eBCSgen v2.2.0

• revised the logic of insert methods (insert_atomic_to_complex, insert_struct_to_complex, insert_atomic_to_struct) to enhance insertion validity and data integrity #91
• enabled the direct usage of complexes in abstract_sequence by modifying the grammar to support complex names as values #92
• model syntax changes: introduced flexibility in the order of sections in BCSL files, new lines are enforced and forbidden in specific places to prevent unclear model definition #94
• full support for bidirectional rules implemented by specifying distinct rates for each direction #96
• ensured that all referenced rule labels in used in regulations exist; restricted regular regulations to accept only valid regular expressions, not expressions consisting of regex characters #97
• expanded grammar to support rates as complex nested rational expression #100
• zooming syntax aligned with original BCSL: zooming uses ::, same as compartment specification, instead of :, syntax ambiguity solved by switching to Earley parser from LALR(1) #99
• added checks to ensure that all used complex aliases are defined before use, raising ComplexParsingError when mismatches are detected #105
• checking for uniqueness of atomic agents within structure agents #105
• defined replication rules to avoid complex replication checks in every rule #107
• implemented parsing for observables (pools and basic arithmetic scaling) #109
• organized test cases for both existing parsing functionalities and feature tests #78
• added test cases for parsing #85
• moved testing objects to objects_testing.py to eliminate redundancy and text models shifted to .txt files #90
• changed tests for rules (replication and bidirectional), syntax for zooming ::, etc; added parsing tests for new feature observables #109

eBCSgen v2.1.0

• changed output format of PCTL parameter synthesis from Storm stdout to a more general CSV file #65

eBCSgen v2.0.4

• fixed transforming rules #61
• created dockerfile with automatic CI build #62
• removed obsolete remote Storm calls #63

eBCSgen v2.0.3

• fixed minor bugs in SBML export #52

eBCSgen v2.0.2

• fixed correct error catching in parsing #54

eBCSgen v2.0.1

• fixed the replication type of rules (A -> 2A) #45
• fixed TransitionSystem.change_to_vector_backend usage in TS generating #50

eBCSgen 2.0

Version 2.0 of eBCSgen tool supporting the following new features:

• regulated models
• SBML-multi export
• CTL model checking

Additionally, overall quality of Galaxy related tools was improved, the tool is available on bioconda, and official documentation was deployed on ReadTheDocs.

eBCSgen package fix

• fixed setup.py file to correctly include whole package

eBCSgen with support of SBML export

• reorganised repository to be a proper Python package; updated conda environment file #46
• added support for SBML export (undocumented) #32
• improved several issues in supported syntax #34
• added ReadTheDocs documentation #48

New eBCSgen version with support of regulations

What is new:

• support of regulated models (undocumented)
• minor performance improvements
• transitions system instead of model as an input to PCTL analysis - allows to reuse the TS for multiple analysis runs
• support of CTL model checking
• created conda environment and automatic tests CI
• edited tutorial accordingly