Tag: BioPax

BioPAX2SBML – Translation of BioPAX into SBML including the Qualitative Models extension

BioPAX2SBML

:: DESCRIPTION

BioPAX2SBML is a  webtool. It is capable of properly translating BioPAX formats (Level 2 and 3) into SBML format (Level 3 Version 1 with qual) including reactions and relations in one model.

::DEVELOPER

the Interfaculty Institute for Biomedical Informatics (IBMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

  BioPAX2SBML

:: MORE INFORMATION

Citation

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, and Zell A.
Qualitative translation of relations from BioPAX to SBML.
Bioinformatics (2012) 28 (20): 2648-2653.

BioPAX-pattern 1.1.0 – Pattern search software for BioPAX models

BioPAX-pattern 1.1.0

:: DESCRIPTION

BioPAX-pattern is an open source and extensible framework for defining and searching graph patterns in BioPAX models.

::DEVELOPER

BioPAX-pattern team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BioPAX-pattern

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 1;30(1):139-40. doi: 10.1093/bioinformatics/btt539. Epub 2013 Sep 16.
Pattern search in BioPAX models.
Babur Ö , Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E.

VISIBIOweb 1.1 – pathway visualization software for BioPAX

VISIBIOweb 1.1

:: DESCRIPTION

VISIBIOweb is a free, open-source, web-based pathway visualization and layout services software for BioPAX (level 2) pathway models

::DEVELOPER

Bilkent Center for Bioinformatics

:: SCREENSHOTS

 VISIBIOweb

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 VISIBIOweb

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W150-4. doi: 10.1093/nar/gkq352. Epub 2010 May 11.
VISIBIOweb: visualization and layout services for BioPAX pathway models.
Dilek A1, Belviranli ME, Dogrusoz U.

ChiBE 2.2 – Chisio BioPAX Editor

ChiBE 2.2

:: DESCRIPTION

ChiBE (Chisio BioPAX Editor)is a free editing and visualization tool for pathway models represented by the BioPAX format, based on Chisio.

::DEVELOPER

Bilkent Center for Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 ChiBE

:: MORE INFORMATION

Citation

O. Babur, U. Dogrusoz, E. Demir, and C. Sander,
“ChiBE: interactive visualization and manipulation of BioPAX pathway models“,
Bioinformatics, 26(3), pp. 429-431, 2010.

Paxtools 5.1.0 / PaxtoolsR 1.26.0 – Accessing & Manipulating BioPAX Data

Paxtools 5.1.0 / PaxtoolsR 1.26.0

:: DESCRIPTION

Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. The Paxtools Java programming library for BioPAX has been developed to help software developers readily support the import, export and validation of BioPAX-formatted data for various uses in their software . Using Paxtools, a range of BioPAX-compatible software has been developed, including browsers, visualizers, querying engines, editors and converters

PaxtoolsR provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC).

::DEVELOPER

Computational Biology Center at MSKCC 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java / R/ BioConductor

:: DOWNLOAD

 Paxtools , PaxtoolsR

:: MORE INFORMATION

Citation:

PaxtoolsR: Pathway Analysis in R Using Pathway Commons.
Luna A, Babur Ö, Aksoy BA, Demir E, Sander C.
Bioinformatics. 2015 Dec 18. pii: btv733.

Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666

BioPAX level 3 – Biological Pathway Exchange Language

BioPAX level 3

:: DESCRIPTION

BioPAX (Biological Pathway Exchange) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

::DEVELOPER

BioPAX Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 BioPAX

:: MORE INFORMATION

Citation:

Demir et al.
The BioPAX community standard for pathway data sharing
Nature Biotechnology 28 , 935–942 (2010) doi:10.1038/nbt.1666

Sig2BioPAX v4 – Java tool for Converting Flat Text files to BioPAX Level 3 format

Sig2BioPAX v4

:: DESCRIPTION

Sig2BioPAX is a Java program that can be used to convert structured text files describing molecular interactions into the BioPAX Level 3 standard format.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

Sig2BioPAX

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Sig2BioPAX

:: MORE INFORMATION

Citation

Source Code Biol Med. 2011 Mar 21;6:5. doi: 10.1186/1751-0473-6-5.
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.
Webb RL, Ma’ayan A.

SBML Converters 20100413 – Conversions to & from SBML

SBML Converters 20100413

:: DESCRIPTION

SBML Converters are several converters which transfer SBML to BioPax 2 and 3, SBML to XPP and SBML to Octave, etc.

Converters list:

  • SBML to Octave  (GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.)
  • SBML to XPP (XPP-Aut is a numerical analysis software. It permits to solve differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.)
  • SBML to SciLab (SciLab is a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.)
  • SBML to CellML & CellML to SBML (CellML is an open standard based on the XML markup language like SBML. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The main difference between CellML and SBML is that the former is based on modules while the latter is based on hierarchical components.)
  • SBML to BioPax (The main objective of the BioPAX initiative is to develop a data exchange format for biological pathways that is flexible, extensible, optionally encapsulated and compatible with other standards and can be widely adopted in a timely manner.)
  • SBML to Dot (GraphViz is an open source graph visualization software. The language used to encode the graphics processed by GraphViz is called DOT. Note that a “dot” file can be used with other graphical software.)
  • SBML to SVG (Scalable Vector Graphics (SVG) is a language for describing two-dimensional graphics and graphical applications in XML. It is an open standard created by the World Wide Web Consortium.)

SBML Converters also have an online version.

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SBML Converters

:: MORE INFORMATION

Please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net