BioNetGen-2.9.2

Minor changes

• Underlying NFsim version updated to version v1.14.2, please see here for changes.

BioNetGen-2.9.1

Fixes a bug that led to invalid SBML files being produced when there were internal variables in a BNGL models. These are produced when anything other than a simple parameter name is used in a RateLaw associated with a rule.

NOTE: These bundles do not include binaries for sbmlTranslator or library files for compiling and linking to the CVODE library. These files are included in previous release bundles if you need them. For import and atomization of SBML models we strongly suggest you use the Atomizer library and tools included in the latest release of PyBioNetGen. Its functionality and reliability is much greater than that of the old sbmlTranslator code.

NOTE2: The linux and mac bundles also contain older versions of the NFsim executable (v.1.12.1). If you need newer versions of NFsim, they can be retrieved from the bin directory of the previous release.

Full Changelog: BioNetGen-2.9.0...BioNetGen-2.9.1

BioNetGen-2.9.0

Major changes

• Species are exported to a SBML initial assignments block. Constant expressions are also exported in initial assignments block as long as they weren't a part of the original species block. This will improve the functionality of the exported SBML output for downstream tools.

Minor changes

• Referring to observables or functions within species will result in an error as it could lead to circular dependency.

BioNetGen-2.8.5

Minor changes

• Underlying NFsim version updated to version v1.14.0, please see here for changes.
• Bugfix: fix to issue #174 was causing multiple patterns with quantifiers to fail incorrectly. Multiple patterns with quantifiers are now correctly parsed with spaces or commas in between but multiple quantifiers within the same pattern is correctly caught and errors out.

BioNetGen-2.8.4

Minor changes

• Bugfix to issue #174 where observables of the form A==N.B==M were accepted but incorrectly parsed. These observables are no longer accepted and will produce an error.
• Bugfix to issue #180 where wildcard bonds in products could be broken, e.g. A(b!+) -> A(b) + B(a). This will now be detected, cause an error and quit.
• Bugfix to issue #189 where negative rate constants were accepted without warning. Rate constants will be evaluated and if they are negative, they will produce a warning but won't quit.

BioNetGen-2.8.3

Minor changes

• Minor bugfix where the parameter scan action didn't check if the parameter getting scanned was defined.

BioNetGen-2.8.2

Minor changes

• Changed observable and species name separators in writeCPYfile action

BioNetGen-2.8.1

New Features

• New action writeCPPfile writes a C++ header file that requires CVODE and encodes the model ODEs.
  This allows for ODE simulations of the model directly from other C++ software
• New action writeCPYfile writes a C file that requires CVODE and encodes the model ODEs.
  This allows for ODE simulations of the model directly from other C software. Additionally, this
  file is written with the Python ctypes module in mind, making it easier to make direct calls to
  a shared C library from Python.

Minor changes

• Updated underlying NFsim version to 1.2.2
• Minor bugfix where the reported unique species didn't account for certain species resulting in an incorrect count.

BioNetGen-2.8.0

New Features

• BNG-XML now exports the entire BNGL model and not just NFsim related features.
  This is to allow other software to read the XML instead of the BNGL model text.

BioNetGen-2.7.2

Minor updates

• BNG-XML now exports population maps and energy patterns for other software to read.