System Biology & Modeling
- Mocapy++ 1.07 – Dynamic Bayesian Network toolkit
- Twixtrix r4 – Context-specific Transcriptional Regulatory Network Inference
- lemon-tree 3.0.1 – Biological Module Network Inference
- PathwayAnalyser 1.0 – Analysis of Metabolic Pathways
- Treegl – Reverse Engineering Tree-Evoloving Gene Networks Underlying Developing Biological Lineages
- TESLA – Recovering Time-varying Networks of Dependencies in Biological studies
- KELLER – Estimate Time-varying Interactions between Genes
- BlastGraph 2.0 – Intensive approximate Pattern Matching in a de-Bruijn graph or a Sequence Graph
- SEREND 1.1 – SEmi-supervised REgulatory Network Discoverer
- Network Archaeology 1.0 – Infer Evolutionary History of a network.
- GHOST 0.1 – Global Network Alignment using Multiscale Spectral Signatures
- PARANA 1.0 – Parsimonious Reconstruction of Ancestral Interaction Networks
- CLAIM – Coupling Co-expression Data and Protein-protein Interaction Networks for Functional Protein Analysis
- sLDA – Sparse Linear Discriminant Analysis
- MetAssimulo 1.2.1 – Metabolomic Analysis software
- RuleMonkey 2.0.25 – Simulate Large-scale Rule-based Models
- IntOGen – Integration and Data Mining of multidimensional Oncogenomic data
- STSE – Spatio-Temporal Simulation Environment
- TIde 2.0 beta – SBML based Identification of Optimal Inhibition Targets
- SemGen 2.0 beta – Semantics of Biological Processes
- FROMP 20130424 – Fragment Recruitment on Metabolic Pathways
- Fast-tFVA 20130114 – Thermodynamically Constrained Flux Variability Analysis
- Inferelator 2013.3.RC3 – Genetic Regulatory Networks Inference algorithm
- FunCProp – Function Computational Propagation
- BioNetBuilder 2 – Cytoscape PlugIn to Create Biological Networks
- cMonkey 1.1 – Biclustering from Diverse System Biology Data
- GGB 1.0 – Visualization of Systems Biology data in context of the Genome
- firegoose 1.0.296 – Firefox Toolbar connects the Gaggle to the web
- TSP/TST (GPU) 1.1 – Top-Scoring Pair and Top-Scoring Triple on the GPU
- TSN 1.0 – Expression Classification method from Small numbers of Biomolecules
- PROM – Probabilistic Regulation of Metabolism
- DIRAC – Studying Gene Expression within Pathways
- AUREA 1.6.6 – Adaptive Unified Relative Expression Analyzer
- GEMINI – Gene Expression and Metabolism Integrated for Network Inference
- SensSB 20120926 – Development and Sensitivity Analysis of Systems Biology Models
- FastSemSim 0.7.1 – Semantic Similarity Measures
- visANT 4.07 – Integrative Visual Analysis Tool for Biological Networks & Pathways
- iRefIndex 10 / iRefScape 1.1.8 / iRefR 1.00 – Downloading Consolidated Protein Interaction data and Visualization
- Paxtools 4.1.6 – Java Library for Accessing & Manipulating BioPAX Data
- CellNOpt 1.7.1 – Creat Logic-based Models of Signal Transduction Networks
- Smoldyn 2.29 – Cell-scale Biochemical Simulator
- MetNetMaker 1.6.2 – Creation of Novel Metabolic Networks in SBML format
- PottersWheel 3.0 – MatLab Toolbox of Mathematical Modeling of Dynamical Systems
- FluxViz/CyFluxViz 0.91 – Cytoscape Plugin for Flux Visualization
- FASIMU 2.3.3 – Flux-balance Analysis based SIMUlations
- BiNoM 2.2 – Cytoscape plug-in for Manipulating and Analysing biological networks
- mlegp 3.1.3 – Statistical Analysis for Computer Models of Biological Systems
- GGL 4.0.1 – Graph Grammar Library
- Caleydo 2.2 – Pathway and Gene Expression Visualization
- SBEToolbox 1.0 – MATLAB Systems Biology & Evolution Toolbox
- KaSim 3.1 – Stochastic Simulator for Rule-based Model
- Facile 0.53 – Network Compiler for Systems Biology
- Cellzilla2D 3.0 – Two-dimensional Tissue Objects Simulator
- LibSBMLSim 1.1.0 – The library for Simulating SBML models
- LibSBML 5.8.0 – API Library for SBML
- JSBML 0.8 – Java library for SBML
- NeAT – Network Analysis Tools
- MCODE 1.32 – Cytoscape plugin that finds Clusters in a Network
- ChiBE 2.0 – Chisio BioPAX Editor
- HEC 0.2 – Haploid Simulation of Bacterial Communities
- PathVisio-Validator – Creation of Pathway Diagrams by ensuring Correct usage of the MIM notation
- BioLayout Express3D 3.0RC6- Biological Network Visualisation and Analysis
- iBioSim 2.4.6 – New Efficient Analysis Methods for Genetic Circuits
- GLAMM 2.2.3 – Interactive Viewer for Metabolic Pathways and Experiments
- BioUML 0.9.4 – Open Source Java Framework for Systems Biology
- VCell 5.1 – Environment for Modeling & Simulation of Cell Biology
- CellDesigner 4.3 – Biochemical Networks Modeling Tool
- YANAsquare 201212 / YANAvergence – Integrated Network Reconstruction, Visualization and Analysis
- Cytoscape 3.0.1 – Platform for Complex-Network Analysis & Visualization
- BioTapestry 6.00 – Genetic Regulatory Networks Tool
- BN/PBN Toolbox – Toolbox of Boolean Networks and Probabilistic Boolean Networks
- Edinburgh Pathway Editor 3.0a13 – Visual Editor for Systems Biology
- CplexA 20121212 – Mathematica Package to Study Macromolecular Assembly Control
- GNU MCSim 5.5.0 – Simulation & Statistical Inference Tool
- SBML-PET-MPI 1.2 – Parallel Parameter Estimation Tool for SBML based Models
- SemanticSBML 2.0 – Annotation Checking& Merging of Systems Biology Models
- xCellerator 0.91 – Mathematica Package for Biological Modeling
- SBSI CellDesigner Plugin 20111025 – Bridge functionalities of CellDesigner & SBSI
- SBMLeditor 2.0-b1 – SBML File Editor
- GOrilla – Gene Ontology enRIchment anaLysis and visuaLizAtion tool
- SB.OS 0.7 – Systems Biology Operational Software DVD ISO Image
- SPEED 20110708 – Signaling Pathway Enrichment using Experimental Datasets
- LPCF – Local Protein Community Finder
- PNNS – Protein Network Neighbor Search
- Personalized PageRank Tool – Compute Personalized PageRank in Protein-protein Interaction Network
- Nascent 1.2 – Protein-Protein Physical Interaction Network Originating Tool
- Dendrix 0.3 – Discovery of Mutated Driver Pathways in Cancer
- Multi-Dendrix 1.0 – Multiple Pathway De novo Driver Exclusivity
- Lattice Microbes 2.1 – Simulation method for the Reaction-diffusion Master Equation
- GeneNet 1.2.6 – Modeling and Inferring Gene Networks
- Cosine 1.0 – COndition-SpecIfic sub-NEtwork Identification using a global Optimization Method
- iFad 2.0 – An integrative Factor Analysis Model for Drug-pathway Association Inference
- FacPad 2.0 – Bayesian Sparse Factor Modeling for the Inference of Pathways responsive to Drug Treatment
- VitaPad 0.6.1c – Visualize and Analyze Biological Pathways
- PAICE 2.92 – Bioinformatics Pathway Visualization
- MAPT 0.58 – Pathway Annotation, Analysis
- SBML Reaction Finder 1.2.1 – Extracts Chemical Reactions from SBML models
- OpenCMISS – Mathematical Modelling Environment for Complex Bioengineering Problems
- mozCellML 0.3.1 – Utility for Manipulating initial conditions and integrating CellML models
- OpenCell 0.8 – Environment for Working with CellML Models
- JSim 2.10 – Simulation System for Building and Analyzing Quantitative Numeric Models
- FLAME – Flexible Large-scale Agent Modelling Environment
- E-Cell 3.2.3 – Whole Cell Simulation
- COPASI 4.9.45 – Biochemical Network Simulator
- Chaste 3.1 – Cancer, Heart and Soft Tissue Environment
- CellSys 5.0 – Cell-based Simulation software for Multi-cellular systems
- Vernan – Specification, Construction, and Exact Reduction of State Transition System models of Biochemical Processes
- ELECANS 1.0.0.2 – Electronic Cancer Simulation Studio
- RobinViz 1.0 – Reliability Oriented Bioinformatic Networks Visualization
- spinal – Scalable Protein Interaction Network Alignment
- MetaNetX – Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks
- PITUFO – Find minimal sets of Precursors of Target Compounds in a Metabolic Network
- MetExplore – Web Server to Link Metabolomic Experiments and Genome-scale Metabolic Networks
- BudHat 2.0 – Online Biochemical Model Version Control System
- BiVeS 0.8 – Biochemical Model Version Control System
- BioGranat 0.1 – Molecular Biology Graph Visualisation and Analysis Tool
- SBSI 1.4.4 – Systems Biology Software Infrastructure
- mirConnX – Analysis of mRNA and microRNA (miRNA) Gene Regulatory Networks
- NCT 1.1.0 – The Network Comparison Toolkit
- GOTreePlus 20081213 – Interactive Gene Ontology Browser
- CePa 0.5 – Centrality-based Pathway Enrichment
- XcisClique – Integrating Gene Expression and Motif Combinations in Arabidopsis thaliana
- Biorithm 1.1 – C++ package to analyze data in Molecular Systems Biology.
- SASSy – Sensitivity Analysis Software for Systems
- GNAT 20121115 – Glycosylation Network Analysis Toolbox
- CellMLCompiler 2.0 – Software Platform for Biological Function Simulation
- KEGGParser 20130225 – Parsing and Editing KEGG Pathway Maps in Matlab
- GESTODifferent 1.0 – Cytoscape plugin for the Identification of Boolean Gene Regulatory Networks describing the stochastic differentiation process
- BioSimWare 201103 – Stochastic Modelling, Simulation and Analysis of Biological Systems
- HitWalker 0.99.0 – Variant Prioritization for Personalized Functional Cancer Genomics
- ProteoLens 1.11 – A Visual Network Data Mining Tool
- PINA 2.0 – Protein Interaction Network Analysis platform
- Moksiskaan 2.00 – Translate Gene Sets to Networks
- SubSeqer – Detection and Identification of Repetitive Elements in low-complexity Sequences
- cuda-sim 0.08 – CUDA GPU accelerated Biochemical Network Simulation
- ABC-SysBio 2.06 – Parameter Inference and Model Selection
- RXA 20100914 – Relative Expression Analysis of Gene Expession Profiles
- CluePedia 1.0.1 – Provide Insights into Pathways by integrating Experimental and in silico Information
- ClueGO 2.0.1 – Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks
- SyBiL 1.1.11 / sybilSBML 1.1.16 / sybilFCF 0.2.1 – Systems Biology Library for R
- AVID – Discover Functional Relationships among Proteins
- Tav4SB 0.2.2 – Web service operations for analysis of the Kinetic models of Biological Systems
- MIRACH 1.0 – Statistical Online Model Checker for Biological Pathway Models
- PlazaSur – Immunology Modeling System
- SIRIUS2 1.0 – Identification of Metabolites using single and Tandem Mass Spectrometry
- JCell 1.0.1 – A Java based framework for Inferring Genetic Networks
- SBMLsimulator 1.0.0 – Java Solver Implementation for SBML
- InCroMAP 1.4.0 – Integrated Analysis of Cross-platform MicroArray and Pathway data
- MIDIA 1.1 – Modularization Identification by Dynamic Independence Algorithms
- TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation
- Acorn 20101108 – Visualation of Genome Scale Metabolic Reaction Networks
- SurreyFBA 1.32 – Constraint-based modeling of Genome-scale Metabolic Reaction Networks
- PNA 1.0 – Principal Network Analysis
- Oog – Power Graphs Plugin for Cytoscape
- TracePilot 1.0 – Analysis of Phenotypes related to Cell Motility
- Rahnuma 1.1.1 – Prediction and Analysis of Metabolic Pathways and Comparison of Metabolic Networks
- RDFScape 0.4.2 – Semantic Web meets Systems Biology
- IOCBio 1.2.2 – Open-source Software from the Laboratory of Systems Biology
- Netsplitter 1.3.3 – Interactive Metabolic Subnets
- NetPathID – Network-based Analysis Identifies common Pathways
- WinSAAM 3.0 – The Simulation, Analysis and Modeling Software
- CytoscapeRPC 1.7 – Create, Query and Modify Cytoscape Networks
- TINGe 1.061 / GeNA 0.1 – Gene Networks Inference and Analysis
- DatasetAssess – Estimate Error Rates in High-throughput Protein Interaction datasets
- Glocal 1.1 – Robustness Analysis and Model Discrimination for Circadian Oscillators
- HYPERSPACE – Exploring Parameter Spaces in Systems Biology
- MinPath 1.2 – Biological Pathway Reconstructions using Protein Family Predictions
- GenCLiP 2.0 – Human Gene Function And Network Analysis
- GENIE3 – Inference of Gene Regulatory Networks from Expression data
- BioNet Reasoning – Modeling Biological Systems
- PaVESy 20060803 – Pathway Visualization Editing System
- DiVa 20121019 – Disconnectivity Valuation tool
- InferPPI 1.0 – Predict Protein Interactions based on Parsimony Tendency of Domain Interactions
- FluxMap 1.14 – Visual Exploration of Flux Distributions in Biological Networks
- SBGN-ED 1.3 – Editing, Translating and Validating of SBGN Maps
- HIVE 1.3 – Handy Integration and Visualisation of multimodal Experimental Data
- MapMan 3.5.1 – Displays large datasets onto Diagrams of Metabolic Pathways
- FFCA 1.01 – Feasibility-based Flux Coupling Analysis of Metabolic Networks
- RProteinInteraction 0.1-2 – Protein Interaction Network based protein Function Prediction algorithms
- Ensemble NMF 0.91 / NMF Tree Browser 0.98 – Clustering and Visualising Protein Interaction Networks
- E-MAPs 1.1 – Imputing Quantitative Genetic Interactions
- Arena3D 2.0 – Visualization of Biological Networks in 3D
- STITCH 3.1 – Search Tool for Interactions of Chemicals and proteins
- iPath 2.0 – Interactive Pathways Explorer
- STRING 9.0 – Search Tool for the Retrieval of Interacting Genes/Proteins
- FBA-SimVis 1.91 – Dynamic Visualisation of Constraint-based Metabolic Models
- VANTED 2.1.0 – Visualization and Analysis of Networks containing Experimental Data
- BioCham 3.4 – Modelling Environment for Systems Biology
- GibbsOS V3 – Robust Identification of Transcriptional Regulatory Networks using a Gibbs Sampler on Outlier Sum Statistic
- yasimSBML 1.0.1 – Simulate Metabolic Network depending on the Flux Distribution
- Q2LM 1.2 – Study Intracellular Signaling Networks and Cell-cytokine Interactions
- HotNet 1.0.0 – Finding Altered Subnetworks
- TinkerCell 20120703 – CAD Software for Synthetic Biology
- SOSlib 1.7.0 – ODE Solver for SBML
- Pysces 0.8.0 – Python Simulator of Cellular Systems
- NetBuilder 0.94 – Graphical Tool for Representing and Simulating Genetic Regulatory Networks
- MesoRD 1.1 – Mesoscopic Reaction Diffusion Simulator
- PET 0.7.4 – Parameter Estimation Toolkit
- BioNetGen 2.2.2 – Rule-Based Modeling of Biochemical Systems
- APP 2.29 – Pathway Viewer
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