conc' argument to parameter_scan() that suppresses the call to resetConcentrations()
    if set to 0 (default value is 1). This allows simulations in the scan to be started from the end point
    of the previous simulation (used in bifurcate(); see below).
  • Added a new bifurcate() action that takes the same arguments as parameter_scan() (except 'reset_conc').
    The method automatically runs two scans, one from 'par_min' to 'par_max' and the other in the reverse
    direction. Each simulation in the scans starts from the end point of the previous simulation by passing
    reset_conc=>0 to parameter_scan(). Output files are then generated for each observable
    containing the parameter values vs. final observable values for both forward and reverse directions.
  • Modified readFile() to allow specific model blocks to be read using the 'blocks' argument.
    ** Example: readFile({file=>"mymodel.bngl",blocks=>["parameters","seed species"]})
  • Added support for method=>"nf" in simulate(). This allows NFsim to be used in
    parameter_scan() and bifurcate() as well.
  • Added support for compartments in writeSBML() and upgraded the supported version of SBML to Level 2 Version 3.

==== Minor Changes ====

  • Upgraded muParser ([http://muparser.beltoforion.de http://muparser.beltoforion.de]) to version 2.2.4.
  • Modified parameter_scan() to set get_final_state=>0 if reset_conc=>1
    (the default). This prevents BNG from unnecessarily reading in the final species populations at the end of
    NFsim simulations if they are going to be reset anyway. This is important as the read step can be extremely
    expensive for models with high degrees of symmetry.
  • Modified setConcentration() to retain parameter names in expressions (rather than evaluating to a number).
    This allows setConcentration() to be used with parameter_scan(). However, observables and functions are
    still evaluated to numbers.
  • Modified NET file output to list all rules that generate a given reaction in the comment following each
    line of the reactions block. This is useful when a reaction is generated by multiple
    different rules. Often this is unintentional and can be problematic since BNG multiplies the rate constant
    by the number of duplicates generated. Listing all rules that generate a reaction can help identify and
    debug situations like this.
  • Added a default PLA configuration for simulate(method=>"pla"). If the 'pla_config'
    argument is not defined, the configuration is set to fEuler|pre-neg:sb|eps=0.03, i.e.,
    a standard tau-leaping method (1st order) with species-based preleap tau calculations, negative-population
    postleap checking, and error control parameter 'eps' of 0.03.
  • Modified validate_examples.pl to only report a stochastic validation failure if the
    validation fails twice in a row.
  • Added functionality to readFile() to convert forward slashes (/) to back slashes (), and vice versa,
    in '''''relative''''' paths, depending on the OS. This improves cross-platform portability and makes it
    easier to share models.

==== Bug Fixes ====

  • An error is now thrown if zero-order synthesis products do not have compartments.
  • BNG will no longer switch to "compartmental" mode if the compartments block is empty.
  • Expressions for compartment volumes are now correctly evaluated when generating a BNG-XML file.
  • Fixed an inconsistency where forward referencing of parameters/observables was allowed for functions
    defined in the functions block but not in the reaction rules block.
  • Fixed a bug where in rare cases a function defined in the reaction rules block would
    be typed as a 'ConstantExpression'. This would cause simulation to fail since it would be placed in the
    parameters block of the generated NET file.
  • Fixed a bug in the handling of 'max_stoich' constraints. In versions 2.2.3, 2.2.4, and 2.2.5, the
    constraints were sometimes ignored during network generation and complexes larger than the maximum
    specified could be constructed. Also added code to check that molecule names passed in the argument are
    valid. This is useful since users often specify patterns, such as 'A()', rather than the actual molecule
    name 'A'. Without an error message this can cause confusion.
  • Fixed a bug where BNG was not passing to NFsim the random seed that it was generating when the 'seed'
    argument was not explicitly set by the user. This made it difficult to debug problems in NFsim since it
    was not outputting a random seed in the error messages.
Aug 7, 2013
Jul 22, 2013