Software

BioSpice. Aim: cellular pathways. Features: pathways are graphically represented, access to databases. Models: 3D fluid-mechanical systems. Language: Matlab/Java - open source software. People: Adam Arkin, project director of Berkeley BioSpice Network Representation and Modeling System (NRMS), see also here

Cellerator. Aim: interacting signal transduction networks. Features: biological modeling via automated equation generation. Models: (ordinary) differential equations. Language: Mathematica. "People": Jet Propulsion Laboratory, California Institute of Technology

E-Cell. Aim: Modeling and simulation environment for biochemical and genetic processes. Features: functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression, other features of cellular metabolism. Models: deterministic ODEs, discrete stochastic systems, many components driven by multiple algorithms with different timescales. Language: C++. People: Masaru Tomita at the Institute for Advanced Biosciences, Keio University

FluxAnalyzer. Aim: A graphical interface for Metabolic Flux Analysis (MFA). Features: Stoichiometric analysis and determination of flux distributions in metabolic networks Models: abstract (symbolic) network representation, network graphics visualizing the metabolic network (metabolic maps). Language: MATLAB - free for academic users. People: Steffen Klamt, Systems Biology group of Ernst Dieter Gilles, MPI "Dynamics of Complex Technical Systems", Magdeburg

Gepasi. Aim: Modeling biochemical systems. Features: many compartments with different volumes, tools to fit models to data, optimize any function of the model, metabolic control analysis, linear stability analysis, parameter studies, SBML support Models: matrices and differential equationsLanguage: source code in C, user interface using Microsoft Windows - free software. People: Pedro Mendes at Aberystwyth Quantitative Biology and Analytical Biotechnology Group, University of Wales Aberystwyth

MCell. Aim: A General Monte Carlo Simulator of Cellular Microphysiology. Features: so far the focus has been on one aspect of biological signal transduction, namely the microphysiology of synaptic transmission. Models: Simulations are positioned at a biological scale above molecular dynamics but below whole cell and higher level studies; Diffusion of individual ligand molecules by Brownian dynamics random walk algorithm, and bulk solution rate constants are converted into Monte Carlo probabilities so that the diffusing ligands can undergo stochastic chemical interactions with individual binding sites such as receptor proteins, enzymes, transporters, etc.Language: obtained as a machine-specific executable program - free software (copying and/or editing of MCell without the authors' consent is expressly forbidden). People: Tom Bartol at Computational Neurobiology Laboratory (CLN) at Salk Institue and Joel R. Stiles at Biomedical Applications, Pittsburgh Supercomputing Center

Metabolizer. Aim: Simulation of complex biological systems Features: Integration of deterministic and stoachastic simulation techniques of metabolic networks into a hybrid simulator, SBML support. Models: Gillespie's first reaction method; ODEs and PDEs models are planed. Language: Java People: Markus Schwehm Department of Computer Architecture, University of Tübingen

ProMoT/DIVA. Aim: Structured dynamic simulation models Features: symbolic transformations, optimization. Models: differential and algebraic rate equations. Language: Lisp/Java - free software under Linux/Unix. People: Virtual Biological Laboratory: Martin Ginkel, Andreas Kremling, Torsten Nutsch at MPI "Dynamics of Complex Technical Systems", Magdeburg

ScrumPy. Aim: biochemical modelling. Features: steady-state determination, time-course simulation, MCA functions, determination of Elementary Modes and enzyme subsets. Language: Python - open-source . People: Metabolic Control Analysis Research Group, Oxford Brookes University, UK

Stochastirator. Aim: chemical and biological reaction networks. Features: stochastic mathematical framework. Language: C++. People: Eric Lyons, Larry Lok

StochSim. Aim: general purpose biochemical simulator Features: individual molecules or molecular complexes are represented as individual software objects; reactions between molecules occur stochastically (employing "pseudo-molecules"). Multiple states of molecules (conformational state, ligand binding, phosphorylation, methylation, or other covalent modification). Models: random selection of two molecules. Language: platform-independent core simulation engine People: Carl Firth (formerly Carl Morton-Firth), Computational cell biology group at the Department of Zoology of the University of Cambridge (USA)

STOCKS. Aim: STOChastic Kinetic Simulation of biochemical processes to simulate time evolution of the system composed of large number of first and second order chemical reactions. Features: several cellular generations using linearly growing volume of reaction environment and simple model of cell division. Substance in equilibrium modelled as random pools with Gaussian distribution. Models: Gillespie's direct method Language: C++ under Unix/Linux - public domain (GNU GPL) software. People: Andrzej M. Kierzek, Institute of Biochemistry and Biophysics, Warszawa

Virtual Cell. Aim: remote user modeling and simulation environment to create biological models of various types and run simulations on a remote server. A transparent general purpose solver is used to translate the initial biological description into a set of concise mathematical problems. Features: mathematical simplification using pseudo-steady approximations and mass conservation relationships. Language: Java based graphical interface. People: Jim Schaff (Virtual Cell Developer) at National Resource for Cell Analysis and Modeling, NRCAM

SBW. "The Systems Biology Workbench (SBW) is a modular, broker-based, message-passing framework for simplified application intercommunications." by ERATO Kitano Systems Biology Project. Contains a good list of links

Other programs are Jarnac (Herbert Sauro). STODE (Carel van Gend, Ursula Kummer). Furhtermore, METACON and EMPATH are no longer being developed, maintained or supported

Guide to Available Mathematical Software. "A cross-index and virtual repository of mathematical and statistical software components of use in computational science and engineering."

Sonstige Internet-Ressourcen

BioMedNet a portal to live sciences. PubMed PubMed, a service of the National Library of Medicine, provides access to over 12 million MEDLINE citations back to the mid-1960's and additional life science journals. PubMed includes links to many sites providing full text articles and other related resources