cy3sbml-v0.3.0 - SBML for Cytoscape

Bugfix and dependency release

• bugfixes
• updated dependencies

cy3sbml-v0.2.7

v0.2.7 [2017/11/12]

Bugfix and dependency release

• bugfixes
• updated dependencies

cy3sbml-v0.2.6

Major bugfix release to handle EBI https and Uniprot https.

• bugfixes
• updated dependencies
• cleanup of unused functionality and dependencies

cy3sbml-v0.2.5

• Bug fixes
• Updated UniProt Information
• Updated HTML display
• Updated VisualStyles
• Tested with latest bigg models (v1.3)

cy3sbml-v0.2.2

v0.2.2 [2016/08/10]

• Complete redesign of information pane (JavaFx instead of Swing with CSS, JS and HTML)
• HTML export of information
• Ontology information retrieved via Ontology Lookup Service
• Proper formating and display of raw xml in annotations
• Support of KineticLaws
• Offline MIRIAM with latest MIRIAM registry (faster access & reduced webservice calls)
• Improved visual styles (distinguish reversible & irreversible reactions)
• Fixed name attributes
• Improved compatibility to SBMLCore reader (identical attributes)
• Updated icons
• UniProt secondary information for RDF
• Caching of webservice information from OLS and UniProt
• Support of *.sbml files
• Multitude of bug fixes
• Improved session saving & loading (now with layout information)
• Unittest coverage increased to 37%
• Simplified maven dependencies
• Testing of serialization & deserialization
• Updated and tested sbml-test-suite 3.2.0
• Licence update to LGPL v3.0
• Dependencies updated
• Improved logging

MD5
06679f0573e736580883de92c815a44a  cy3sbml-0.2.2.jar
SHA1
058518bc27067158d81335ef833b5378fea216c2  cy3sbml-0.2.2.jar
SHA256
3a0b848288f5149bada7a0d4ee5a6fef8f1fcab65ecdf932f6b17a778e1b2af1  cy3sbml-0.2.2.jar

bugfix release

• bug fixes (autofocus)

MD5
f8ca1d075950fb17cb4e121d3c062e37  cy3sbml-0.2.1.jar
SHA1
b16fc4ab26bf99d15c0741619ae0d078899095fa  cy3sbml-0.2.1.jar
SHA256
4f85830fbc1166b0cd857ca3d67fe71d9d52b74d5895c4cae610fe3f691c2aae  cy3sbml-0.2.1.jar

bugfix release

• logging bugfixes

cy3sabiork & Testing release

v0.1.9 [2016/06/28]

• updated test models to BiGG v1.2
• updated test BioModels to release 30
• improved unit tests against test models
• bug fixes related to new test models, SBOTerms, LocalParameters & annotations
• additional support for cy3sabiork
• updated JSBML dependencies and pom files

Bug fix release & cy3sabiork support

v0.1.8 [2016/06/07]

• visualStyles for new and reopened sessions
• display of RDF & non-RDF annotation information
• kineticLaws as first class objects (with annotation display)
• FunctionDefinitions are now parsed correctly
• refactoring of CyNode to SBase mapping (performance increase)
• multitude of smaller bugfixes

Visual representation (layout & styles)

v0.1.7 [2016/03/24]

• position saving and restoring ported from cy2sbml (saving & restoring layouts)
• dark VisualStyle implemented (cy3sbml-dark)
• improved visual styles & dynamic compartment colors
• saving and restoring of full session with SBML files
• COBRA information parsed into attributes
• multiple bugfixes
• first version of cofactor nodes
• tested with Cy3.3 and Cy3.4-milestone-2