Biochemical

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded...

Scaffold Hunter is an accessible Java-based application built for the analysis of structure-related biochemical data. The program is able to facilitate the interactive exploration of chemical space by enabling generation of and navigation in a scaffold tree hierarchy annotated with various...

rxncon is a specialized program that's been designed to generate contingency matrices. rxncon can also generate graphical representations of biochemical signaling networks. As its input it uses specially formatted Excel files. To start using rxncon you first have to upload a specially formated...


Platforms: Windows

PyBact is a Python written program designed for bacterial identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test


Platforms: Windows

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host...


Platforms: *nix

ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.


Platforms: Mac, Linux

HalX is a LIMS (Laboratory Information Management System). It is meant to be able to keep track of all the experimental details of any type of biochemical, molecular biology or structural biology experiment (but not all are available now...)


Platforms: Windows, Mac, Linux

StochPy (Stochastic modelling in Python) is an easy-to-use package, which provides several stochastic simulation algorithms (SSAs), which can be used to simulate biochemical systems in a stochastic manner. Further, several unique and easy-to-use analysis techniques are provided by StochPy....


Platforms: Linux

StochPy (Stochastic modelling in Python) is an easy-to-use package, which provides several stochastic simulation algorithms (SSAs), which can be used to simulate biochemical systems in a stochastic manner. Further, several unique and easy-to-use analysis techniques are provided by StochPy....


Platforms: Mac

StochPy (Stochastic modelling in Python) is an easy-to-use package, which provides several stochastic simulation algorithms (SSAs), which can be used to simulate biochemical systems in a stochastic manner. Further, several unique and easy-to-use analysis techniques are provided by StochPy....


Platforms: Windows

QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.


Platforms: Windows, Mac, BSD, Linux

A command-line biochemical network compiler for systems biology.


Platforms: Windows, Mac, Linux

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.


Platforms: Windows, Mac, BSD, Linux

A Perl Extension for modeling enzymatic (biochemical) reaction networks


Platforms: Windows, Mac, Linux

Stability of the system obtained from the a typical biochemical network was checked using simulink


Platforms: Matlab

A rule-based modelling framework for allosteric proteins and biochemical networks.


Platforms: Windows, Mac, Linux

Cellontro models and simulates cells, other biological entities, and biochemical networks. Specify your models using XML and Java, or SBML. Cellontro is now completely contained within the Xholon sourceforge project.


Platforms: Windows, Mac, Linux

Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.


Platforms: *nix

The Biochemical Abstract Machine (BioCham) is a modelling environment for systems biology, with some unique features for static analysis or for inferring unknown model parameters from temporal logic constraints. BioCham is mainly composed of : a rule-based language for modeling biochemical...


Platforms: Mac

MetMAP is a MATLAB Toolbox for Metabolical Modeling, Analysis and oPtimization (Met. M. A. P.).You can use this package to study metabolical systems from a theoretical point of view, analysing the pathway's structure and dynamics, but you can also use it for biotechnological purposes, evaluating...


Platforms: Matlab