Posts
- Category: System Biology & Modeling (continued)
- ANAT 3.0 - Inference and Analysis of Functional Networks of Proteins
- ANC 1.01 - Allosteric Network Compiler
- APID2NET - Unified Interactome Graphic Analyzer
- APP 2.30 - Pathway Viewer
- ARACNE 2 - Reconstruction of Accurate Cellular Networks
- Arcadia 1.0rc2 - Visualisation Tool for Metabolic Pathways
- Arena3D 2.0 - Visualization of Biological Networks in 3D
- Arete 4.0 - An Analysis Toolkit for Network-based Gene Prioritisation
- Argot2 - Functional Annotation of Proteins using the Semantic Similarity in the Gene Ontology
- ARTIMMUS - Artificial Murine Multiple Sclerosis Simulation
- ASSIGN 1.6.0 - Adaptive Profiling of Genomic Signatures
- Athena r4 - Modular CAD/CAM software for Synthetic Biology
- AUREA 1.6.7 - Adaptive Unified Relative Expression Analyzer
- Author tool 4.0 - Input data into Reactome
- Autoosc 0.1 - Automated Analysis of Biological Oscillator Models using Mode Decomposition
- AVID - Discover Functional Relationships among Proteins
- AVIS 2 - AJAX viewer of Interactive Signaling Networks
- B-NEM - Boolean Nested Effect Models
- BALSA - Cell Systems Modeling Environment
- BaMFA - Bayesian Metabolic Flux Analysis
- Banjo 2.2.0 - Bayesian Network Inference with Java Objects
- bcbn 0.02 - Bayesian inference for Conjunctive Bayesian Networks
- BCT 4.4 - Bacterial Chemotaxis Modelling & Simulator
- BDTree 1.01 - Modeling of Gene Expression Regulation
- BetaWB - Study Dynamics of Biological Systems
- BFRM 2.0 - Bayesian Factor Regression Models
- BGmix 1.52.0 - Bayesian Mixture Model for Differential Expression
- BIANA 1.4.5 - Biologic Interaction and Network Analysis
- BiGG Models 1.6 - A Platform for integrating, standardizing and sharing Genome-scale Models
- BiLayout 1.0 - Cytoscape plugin for Analysis & Visualization of Molecular Interaction Networks
- BiNA 2.4.1.1 - Biological Network Analyzer
- BinAligner 1.0.0 - Bioinformatics software for BIological Network ALIGNment
- BINAT 1.0 - Biological Networks Analysis Tool
- BiNoM 2.5 - Cytoscape plug-in for Manipulating and Analysing biological networks
- Bio-PEPA Workbench 1.0 - Bench of Language for the Modelling & the Analysis of Biochemical Networks
- Bio-SPICE Dashboard 7.0 - Viological Simulation Program for Intra- & Inter-Cellular Evaluation
- Bio2RDF r3 - Largest network of Linked Data for the Life Sciences
- Biocellion 1.2 - Computer Simulation of Living Cell Systems
- BioCham 4.5.17 - Modelling Environment for Systems Biology
- BioFabric 1.0.0 - Open-source Network Visualization tool
- BioGranat 0.1 - Molecular Biology Graph Visualisation and Analysis Tool
- BioJazz - Evolve and Design Biochemical Reaction Networks
- BioLayout 3.4 - Biological Network Visualisation and Analysis
- Biolearn 1.0 - Structure Learning for Bayesian Networks
- Biomarker - Biomarker Selection using Logit-Laplacian-net
- Bionet 3.0a - Biological Cell Network Pathway Simulation
- BioNet Reasoning - Modeling Biological Systems
- BioNetCAD 1.1 - Design, Simulation and Experimental Validation of Synthetic Biochemical Networks
- BioNetGen 2.5.0 - Rule-Based Modeling of Biochemical Systems
- BioOpt - Flux Balance Analysis
- BioPAX level 3 - Biological Pathway Exchange Language
- BioPAX-pattern 1.1.0 - Pattern search software for BioPAX models
- BioPreDyn-Bench v15102014B - Dynamic Modelling in Systems Biology
- BioQuali 2 - Cytoscape Plugin for Analysing the Global Consistency of Regulatory Networks
- Biorithm 1.1 - C++ package to analyze data in Molecular Systems Biology.
- bioSDP 0.3 - Analysis of uncertain Biochemical Networks via Semidefinite Programming
- BioSPI - SIMULATION OF BIOCHEMICAL PROCESSES
- BioTapestry 7.1.2 - Genetic Regulatory Networks Tool
- BioUML 0.9.10 - Open Source Java Framework for Systems Biology
- BIPS - Predict putative protein-protein interactions based on Homology
- BIRTA 1.16.0 - Bayesian Inference of Regulation of Transcriptional Activity
- biRte 1.18.0 - Bayesian Inference of Regulatory Influence on Expression
- BiVeS 1.13.3 - Biochemical Model Version Control System
- Blast2GO 5.2.5 - Functional Annotation Tool
- Blast2KEGG 0.1 - Enhanced Pathways Prediction from Nr and ENZYME Nomenclature Database
- BlastGraph 2.0 - Intensive approximate Pattern Matching in a de-Bruijn graph or a Sequence Graph
- BMRF / C++/JAVA 1.0 - Pathway Network Identification
- BN/PBN Toolbox - Toolbox of Boolean Networks and Probabilistic Boolean Networks
- BN++ 1.1 - Biochemical Network Library
- BNA 20060216 - Biological Network Analysis
- BNArray 1.0 - Constructing Gene Regulatory Networks from Microarray data by using Bayesian network
- BNCA - Bayesian Sparse Hidden Components analysis
- BoolNet 2.1.5 - Generation,Reconstruction and analysis of Boolean networks
- BoolSpace v1 - Boolean Modeling of the Cancer State Space
- BOQA - Bayesian Ontology Query Algorithm
- BOSS - Predicting Biological System Objectives de novo from internal State Measurements
- BPMs - Validating a particular set of PPI Motifs
- BRAIN 1.0.5 /BRAIN Library 1.5 - Biologically Relevant Analysis of Interaction Networks
- BSubtilis 1.0 - Multi-Scale, Agent Based Model of B. Subtilis Phenotype Switching
- BudHat 2.0 - Online Biochemical Model Version Control System
- ByoDyn 5.12 - Study of Biochemical Networks within the framework of Systems Biology
- C13 - Quantification of in vivo Metabolic Fluxes
- CABERNET 1.1 - A Cytoscape APP for Augmented Boolean Models of Gene Regulatory Networks
- CADLIVE 2.75 - Computer-Aided Design of LIVing systEm
- Caleydo 3.1.5 - Pathway and Gene Expression Visualization
- Camelot - Model Complex Traits and Identify the Potential underlying Causal Factors
- CAMPways - Constrained Alignment of Metabolic Pathways
- Cancerin - Infer Competing Endogenous RNA (ceRNA) interactions in Cancer
- capDSD - Confidence, Augmented Pathway Diffusion State Distance
- CarGene 1.0 - Characterization of Sets of Genes based on Metabolic Pathways Analysis
- CARMEN - Comparative Analysis and Reconstruction of MEtabolic Network
- Cascade 2.0 - Selection, Reverse-Engineering and Prediction in Cascade networks.
- Catapult - Associating new Genes with Traits, Phenotypes, and Diseases
- cddApp 1.1.4 - Integration between Cytoscape and the NCBI Conserved Domain Database
- CellBlender 3.5.0 - Blender addon for Creation, Simulation, Visualization, and analysis of 3D Cell Models
- CellDesigner 4.4.2 - Biochemical Networks Modeling Tool
- CellLine - Stochastic Cell Lineage Simulator
- CELLmicrocosmos 4.2 PathwayIntegration - Localization and Visualization of Protein-Interaction Networks in a Virtual Cell
- CellMLCompiler 2.0 - Software Platform for Biological Function Simulation
- CellNetAnalyzer 2021.1 - Structural & Functional Analysis of Cellular Networks
- CellNOpt 1.4.0 / CellNOptR 1.38.0 - Creat Logic-based Models of Signal Transduction Networks
- CellPublisher 2.0 - Representations of Biochemical Processes
- CellSys 5.0 - Modular software for Physics-based Tissue Modelling in 3D
- Cellware 3.0.1 - Modeling & Simulation Tool for Modeling Cellular Transactions
- CellWhere 2019.10 - Graphical Display of Interaction Networks organized on Subcellular Localizations
- Cellzilla2D 3.0 - Two-dimensional Tissue Objects Simulator
- CentiBiN 1.4.3 - Centralities in Biological Networks
- CentiLib - Computation of network centralities
- CentiScaPe 2.2 - Centralities for Cytoscape
- CePa 0.7.0 - Centrality-based Pathway Enrichment
- Cerebral 2.8.2 - Cytoscape Plugin for Layout of and Interaction with Biological Networks
- Cerebral 2.8.2 / CerebralWeb 1.0 - Cytoscape Molecular Interaction Viewer
- CHARON 1.0 - Language for Modular Specification of Interacting Hybrid System
- Chaste 2021.1 - Cancer, Heart and Soft Tissue Environment
- ChemChains 1.22 - Simulation & Analysis of Logical Models
- ChiBE 2.2 - Chisio BioPAX Editor
- ChiLay 2.0 - Automated Layout of Process Description Maps Drawn in SBGN
- ChIPModule 20130227 - Systematic discovery of Transcription Factors and their Cofactors from ChIP-seq data
- CHRONOS 1.22.0 - microRNA-mediated sub-pathway Enrichment Analysis
- CIPHER - Correlating Protein Interaction Network and Phenotype Network to predict Disease Genes
- Circadian Modelling 2.0 - Simulations using Mathematical Models of Biological Clocks
- cisMetalysis 1.3 - Meta Analysis of Gene Expression data sets
- CLAIM 20131010 - Coupling Co-expression Data and Protein-protein Interaction Networks for Functional Protein Analysis
- Cloud-COPASI 2020 - Biochemical Simulation and Analysis using Cloud Computing
- ClueGO 2.0.5 - Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks
- CluePedia 1.0.5 - Provide Insights into Pathways by integrating Experimental and in silico Information
- CluMa-GO 1.5 - Visualization of Mappings between the Gene Ontology and Cluster Trees
- ClusterONE 1.0 - Detecting Overlapping Protein Complexes in Protein-protein Interaction Networks
- clusterProfiler 3.14.0 - Statistical Analysis and Visulization of Functional Profiles for Genes and Gene Clusters
- ClusterViz 1.0.3 - Clustering Analysis of Biological Network
- ClustEx 2.0 - Responsive Gene Module Identification package
- CMGRN - Constructing Multilevel Gene Regulatory Networks
- CMI2NI - Inferring Gene Regulatory Networks from Gene Expression data
- cMonkey 2 1.2.2 - Biclustering from Diverse System Biology Data
- CN - Inferring Gene Regulatory Networks using SORDER algorithm
- CNApy 1.0.6 - Integrated Environment for Metabolic Network analysis
- CNetQ / Corbi 0.6-1 - Network Querying tool based on Conditional Random Fields
- COBRA Toolbox 3.0.6 / COBRApy 0.17.1 - MATLAB Scripts for Constraint-based Modeling of Metabolic Networks
- Cobweb 1.1.1 - Network Exploration and Visualisation
- CODENSE 1.0 - Mine Coherent Dense Subgraphs from Multiple Biological Networks
- Coev2Net - Boosting Confidence in High-throughput Protein-protein Interaction datasets
- CoExpNetViz 1.0.4 - Comparative Co-Expression Network Construction and Visualization
- CoMDP - Co-occurring Mutated Driver Pathway
- CommFinder - Visualizing Community Structures in Biological Networks
- CoMoFinder - Identify Composite Network Motifs in Genome-scale Co-regulatory Networks
- CompareSVM - Support Vector Machine (SVM) Inference of Gene Regularity Networks
- CompNet - A GUI based tool to Compare Multiple Biological Interaction Networks
- ContextTRAP - Pathway based analysis of Gene Expression data
- CONTOUR v2 - Cancer (Onco) geNes from disrupTed mOdUles and their Relationships
- COPASI 4.33 - Biochemical Network Simulator
- Core 0.10 - Predict Protein Complex from PPI network
- CoReCo - Comparative ReConstruction of Genome-scale Metabolic Networks
- CoRegNet 1.30.0 - Reconstruction and Integrated Analysis of Co-regulatory Networks
- CorNet 2.01 - Correlation Network Graphs
- CorTo 1.03 - Transcript and Metabolite Network Reverse Engineering
- CoryneRegNet 6.0 - Corynebacterial Transcriptional Gene Regulatory Interactions
- Cosine 2.1 - COndition-SpecIfic sub-NEtwork Identification using a global Optimization Method
- COSSY - COntext-Specific Subnetwork discoverY
- COVAIN 20170509 - Multivariate Statistical Analysis of Metabolomics Covariance data
- cPath2 pc11 - Pathway Database Designed for Systems Biology Research
- CplexA 20121212 - Mathematica Package to Study Macromolecular Assembly Control
- CRNreals v2 - Distinguishability Analysis of Biochemical Reaction Networks
- CrossTalkZ 1.4 - Statistical tool to assess Crosstalk Enrichment between Node Groupings in a Network
- cuda-sim 0.08 - CUDA GPU accelerated Biochemical Network Simulation
- Curator tool 3.1 - Annotate Biological Pathways based on the Reactome Schema
- Cyclone 1.0 beta - Java-based Querying and Computing with Pathway/Genome databases
- CyClus3D 3.3 - Cytoscape plugin for Identifying Functional Modules
- CyNeo4j 1.3 - A Cytoscape app to connect to a Neo4j database
- Cyni 1.0.0.beta6 - Cytoscape Network Inference Toolbox
- Cyrface 2.0 - Bridging Cytoscape with R
- CySabioRK 0.1 - Cytoscape plugin for loading Reaction Kinetics Networks
- CySBGN 1.2 - SBGN diagrams in Cytoscape
- CySBML 1.4.1 - Cytoscape Plugin for SBML
- CytoHiC 1.1 - Visual Comparison of Hi-C Networks
- CytoKavosh 1.1 / Kavosh - Finding Network Motifs in Large Biological Networks
- CytoNCA 2.1.6 - Cytoscape Apps for Network Centrality Analysis and Evaluation
- Cytoprophet 1.0 - A Cytoscape plug-in for Protein and Domain Interaction Networks Inference
- CytoSaddleSum 1.5 - Functional Enrichment Analysis plugin for Cytoscape
- Cytoscape 3.8.2 - Platform for Complex-Network Analysis & Visualization
- CytoscapeRPC 1.8 - Create, Query and Modify Cytoscape Networks
- D2D - Quantitative Dynamic Modeling of Biochemical processes
- DA 1.0 - Estimate Unknown parameters in a Pathway Model
- DANCE - GWAS-hits, Human Complex Phenotypes and Population Genetic Variability
- Data2Dynamics 170117 - Modeling Environment Tailored to Parameter Estimation in Dynamical System
- DataRail 1.3 - Analysis of High-throughput data encountered in Systems Biology
- DatasetAssess - Estimate Error Rates in High-throughput Protein Interaction datasets
- DBsolve Optimum 2020 - Development & Analysis of Kinetic Models of Biochemical Pathways
- DDN - Identify Condition-specific Topological Changes in Biological Networks
- DeDaL - Producing an Morphing data-driven and structure-driven Network Layouts
- Deduce - Deduction of Molecular Reaction Network Structure from Measured Time-series
- DeltaNet 1.0 - Predicting Genetic Perturbations from Gene Expression data
- Dendrix 0.3 - Discovery of Mutated Driver Pathways in Cancer
- DeNovo - Virus-Host Sequence-Based Protein-Protein Interaction Prediction
- DERA 1.0 - Differentially Expressed Regulation Analysis
- DeterminePPI 1.0 - Inferring Protein-protein Interactions by Parsimony Principle
- DGPsubNet 0.0.1 - Drug-Gene-Disease Coherent SUBNETworks
- Diffany 1.0.0 - Calculating and Visualizing Differential Molecular Networks
- DiME - Disease Module Identification
- DINIES - Drug-target Interaction Network Inference Engine based on Supervised Analysis
- DIRAC - Studying Gene Expression within Pathways
- directPA 1.5 - Direction Pathway Analysis
- DisGeNET 6.0 / DisGeNET2R 0.99.0 - Query and Analyze a Network representation of human Gene-disease databases
- DISRUPT 1.01 - Prediction of Network Disruptions
- DISTILLER 2.0 - Data Integration System To Identify Links in Expression Regulation
- Dizzy 1.11.4 - Chemical Kinetics Stochastic Simulation
- Dizzy-Beats 20150113 - Systems Biology Computing the Bayesian Evidence and parameter posteriors for Systems Models
- DomainGraph 3.01 - Cytoscape Plugin of Analysis and Visualization of Molecular Interaction Networks
- DOTcvpSB 2010_E4 - Matlab Toolbox for Dynamic Optimization in Systems Biology
- DREM 2.0.4 / mirDREM - Dynamic Regulatory Events Miner
- DRWPClass 1.0 - Pathway-based Disease Classification
- DSD 0.5 - Diffusion State Distance Calculation Program
- DT-Hybrid 0.99.2 - Drug-target Interaction Prediction
- DualAligner v1.0 - Dual Alignment-based Strategy to Align Protein Interaction Networks
- Dunnart 2.0 - Constraint-Based Diagram Editor
- DyGloSA - Dynamical Global parameter Sensitivity Analysis of ODE models of biological systems
- DynaSIN - The Dynamic Structure Interaction Network
- Dynetica 2.0 Beta - A Simulator of Dynamic Networks
- E-Cell 3D demo - 3D Cell Simulation
- E-Cell4 v1.2.0b1 - Whole Cell Simulation
- E-MAPs 1.1 - Imputing Quantitative Genetic Interactions
- E-zyme 20150501 - Enzymatic Reaction Prediction between Chemical Compounds
- E3Miner - Text Mining tool for Ubiquitin-protein Ligases
- E3NET - A System for Exploring E3-mediated Regulatory Networks of Cellular Functions
- EASE 2.0 - Functional Annotation tool
- ebdbNet 1.2.3 - Empirical Bayes Dynamic Bayesian Network Inference
- EC2KEGG v1 - Comparative Analysis of Enzyme Lists
- Edinburgh Pathway Editor 3.0a13 - Visual Editor for Systems Biology
- efmtool 4.7.1 — Elementary Flux Mode Tool
- EGAN 1.5 - Exploratory Gene Association Networks
- EI_EXCHANGE 1.0 - Calculate Elementary Mode
- ELECANS 1.0.0.2 - Electronic Cancer Simulation Studio
- EmbryoMaker 1.0 - Computational Modeling of development by Epithelia, Mesenchyme and their Interactions
- ENA 1.3-0 - Ensemble Network Aggregation
- enhancedGraphics 1.5.4 - Cytoscape app for enhanced Node Graphics
- Enrichment Map 3.2.1 - Cytoscape plugin for Functional Enrichment Visualization
- EnrichNet 1.1 - Network-based Enrichment Analysis
- Ensemble NMF 0.91 / NMF Tree Browser 0.98 - Clustering and Visualising Protein Interaction Networks
- ENViz 3.1.5 - Integrated Statistical Analysis and Visualization of Sample-Matched Data with Multiple Data Types
- EPISIM 1.5.2 - Multi-Scale Modeling and Simulation Platform
- epistasisGA - Detecting Gene-gene Interactions in Case-parent Triad or Affected/unaffected Sibling studies
- ETAscape - Cytoscape plugin for Predicting Protein Function based on Evolutionarily Important Structural Motifs
- EvoFBA - Simulating Evolution of Constraint Based Models of Cellular Metabolism
- EvoPPI 1.0 - Inter-specific comparisons from PPI Databases
- eXamine 2.1.2 - Cytoscape app for Exploring Annotated Modules in Nnetworks
- ExPA 050216 - Extreme Pathway Analysis for Metabolic Networks
- FACETS v1.0 - Multi-faceted Functional Decomposition of Protein Interaction Networks
- Facile 0.53 - Network Compiler for Systems Biology
- FacPad 3.0 - Bayesian Sparse Factor Modeling for the Inference of Pathways responsive to Drug Treatment
- FASIMU 2.3.4 - Flux-balance Analysis based SIMUlations
- FASPAD 20070415 - Detection of Linear Signaling Pathways in Protein Interaction Networks
- Fast-SL – Identify Synthetic Lethal sets in Metabolic Networks
- Fast-tFVA 20130114 - Thermodynamically Constrained Flux Variability Analysis
- FASTCORE 1.0 - Fast Reconstruction of Compact Context-Specific Metabolic Network Models
- FastGGM 20151105 - Algorithm for the inference of Gaussian Graphical Model in Biological Networks
- FastPros 1.0.0 - Screening of Reaction Knockout Strategies for Metabolic Engineering
- FastSemSim 1.0 - Semantic Similarity Measures
- FBA 2.0 - Flux Balance Analysis E.coli Model
- FBA-SimVis 1.91 - Dynamic Visualisation of Constraint-based Metabolic Models
- fcsampling - Generate Function-constrained Samples that match a Target Distribution
- FERN 1.4 - Stochastic Simulation & Evaluation of Reaction Networks
- FFCA 1.01 - Feasibility-based Flux Coupling Analysis of Metabolic Networks
- FGNet 3.26.0 - Functional Gene Networks derived from Biological Enrichment Analyses
- FindPath - in silico Design of Synthetic Metabolic Pathways
- FLAME - Flexible Large-scale Agent Modelling Environment
- Flux Simulator 1.2.1 - Modeling RNA-Seq Experiments
- FluxMap 1.15 - Visual Exploration of Flux Distributions in Biological Networks
- FluxModeCalculator - Large-scale Flux mode Computation
- FluxViz/CyFluxViz 1.00 - Cytoscape Plugin for Flux Visualization
- FlyNet - Versatile Network Prioritization server for Drosophila Melanogaster
- FNV 1.0 - Light-weight Flash-based Network and Pathway Viewer
- FpClass - Interactions and Properties of Human Proteins
- FROMP 20130424 - Fragment Recruitment on Metabolic Pathways
- FTGI - Finding a Three-way Gene Interaction
- FunCProp - Function Computational Propagation
- FungiFun 2.2.8 BETA - Functional Categorization of Fungal Genes and Proteins
- FunMod 2.8.3 - Cytoscape plugin for Identifying Functional Modules in undirected Protein-protein Networks
- FunNet 1.00-3 - Functional Analysis of Transcriptional Networks
- FuseNet - Gene Network Inference by Fusing data from Diverse Distributions
- GAP 0.0.1 - Gene functional Association Predictor
- GAPI - Explores Hyperbolic Mapping of the human Potein Interaction Network
- GASOLINE 2.0 - Optimal Local multiple Alignment of Interaction NEtworks
- GDBB 1.01 - Genetic Design through Branch and Bound
- GDLS 1.11 - Genetic Design through Local Search
- GECS - Glycan Structure Prediction from Microarray data
- GEDEVO / GEDEVO-M / CytoGEDEVO 1.0.3.1 - Global Alignment of Biological Networks with Cytoscape
- GEM 1.4.1 - Gene-Environment interaction analysis for Millions of samples
- GEMINI - Gene Expression and Metabolism Integrated for Network Inference
- GEMSiRV 20130911 - GEnome-scale Metabolic Model Simulation, Reconstruction and Visualization
- GEMSTAT 1.5.0 - Thermodynamics-based Modeling of Gene Expression from Regulatory Sequences
- GenCLiP 3 - Human Gene Function And Network Analysis
- Genecentric 1.0.3 - Uncover Graph-theoretic Structure in High-throughput Epistasis data
- geneDBN V01.9R01 - Build Gene Regulatory Networks
- GeneFAtt - Computing Attractors of Synchronous and Asynchronous Boolean Networks
- GeneInfoViz - Constructing and Visualizing Gene Relation Networks
- GeneMANIA 3.5.1 - Gene Function Prediction
- GeneNet 1.2.14 - Modeling and Inferring Gene Networks
- GeneNet Toolbox - Analysis of Gene Connectivity in Biological Networks
- GeneNetFinder 2.0 - Qualitive Reasoning of Dynamic Gene Regulatory Interations form Gene Expression Data
- GeneNetStudio 2011 - Visual Reconstruction and Analysis of Gene Networks
- GeneNetVal - Gene Network Biological Validity based on Gene-gene Interaction Relevance
- GeneNetWeaver 3.1.3 Beta - in silico benchmark Generation and performance profiling of Network Inference Methods
- GeneNT 1.4.1 - Relevance or Dependency network and Signaling Pathway Discovery
- GenePath - Analysis of Genetic Data and Discovery of Genetic Networks
- GenePro 2.5.2 - Visualization and Analysis of Protein and Gene Interaction Networks
- geneRegulationSimulation - Perform Simulations for Transcription Regulation Network
- Genes2Networks 1.5 - Connecting Lists of Gene Symbols using Mammalian Protein Interactions databases
- GENIE3 - Inference of Gene Regulatory Networks from Expression data
- GENIES - Gene Network Inference Engine based on Supervised Analysis
- GENOM 2005 3.42 - Affymetrix Microarray Analysis
- GenomicInteractions 1.26.0 - Exploring Chromatin interaction data
- GenRev 1.0.1 - Explore Functional Relevance of Genes in Molecular Networks
- GENS 2.3.1 - Simulate Gene-environment and Gene-gene Interactions
- GenSSI 2.0 - Structural Identifiability Analysis of Biological Models
- GEOMI 07 - Visual Analytic tool for Biological Networks
- GEsnpx 1.1 / GEsnpxPara 1.3 - Genetic Ensemble approach for Gene-gene Interaction Identification
- GESSA 1.0.0 - Hybrid Model of Transcriptional Reprogramming due to Cell Signaling
- GFD-Net 1.4.1 - Measuring Semantic Dissimilarity of Gene Networks
- GGEA / EnrichmentBrowser 2.22.2 - Gene Graph Enrichment Analysis
- GGL 4.1.2 - Graph Grammar Library
- GHOST v1.1.0 - Global Network Alignment using Multiscale Spectral Signatures
- GibbsOS V3 - Robust Identification of Transcriptional Regulatory Networks using a Gibbs Sampler on Outlier Sum Statistic
- GINsim 3.0.0b - Qualitative Analysis of Regulatory Graphs
- GIPro 1.0 - Visualization of High-throughput Genetic and Physical Interaction data
- GLAMM 2.2.4 - Interactive Viewer for Metabolic Pathways and Experiments
- GLIEP - Navigation and Exploration of Interconnected Pathway Visualization
- Glocal 1.1 - Robustness Analysis and Model Discrimination for Circadian Oscillators
- Gmix - Bayesian Analysis of Univariate Normal Mixtures
- GNA 8.7.1.1 - Modelling & Simulation of Genetic Regulatory Networks
- GNAT 20131101 - Glycosylation Network Analysis Toolbox
- GNC 1.3 - Gene Network Coherence with direct and indirect Relationships
- GNLab -Computational Pipeline for Large-Scale Gene Network Analysis
- GNTInfer 1.1 - Gene Network Reconstruction tool
- GNU MCSim 5.5.0 - Simulation & Statistical Inference Tool
- GO-Elite 1.2.6 - Software for Extended Pathway Analysis
- go2ppi 1.06 - Prediction of Protein-protein Interactions
- Gobbolino - Enumeration of Metabolic Storie
- GOrilla - Gene Ontology enRIchment anaLysis and visuaLizAtion tool
- GOTreePlus 20080131 - Interactive Gene Ontology Browser
- GPLEXUS - The High-performance Gene Association Network Analysis Server
- GPODE 20090927 - Learning Gene Regulatory Networks from Gene Expression Measurements
- GPRuler - Metabolic Gene-Protein-Reaction Rules Automatic Reconstruction
- GPU-FAN 1.0 - GPU-based Fast Analysis of Networks
- GRAAL / C-GRAAL / MI-GRAAL/ L-GRAAL - Matching-based Integrative / GRAph ALigner
- Graemlin 2.01 - Aligning Multiple Global Protein Interaction Networks
- GRAM 0.6 - Discovery of Gene Modules and Regulatory Networks
- GRaPe 1.0 – Generation of Generic Rate Equations for all Reactions in a Model
- Graph 1.0 - Constructs, Visualizes and Modifies Graphs
- GraphCrunch 2.1.1 - Network Modeling, Alignment and Clustering
- GRENDEL 0.2 - Gene Regulatory Network Decoding Evaluations tooL
- GRNInfer 1.0 - Gene Regulatory Network Inference tool from multiple microarray datasets
- grnl1 - Gene Regulatory Network modeling using L1 Regularized Graphical Models
- GUILD - Genes Underlying Inheritance Linked Disorders framework
- HBN - Integration of Relational and Hierarchical Network Information for Protein Function Prediction
- HEC 2.0.1 - Haploid Simulation of Bacterial Communities
- Hi-Jack - Pathway-based Inference of Host-pathogen Interactions
- HillSim 1.0 - Signaling System Analyzer
- HIPPIE 2.2 - study and filter the Network of Human Protein-protein Interaction data
- HitWalker2 1.0 - Variant Prioritization for Personalized Functional Cancer Genomics
- Hive plots 0.02 / jhive v0.3.0 - Rational Network Visualization
- HotNet2 1.2.1 - Finding Altered Subnetworks
- HRM - Hybrid Regulatory Models
- HSimulator 1.0 - Multithread Hybrid stochastic/deterministic simulation of Biochemical Reaction Networks
- HTSanalyzeR 2.38.0 - Network analysis of High Throughput Screens
- HumanNet v2 - Human Gene Networks for Disease Research
- Hyperscape - Visualization for Complex Biological Network
- HYPERSPACE - Exploring Parameter Spaces in Systems Biology
- iBioSim 3.1.0 - New Efficient Analysis Methods for Genetic Circuits
- icbn 0.2-13 - Isotonic regression Conjunctive Bayesian Network models
- ICE 1.0.2 - Iterative Clique Enumeration
- iCTNet 0.1 - Analyze Integrative Complex Traits Networks
- IDEM - Identifying Direction from Expression and Methylation
- idFBA - Dynamic analysis of integrated Signaling, Metabolic, and Regulatory Networks
- iDINGO 1.0.4 - Integrative Differential Network Analysis in Genomics
- iFad 3.0 - An integrative Factor Analysis Model for Drug-pathway Association Inference
- iFBA 1.0 - Integrated Flux Balance Analysis Model of Escherichia coli
- Ilya - Reaction-Diffusion Simulator
- IMP 2.0 - Integrative Multi-species Prediction
- IMPaLA 9 - Integrated Molecular Pathway Level Analysis
- Import Notes 1.1 - CellDesigner Plugin, Import Notes Data from CSV File
- InCroMAP 1.5 - Integrated Analysis of Cross-platform MicroArray and Pathway data
- Inferelator 2015.08.05 - Genetic Regulatory Networks Inference algorithm
- InferPPI 1.0 - Predict Protein Interactions based on Parsimony Tendency of Domain Interactions
- influx_s 5.4.0 - Estimation of Metabolic Fluxes and Metabolite Concentrations
- Infobiotics v1.0.3 - Modelling platform for Systems and Synthetic Biology
- Interference 1.0 - Virtual Knock-out experiments on Biological networks, based on the Centralities Interference notion
- INTERSPIA - INTER-Species Protein Interaction Analysis
- InterSPPI v1.3 - AraPathogen predicts PPIs between Arabidopsis thaliana and pathogens
- InterView 1.0 - Interactive 2D Visualisation of Network data
- IntOGen 2020-02-01 - Integration and Data Mining of multidimensional Oncogenomic data
- IOCBio 1.2.2 - Open-source Software from the Laboratory of Systems Biology
- iPath 3.0 - Interactive Pathways Explorer
- IPATHCONS 1.0.6 - Insect Pathway Construction tool
- iPathways 1.2.1 - Biological Pathways on the iPhone
- IPCA-CMI - Inferring Gene Regulatory Networks based on Combination of PCA-CMI and MIT score
- iRefIndex 14 / iRefScape 1.18 / iRefR 1.13 - Downloading Consolidated Protein Interaction data and Visualization
- iRegulon 1.3 - Sequence-based Discovery of Human Regulons
- ISBJava 2.4.4 - Java library for Research in Computational Biology
- ISM - One-Carbon and Glutathione Metabolism Modeling Software
- IsoRank 2008 / IsoRankN 2009 - Global Alignment of multiple PPI Networks / on Spectral methods
- iVUN 1.2 - interactive Visualization of Uncertain Biochemical Reaction Networks
- iWRAP - Prediction of Cancer-related Protein-protein Interactions
- jagn 1.02 - Java-Based Model for Artificial Gene Networks Generation
- JANet - Javascript AgeFactDB Network-viewer
- JavaCycO 0.1.0 - Java Library for connecting to BioCyc Pathway Geneome Databases (PGDBs).
- JCell 1.0.1 - A Java based framework for Inferring Genetic Networks
- JEPETTO 1.3.1 - Java Enrichment of Pathways Extended To Topology
- JiffyNet - Jiffy (instant) Gene Network Modeler for newly Sequenced Species
- JigCell 7.1.0 - Modeling and Simulation software
- JMassBalance 20130207 - Mass-balanced Randomization and Analysis of Metabolic Networks
- JNets 1.0 - Visualise, Manipulate and Analyze Networks by Overlaying Annotation
- JSBML 1.5 - Java library for SBML
- JSim 2.21 - Simulation System for Building and Analyzing Quantitative Numeric Models
- jSquid 20081203 - Visualize Networks & Edge Scores
- jump3 - Inference of Gene Regulatory Networks
- KAAS 20140224 - KEGG Automatic Annotation Server
- KaSim 4.1.2 - Stochastic Simulator for Rule-based Model
- KATSURA 1.0.1 - KEGG Pathway Coverage & Expression Analysis
- KDDN 1.1.0 - Knowledge-fused Differential Dependency Network
- KEGG2SBML 1.5.0 - Convert KEGG Pathway Database to SBML
- KEGGgraph 1.52.0 - A Graph Approach to KEGG PATHWAY in R and Bioconductor
- KEGGParser 20140324 - Parsing and Editing KEGG Pathway Maps in Matlab
- KEGGscape 0.9.1 - File Reader and Pathway Vsualizer for KEGG XML (KGML) files
- KeyPathwayMiner 5.0.1 - Combining networks with OMICS data
- KGML-ED 1.0 - Edit, Process, and Visualize KGML pathway files
- KiMoSys - Quantitative KInetic MOdels of Biological SYStems
- KInfer - Calibration of Dynamic Models of Biological Systems
- Kinsolver - Simulator for Biochemical and Gene Regulatory Networks
- Kiwi 0.3.6 - Visualization of Network Topology and Gene-set Analysis
- kMech - Enzyme Mechanism language for the Mathematical Modeling of Metabolic Pathways
- Knet - Finds Pairs of Genes with Similar Behavior across a Gene Expression dataset
- KOBAS 2.0 - Annotation and Identification of Enriched Pathways and Diseases
- Lattice Microbes 2.3 - Simulation method for the Reaction-diffusion Master Equation
- LBIBCell 0.2 - Cell-Based Simulation Environment for Morphogenetic Problems
- LDGM - Identifying Gene Regulatory Network Rewiring using Latent Differential Graphical Models
- lemon-tree 3.1.1 - Biological Module Network Inference
- libRoadRunner 1.4.18 - High performance SBML JIT Compiler & Simulation Engine
- LibSBGN Milestone 3.2 - Standard Electronic Implementation for SBGN
- LibSBML 5.19.0 - API Library for SBML
- LibSBMLSim 1.4.0 - The library for Simulating SBML models
- libScopes 0.1.1 - C++ Library for Calculation of Biochemical Scopes
- LIGAP 20130505 - Identify Condition/Lineage Specific Time-course Profiles
- LIME 1.0 - Stochastic Dynamical Modelling in Ecology
- linkcomm 1.0-11 - Tools for Generating, Visualizing, and Analysing Link Communities in Networks
- LLDA - Latent Variable Model for Chemogenomic Profiling
- LocalAli - Local Alignment tool for Multiple Networks
- LocFuse - Human protein-protein Interaction Prediction
- lol 1.34.0 - Lots Of Lasso
- Loregic 1.0 - Characterize the Cooperative Logic of Regulatory Factors
- LPCF - Local Protein Community Finder
- LPIA v1 - Latent Pathway Identification Analysis
- lpNet 2.18.0 - Linear Programming Model for Network Inference
- LR_PPI - large-scale Prediction of Human protein-protein interaction
- LRpath - Pathway Analysis using Logistic Regression
- Lynx v3.0 - Integrated Systems Biology Platform
- M-Module - Integrative Analysis algorithm for Multiple Networks
- MaBoSS 2.0 - Apply Kinetic Monte-Carlo on the Boolean State Space
- MADE 20110209 - Metabolic Adjustment by Differential Expression
- MANYCELL 1.0 - Simulator for Cellular Systems
- MapMan 3.6.0RC1 - Displays large datasets onto Diagrams of Metabolic Pathways
- Mapping Tool 1.3 - Map Different Nomenclatures
- MAPT 0.58 - Pathway Annotation, Analysis
- MATISSE 1.1 - Detection of Functional Modules using Interaction Networks and Expression data
- MatNet - MATLAB-NetLogo Model of Pseudomonas Biofilm Formation
- MAVisto 2.7.0 - Motif Analysis and VISualisation TOolkit
- MaxLink 1.0.0 - Network-based Identification of Functionally Related Genes
- MCell 4.0.1 - Monte Carlo Simulator of Cellular Microphysiology
- MCODE 1.5.1 - Cytoscape plugin that finds Clusters in a Network
- MDCinfer 1.0 - PPI Prediction tool based on Multiple Domain Cooperation analysis
- MDPFinder - Mutated Driver Pathway Finder
- mDraw 1.0 - Network Visualization Tool
- MEAGA 1.2 - Minimum distance-based Enrichment Analysis for Genetic Association
- MEDUSA - Motif Element Detection Using Sequence Agglomeration
- Medusa 3.0 - Visualization and Clustering Analysis of Biological Network
- MemGen - Setting up Membrane Simulation systems
- MEMOSys 2.1.1 - Metabolic Model System
- Merge Models 1.03 - CellDesigner Plugin to Merge Models
- MesoRD 1.1 - Mesoscopic Reaction Diffusion Simulator
- Meta-All 1.2 - Store and Access Information about Metabolic Pathways
- metabnorm 20141112 - A mixed model Normalization method for Metabolomics data
- Metaboflux 2.0.6 - Predict Flux Distribution in Metabolic Networks
- Metabomxtr 1.29.0 - R package for Mixture-model Analysis of non-targeted Metabolomics Data
- MetaCrop 2.0 - Browsing and Working with Information from the MetaCrop database
- MetaDecon - Reconstruct the Genomic Content of Community Members
- Metafinder 0.21 - Design and Annotate Metabolic Pathways from Genome Annotations
- MetaMapp - Mapping and Visualizing Metabolomic data
- MetaMapR 1.4 - Pathway Independent Metabolomic Network Analysis Incorporating Unknowns
- MetaNetSam 1.1 - Metabolic Network Sampling
- MetaNetX - Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks
- MetAnnoGen - Metabolic Network Annotation
- metano 1.3.0 - Analyzing the Capabilities of Metabolic Networks
- MetaPAT 20070215 - Tool for the Alignment of Metabolic Pathways
- MetaPath 0.83 - Comparative Analysis of Metabolic Pathways in Metagenomics
- MetaPath 1.0 - Meta-analysis for Pathway Analysis
- MetaPathways 2.5.2 - Analysis of Environmental Sequence Information
- MetaReg - Graphical Interface for Modeling and Evaluation of Biological Systems
- MetAssimulo 1.2.1 - Metabolomic Analysis software
- METATOOL 5.1 - Biochemical Reaction Networks Elementary Modes Analysis
- MetaViz - Visualization software for Metabolic Network
- MetDisease 1.1.0 - Connecting Metabolites to Diseases via Literature
- MetDraw 1.0.0 - Automated Metabolic Maps and Data Visualization
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