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Systems Biology Tools

Name Description Developer Publications Comment
3Omics 3Omics is a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. PUBMED JOURNAL
Biographer Biographer is a tool for web-based editing and rendering of SBGN compliant biochemical networks. The software enables visualizations based on the emerging standard Systems Biology Graphical Notation. Theoretical Biophysics Group Berlin PUBMED JOURNAL Biographer Project Website
Biological Simulation Program for Intra- and Inter-Cellular Evaluation (Bio-SPICE) Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. It is a comprehensive software environment that integrates a suite of analytical, simulation, and visualization tools and services to aid biological researchers engaged in building computable descriptions of cellular functions.
BioSmalltalk BioSmalltalk is a pure object system and library for bioinformatics. The Software enables to build bioinformatics scripts and applications using the Smalltalk programming environment. PUBMED JOURNAL
BioUML platform BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses.
CellDesigner CellDesigner is a modeling tool of biochemical networks. It is a structured diagram editor for drawing gene-regulatory and biochemical networks. JOURNAL JOURNAL
Condor-copasi Condor-COPASI is a web-based interface for integrating COPASI with the Condor High Throughput Computing (HTC) environment. It provides COPASI users with a simple environment for utilising the power of High Throughput Computing, without requiring any technical knowledge of Condor of other HTC tools. PUBMED JOURNAL
ContextNet ContextNet is based on a dynamic programming algorithm for identifying signalling paths linking proteins to their downstream target genes. ContextNet finds high-ranking context-sensitive paths in the interactome, thereby revealing the intermediate proteins in the path and their path-specific contexts. PUBMED JOURNAL
COPASI COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie‘s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. PUBMED JOURNAL
GRN2SBML GRN2SBML is a tool that aims to ease the encoding of gene regulatory networks (GRN) in the systems biology markup language (SBML) HKI Jena PUBMED JOURNAL
JSim JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim‘s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. National Simulation Resource at the University of Washington PUBMED JOURNAL
LibSBMLSim LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim is a simple command-line tool and provides several APIs to load an SBML model, perform numerical integration and export the results. Both explicit and implicit methods are supported. Funahashi Lab (Keio University) PUBMED JOURNAL
Lynx - an Integrated Systems Biology Platform Lynx is a database and knowledge extraction engine for integrative medicine. The platform supports the analysis of common heritable disorders from the systems biology perspective. Bioinformatics group (Gilliam Lab), University of Chicago
MeltDB MeltDB is a web-based software platform for the analysis and annotation of datasets from metabolomics experiments. MeltDB facilitates the integration and evaluation of existing preprocessing methods. The system provides researchers with means to consistently describe and store their experimental datasets. PUBMED JOURNAL
Metingear Metingear is an open source desktop application for creating and curating genome scale metabolic networks with chemical structure. PUBMED JOURNAL
Morpheus Morpheus is a modeling and simulation environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems to study multiscale and multicellular systems. Jörn Starruß & Walter de Back PUBMED JOURNAL
Network Portal Network Portal provides analysis and visualization tools for selected gene regulatory networks to aid researchers in biological discovery and hypothesis development.
ODEion ODEion is a software tool for structural identification of ordinary differential equations, where the model space is implicitly defined by arbitrary user-defined functions. The program searches for possible interactions between the variables and suggests a suitable form of the ODEs, including estimates of the parameters. Peter Gennemark & Dag Wedelin PUBMED JOURNAL
Paintomics Paintomics is a web tool for the integration and visualization of transcriptomics and metabolomics data. PUBMED JOURNAL
PathCase-SB Simulation and Composition Tools The Model Composition Tool (Interface) helps users compose systems biology models to facilitate the complex process of merging systems biology models. Three tools support the model composition tool: (1) Model Simulation Interface that generates a visual plot of the simulation according to user‘s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. PUBMED JOURNAL
PhenoTimer PhenoTimer is a visualization tool for time-resolved phenotypic data. It displays connections between phenotypes through time and the genetic context in which they occur through dynamic network highlighting. EMBL PUBMED JOURNAL
POMO - Plot Omic-associations on Multiple Organisms POMO is an interactive web-based application to visually explore omics data analysis results and associations in circular, network and grid views. PUBMED JOURNAL
SBEToolbox SBEToolbox (Systems Biology and Evolution Toolbox) is an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. PUBMED JOURNAL
SIMScells Bringing Systems Biology to Lab Researchers SIMScells is an on-line computer tool addressed to academic and clinical researchers working in the field of biomedicine. It provides a platform where scientists can design and perform in silico the same experiments that they would perform in their wet labs. SIMScells simulates the full cell behaviour, and offers researchers a systems biology analysis of their results, putting their genes, proteins, drugs or pathologies of interest in the context of the global human organism or another specific biological system such as a cell or a tissue. ANAXOMICS
SPNConverter (signaling Petri net) SPNConverter is a tool to convert graphs into the GraphML format. It is a Cytoscape plug-in that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language. PUBMED JOURNAL
Systems Biology Research Tool (SBRT) SBRT is a free, easy-to-use, open-source, integrated software platform, which facilitates the computational aspects of systems biology. The SBRT currently performs several methods for analyzing stoichiometric networks and methods from fields of graph theory, geometry, algebra, and combinatorics. PUBMED JOURNAL
Systems Biology Software Infrastructure (SBSI) SBSI is a modular software suite that facilitates the parameter-fitting process. SBSI composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. PUBMED JOURNAL
Systems Biology Workbench (SBW) SBW is a software framework that allows heterogeneous application components - written in diverse programming languages and running on different platforms - to communicate and use each others‘ capabilities via a fast binary encoded-message system. PUBMED JOURNAL