Pajek Writer – Generation of Structural Representation of Biochemical Processes in Format Pajek

Pajek Writer

:: DESCRIPTION

Pajek Writer – software for generation of structural representation of biochemical processes in format Pajek on a set of the proceeding reactions presented in the form of the list of biochemical reactions.

::DEVELOPER

Group of Molecular Genetic Systems Modeling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 Pajek Writer

:: MORE INFORMATION

Vernan – Specification, Construction, and Exact Reduction of State Transition System models of Biochemical Processes

Vernan

:: DESCRIPTION

Vernan is a MATLAB tool for the specification, construction, and exact reduction of state transition system models of biochemical processes

::DEVELOPER

The Virtual Physiological Rat Project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

 Vernan

:: MORE INFORMATION

Citation

Bugenhagen SM, Beard DA.
Specification, construction, and exact reduction of state transition system models of biochemical processes.
J. Chem. Phys. 137, 2012

CellPublisher 2.0 – Representations of Biochemical Processes

CellPublisher 2.0

:: DESCRIPTION

CellPublisher is a free and open program to make highly interactive representations of biochemical processes. It converts a file created in the popular modelling tool CellDesigner into a Google maps-based version inside a browser.

::DEVELOPER

Lope A. Flórez, Christoph R. Lammers, Raphael Michna and Jörg Stülke, Department of General Microbiology, Georg-August University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CellPublisher

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Dec 1;26(23):2997-9. Epub 2010 Oct 14.
CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways.
Flórez LA, Lammers CR, Michna R, Stülke J.

STOCKS 2.0 – STOChastic Kinetic Simulation of Biochemical Processes

STOCKS 2.0

:: DESCRIPTION

STOCKS (STOChastic Kinetic Simulation) is a public domain (GNU GPL) software for stochastic simulations of biochemical processes.

::DEVELOPER

STOCKS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • JAVA

:: DOWNLOAD

 STOCKS

:: MORE INFORMATION

Citation:

Kierzek A.M. (2002)
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.
Bioinformatics 18, 470-481

BioSPI – SIMULATION OF BIOCHEMICAL PROCESSES

BioSPI

:: DESCRIPTION

BioSPI is a computer application we have developed for simulating the behavior of biochemical systems specified in the pi calculus. It is based on the Logix system, which implements Flat Concurrent Prolog (FCP). The use of FCP allows both mobility and synchronized communication, two of the major features of the pi-calculus.  To the best of our knowledge this is the only implementation of the full synchronous calculus, including mixed choice.

::DEVELOPER

BioSPI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Sun Solaris/ Linux/SGI

:: DOWNLOAD

BioSPI

:: MORE INFORMATION

In order to obtain the PSI system, please write BioSPI Team, and specify your name, affiliation, and preferred platform.