cy3sbml - cy3sbml-v0.4.0 - SBML for Cytoscape

Release notes for cy3sbml v0.4.0

We are pleased to release a new version of cy3sbml including the following changes:

• updated documentation
• updated licensing (MIT)
• library updates

Your cy3sbml team

- Java
Published by matthiaskoenig 12 months ago

cy3sbml - cy3sbml-v0.3.0 - SBML for Cytoscape

Bugfix and dependency release * bugfixes * updated dependencies

- Java
Published by matthiaskoenig over 6 years ago

cy3sbml - cy3sbml-v0.2.7

v0.2.7 [2017/11/12]

Bugfix and dependency release * bugfixes * updated dependencies

- Java
Published by matthiaskoenig over 8 years ago

cy3sbml - cy3sbml-v0.2.6

Major bugfix release to handle EBI https and Uniprot https. - bugfixes - updated dependencies - cleanup of unused functionality and dependencies

- Java
Published by matthiaskoenig over 8 years ago

cy3sbml - cy3sbml-v0.2.5

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

- Java
Published by matthiaskoenig over 8 years ago

cy3sbml - 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

- Java
Published by matthiaskoenig over 9 years ago

cy3sbml - 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

- Java
Published by matthiaskoenig over 9 years ago

cy3sbml - bugfix release

• logging bugfixes

- Java
Published by matthiaskoenig over 9 years ago

cy3sbml - 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

- Java
Published by matthiaskoenig over 9 years ago

cy3sbml - 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

- Java
Published by matthiaskoenig over 9 years ago

cy3sbml - 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

- Java
Published by matthiaskoenig almost 10 years ago

cy3sbml - Test & bugfix release

v0.1.6 [2015/08/27] Full testing of large scale model repositories and fixing of discovered bugs. - Testing, bug fixes and documentation - sbml-test-cases models successfully parsed - BIGG models successfully parsed - cobrapy test models parsed - full SBML FBC v2 support - basic SBML distrib support

- Java
Published by matthiaskoenig over 10 years ago

cy3sbml - FBC support, SBML Validator, SBML master graph

• SBO Name and definitions for information
• Parsing of rateRules, InitialAssignments and kineticLaws
• Display of NamedSBase attributes in information
• Example loader (menu) & examples added
• FBC support
• NetworkReader tests (passed all BioModels r29 curated models)
• master SBML graph (compartments, kinetics, parameters, ...)
• File selection & multiple file import ported
• SBML validator ported

- Java
Published by matthiaskoenig over 10 years ago

cy3sbml - Biomodel Webservice & Qual release

• support of multiple networks, views and subnetworks
• qualitative model support
• biomodel webservice search & retrieval
• redesign & bug fixes

- Java
Published by matthiaskoenig over 10 years ago

cy3sbml - Release of cy3sbml core functionality

Porting of core parts of cy3sbml are finished. Amongst others - cy3sbml VisualStyles implemented and applied - Support of multiple networks and views (sub networks) - Model information is now displayed - RDF annotations displayed (MIRIAM) - proxy support - first unit tests created and integrated with maven - logging with log4j and slf4j implemented (cy3sbml.log) - support of cy3sbml properties for general settings like preferred VisualStyle - node EventListener for updating annotation information - application of layout after generating views

- Java
Published by matthiaskoenig over 10 years ago

cy3sbml - Documentation Update Release

Detailed build instructions and documentation added.

- Java
Published by matthiaskoenig over 10 years ago