Biological software supporting BioPAX

In addition to the databases supporting BioPAX listed on BioPAX Database Conversion Status, the following biological software tools support BioPAX. If you have a tool that supports BioPAX, please add it to the list.

Libraries

 * Paxtools - Paxtools provides a complete domain object model (DOM) in Java that enables users manipulating and evaluating BioPAX models easily. It also facilitates using state-of-the-art software technologies that require a DOM such as Java Persistence API or Java Message Service. Finally Paxtools implement a fail-fast validation framework, mitigating the cost of potential pitfalls for the developers. Paxtools was designed to be modular, lightweight and platform independent to be easily embedded into applications. Paxtools is currently in development at BioPAX sourceforge site.
 * BiNoM - see description below
 * BioPAX Validator - an open source application and API aimed at BioPAX Level3 data validation (conversion and normalization may be added in next versions).
 * rBiopaxParser
 * BioPAX-pattern - an open source library for defining and searching graph patterns in a BioPAX model.

Pathway/Network Visualization and Analysis

 * Cytoscape - Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.  Supports (via BioPAX plugin) input from file or URL and layout of BioPAX pathway information.
 * Pathway Tools - The Pathway Tools is a reusable, production quality software environment for creating a type of model-organism databases (MOD) called a Pathway/Genome Database (PGDB). A PGDB integrates an evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism.
 * PATIKA - Pathway layout and editing. Features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. Supports export of PATIKA information in BioPAX format.
 * VisANT - Biological network and pathway visualization and analysis tool integrated with a database of biological relationships for many different species. Supports BioPAX input from file or URL and layout of BioPAX pathway information.
 * BCDE - Biological Concept Diagram Editor (BCDE) is a tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes. Besides standard diagramming functions, it has powerful data capture and annotation capabilities. BCDE is compatible with BioPAX and it also exports to Powerpoint and Visio.
 * BiNoM - is a Cytoscape plugin distributed under LGPL, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. In particular, BiNoM allows importing, exporting, editing, merging BioPAX files, and can query huge BioPAX files such as whole Reactome or NetPath databases. It also provides CellDesigner->BioPAX, BioPAX->SBML(level2) conversion. BiNoM can be also used as a library independent from Cytoscape with various I/O and analysis functions. Extensive documentation and examples of use are provided.
 * ExPlain Analysis System - BioBase molecular profile analysis system. Supports loading BioPAX Pathways from external sources.
 * BioUML - starting from version 0.7.7 (support for BioPAX Level 2)
 * SHARKview
 * GeneSpring GX
 * ChiBE - Chisio BioPAX Editor. Visual notation is similar to SBGN-PD. Can run several graph queries on the BioPAX model. Auto-layout. Overlay data. Can talk to Pathway Commons, Gene Expression Omnibus, and cBio Portal.
 * CyPath2 - a Cytoscape 3 app.

Pathway Data Management

 * cPath - database software for local management of pathway information supporting PSI-MI and BioPAX L1/L2 formats. This was used to create original Pathway Commons resource.
 * cPath2 - free BioPAX Level3, Paxtools, Spring, JPA, BioPAX Validator, MIRIAM and Identifiers.org based software developed within Pathway Commons project to build and provide the new web services.
 * Biowarehouse - The BioWarehouse is a toolkit for constructing a warehouse of bioinformatics databases. It consists of a relational schema definition for bioinformatics datatypes, loaders for each component database, and Perl/SQL code to query the warehouse for testing and demonstrations. Both Oracle and MySQL are supported. The BioWarehouse contains a set of loader programs. Each loader reads one or more input database file(s), translates the data into the warehouse schema, and inserts the data into the warehouse database. The BioWarehouse also contains sample SQL and perl code to query the database. The BioPAX loader utilizes SPARQL and the Spring Framework to extract, transform, and load BioPAX queries into SQL.

Other

 * OHSU BioPAX validator - Open source (LGPL license) validator for Levels 1 and 2.
 * The Gateway to Biological Pathways Description at http://research.microsoft.com/workshops/escience2005/, video presentation at http://research.microsoft.com/workshops/escience2005/videos/12809/lecture.htm

Tools planning BioPAX support

 * The Semantic Synapse Portal - Portal for the visualisation of heterogenous OWL data with an emphasis on neuroscientific research. Planned date of support for BioPAX: 12/2005

Please add your tool and a note about the expected support date here if you plan to support BioPAX.