Posts
- Category: System Biology & Modeling (continued)
- MetExplore 2.22.8 - Web Server to Link Metabolomic Experiments and Genome-scale Metabolic Networks
- Metingear 1.1.6 - The Metabolic Development Environment
- MetNetMaker 1.6.2 - Creation of Novel Metabolic Networks in SBML format
- MetScape 3.1.3 - Analysis and Visualization of Metabolomics and Gene Expression data
- mfinder 1.21 - Network Motifs Detection tool
- MFlux - Rapid Prediction of Bacterial Heterotrophic Fluxomics
- MGclus - Network Clustering Employing shared Neighbors
- MIDAS - MIning Differentially Activated Subpaths of KEGG pathways from multi-class RNA-seq data
- MIDER v2 - Mutual Information Distance and Entropy Reduction
- MIDIA 1.1 - Modularization Identification by Dynamic Independence Algorithms
- MIMO 1.0 - Molecular Interaction Maps Overlap
- MIMTool 1.0.2 - Molecular Interaction Map drawing Tool
- MINDY 2 - Genome-wide Discovery of Modulators of Transcriptional Interactions
- MinPath 1.4 - Biological Pathway Reconstructions using Protein Family Predictions
- minRect 1.0.2.1 - Metabolic Network Pathway Design tool on a Boolean model
- miR2Gene 201107 - Gene Pattern discovery by Enrichment Analysis of their microRNA Regulators
- MIRACH 1.0 - Statistical Online Model Checker for Biological Pathway Models
- mirConnX - Analysis of mRNA and microRNA (miRNA) Gene Regulatory Networks
- miRHiC 1.2 - Enrichment Analysis of miRNA Targets in Hierarchical Gene Co-expression Signatures
- MITHrIL 1.0 - Mirna enrIched paTHway Impact anaLysis
- MixNet 1.1.2 / MixeR 1.9 - Analyzes Biological Networks using Mixture Models
- ml-SVR - Identify Condition-Specific Regulatory Networks
- mlegp 3.1.8 - Statistical Analysis for Computer Models of Biological Systems
- MNI - Identify the Gene Targets of a Drug Treatment based on Gene-expression data
- Möbius 2.5 - Integrated Discrete-event Modeling Environment
- Mocapy++ 1.07 - Dynamic Bayesian Network toolkit
- MODA - Network Motif Discovery in Biological Networks
- modelBorgifier 1.0 - Comparing and Merging Metabolic Models
- modelMaGe 1.0 beta - Automatic Model Management & Generation
- ModEnt - Reconstructing Gene Regulatory Networks
- ModMap - Detecting maps of Modules in Biological Networks
- Modulerole 1.3.1 - Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks
- ModuleSearch - Finding Functional Modules in Protein-protein Interaction Network
- Moksiskaan 2.04 - Translate Gene Sets to Networks
- Moleculizer 1.1.3 - Cellular Reaction Network Stochastic Simulator
- MOMA - Minimal Perturbation Analysis
- MonaLisa r5_100 - Visualization and Analysis of Functional Modules in Biochemical Networks
- MONET 2.01 - Modularized Learning of Genetic Interaction Networks
- MoNetFamily - Homologous Modules and Module-module Interaction Networks in Vertebrates
- MONGOOSE 1.1 - Structural Analysis and Refinement of Constraint-based Metabolic Networks
- Moose 3.2.0 - Multiscale Object-Oriented Simulation Environment
- MoReNet - Funtional Gene Network of Mouse Retina
- MORPH - Predict Protein Interaction Partners between members of two Protein Families
- MORPH / MORPH-R 10.7 - MOdule guided Ranking of Candidate PatHway Genes
- Morpheus 2.0 RC2 - Modeling Environment for Multiscale and Multicellular Systems Biology
- MORPHIN - Model Organisms Projected on a Human Integrated Gene Network
- MOSAIC 1.1 - GO network Annotation and Partition in Cytoscape
- MOST 2.0 alpha-9- Metabolic Optimization and Simulation Tool
- MotifNet - Web-server for Network Motif analysis
- MotifNetwork - Analyze Promoter Motifs over Arabidopsis Gene Co-expression Network
- MOTUS 1.1.3 - Motif search in Metabolic Networks
- mozCellML 0.3.1 - Utility for Manipulating initial conditions and integrating CellML models
- MPEA - Metabolite Pathway Enrichment Analysis
- mSD - Regulatory Module Identification
- Multi-Dendrix 1.0 - Multiple Pathway De novo Driver Exclusivity
- Multi-netclust - Finding Connected Clusters in multi-parametric Networks
- MultiTF-PPI - Competitive Transcription Factor Binding Prediction
- MUSiCC - Metagenomic Universal Single-Copy Correction
- MutaNET 1.1.2 - Automated analysis of Genomic Mutations in Gene Regulatory NETworks
- MyProteinNet 2 - Build Up-to-date PIN for Organisms, Tissues, Cells Subsets and user-defined contexts
- N-Sieve 0.1 - Network Inference tool that uses an attenuation based structural prior
- NAIL 1.01 - Network Analysis in the Life Sciences
- NaNOS - Joint Pathway and Gene Selection
- NAPAbench 1.0 - Network Alignment Performance Assessment Benchmark
- NARROMI - Inferring Gene Regulatory Networks from Gene Expression data
- Nascent 1.2 - Protein-Protein Physical Interaction Network Originating Tool
- NASFinder - Identify Tissue-specific, Omics-determined Sub-networks
- NatalieQ - Topology-based Protein-protein Interaction Network Querying
- NaviCell - Web Tool for Exploring large maps of Molecular Interactions
- NaviCluster 2.0 - Interactive, Multi-Scale Navigation for Large and Complicated Biological Networks
- NAViGaTOR 3.0 - Visualize and Analyze Protein-protein Interaction Networks.
- NCT 1.1.0 - The Network Comparison Toolkit
- NeAT - Network Analysis Tools
- nem 2.60.0 - Nested Effects Models
- NEST 1.0 - Network Essentiality Scoring Tool
- NET-SYNTHESIS - Synthesis, Inference and Simplification of Signal Transduction Networks
- NetAligner 1.0 - Fast and Accurate Alignment of Protein Interaction Networks
- NetAutoProbit - Network Auto-Probit Modeling for Binary Network Processes
- NetBox 1.0 - Perform Network Analysis on Human Interaction Networks
- NetBuilder 0.94 - Graphical Tool for Representing and Simulating Genetic Regulatory Networks
- NetCirChro 1.2 - Cytoscape plugin for Network Visualization on Circular Chromosomes
- NetConfer - Exploration and Comparisons of Biological Networks
- NetDecoder - Network-based Platform to Decode Context-Specific Biological Networks and Gene Activities
- NetEffects - Analysing the Effects of Gene Perturbations on Longevity and Components of the Insulin Pathway
- NetGestalt / NetSAM 1.32.0 - Integrating Multidimensional Omics data over Biological Networks
- NetGSRforGGInt - Detection of Gene-Gene Interactions
- NETI 1.2 - Network Inference
- NetMatchStar 3.2 - An enhanced Cytoscape network querying app
- NetPathID - Network-based Analysis Identifies common Pathways
- NetPathMiner 1.22.0 - R package for Network Path Mining through Gene Expression
- NetPhorest 2.1 - Model Phosphorylation driven Cellular Signaling Networks
- NetQTL - Uncovering Genotype-Phenotype Relationships in Complex Diseases
- NetResponse 1.53.2 - Probabilistic algorithms for Functional Network Analysis
- NetSeed - Identify the Seed sets of Networks
- Netsim 1.5.2 - Gene Network Simulator
- Netsplitter 1.3.3 - Interactive Metabolic Subnets
- Netter - Re-ranking Gene Network Inference Predictions
- netVar - Using Gene Co-Expression Networks for Variable Selection
- Netview - Explore the Human and Mouse Gene Regulatory Networks
- NetWalker 1.0 - Random Walk Analysis
- Network2Canvas - Network Visualization on a Canvas with Enrichment Analysis
- NetworkAnalyst 1.0 - Statistical, Visual & Network-based approaches for Gene Expression Meta analysis
- NetworkBLAST / Networkblast-M - Comparative Analysis of Protein Networks
- NetworKIN 3.1 - Exploring Cellular Phosphorylation Networks
- NetworkPrioritizer 1.01 - Network-based Prioritization of Candidate Disease Genes or other molecules
- NetworkTrail 1.3 - Detection of Deregulated Pathways and Subgraphs in Biological Networks
- NetwPartLearn 0.0.1 - Simulation Tool for Reverse Engineering of Genetic Networks
- NEURON 7.7.2 - Simulations of Neurons and Networks of Neurons
- NEXCADE 2.1 - Perturbation Analysis for Complex Networks
- NFsim 1.11 - Biochemical Reaction Simulator
- NIACS - Network Interference Analysis and Correction Software
- NIMEFI - Gene Regulatory Network inference using Multiple Ensemble Feature Importance Algorithms
- NIR - Network Inference by Reverse-engineering
- NOA 1.1 - Cytoscape plugin for Network Ontology Analysis
- NP-method - Inferring Perturbed miRNA Regulatory Networks
- NRWRH - Network-based Random Walk with Restart on the Heterogeneous network
- OCSANA - Optimal Combinations of Interventions from Network Analysis
- Odefy 1.20 - From Discrete to Continuous Models
- Ometer 0.6 - Multivariate Data Analysis
- Omix 2.0.5 - Solutions for Systems Biology
- OntoCAT 0.9.9.2 - Ontology Toolkit
- Ontologizer 2.1 - Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology
- OpenCell 0.8 - Environment for Working with CellML Models
- OpenCMISS 1.3.0 - Mathematical Modelling Environment for Complex Bioengineering Problems
- OptDis - Optimally Discriminative Subnetwork Biomarkers
- optGpSampler 1.1 - Sampling Constraint-based Genome-scale Metabolic Networks
- OptiMage 1.1 - Tool for Producing 3D Layouts of network date
- optnetaligncpp - Optimizing Network Aligner
- OrthoNets 1.0 - Simultaneous Visual Analysis of Orthologs and their Interaction Neighborhoods across different organisms
- Osprey 1.2.0 - Protein-protein Interaction Networks Visualization System
- PAICE 2.92 - Bioinformatics Pathway Visualization
- Paintomics 3 v0.4.5 - Painting Omics Data in Biological Pathways
- PAN 1.32.0 - Posterior Association Networks
- PANDA v2 / PyPanda / PandaR 1.18.0 - Passing Attributes between Networks for Data Assimilation
- PANDA XPLORER - Pathway AND Annotation Xplorer
- PanGIA 3.0 - Analysis of Physical and Genetic Interactions to infer Genetic Module Maps
- PARANA 2-1.0.0 - Parsimonious Reconstruction of Ancestral Interaction Networks
- ParCorA - Partial Correlation Analysis for the purpose of Biochemical Network Inference
- ParMSpindle 1.0 - Simulation of the ParM mediated Segregation of Bacterial Plasmids
- PATH2PPI 1.20.0 - Prediction of Pathway-specific Protein-protein Interaction Networks
- PathBuilder 1.0 - open source Software for Annotating and Developing Pathway Resources
- pathClass 0.9.4 - Classification using Biological Pathways as prior knowledge
- PathExpand - Extending Cellular Pathways in Interaction Networks
- Pathicular 1.55 - Cytoscape plug-in of Identifies Path Motifs
- PATHiVar - Assessing Functional Impact of Mutations over Human Signalling Network
- PATHiWAYS - web-based Signaling Pathway visualization system
- PathJam - Biological Pathway Integration Tool
- PathNER - Systematic Identification of Biological Pathway Mentions
- PathPred - Pathway Prediction server
- PathRanker 0.1 - Mining Metabolic Pathways through Gene Expression
- PathRings 1.0 - A web-version of Biological Data Visualization Framework
- PathRNet - Robust Inference of the Context Specific Structure and Temporal Dynamics of Gene Regulatory Network
- Pathview 1.24.0 - R package for Pathway based Data Integration and Visualization
- PathVisio 3.3.0 - a tool to Edit and Analyze Biological Pathways
- PathVisio-MIM 2.0.11 - Pathvisio Plugin which Adds the Ability to Draw MIM Glyph
- PathVisioRPC - XML-RPC interface for Pathway Analysis tool PathVisio
- Pathway Projector - Zoomable Pathway Browser using KEGG Atlas
- Pathway Tools 25.0 - Editing, Querying, Visualization, and Analysis of PGDBs
- PathwayAnalyser 1.0 - Analysis of Metabolic Pathways
- PathwayExplorer 3.0.2 - Construction of Biological Pathway Diagrams
- PathwayLab 1.3 - Pathway Analysis tool
- PathwayMatrix - Visualizing Binary Relationships between Proteins in Biological Pathways
- PathwaysWeb 2.0 - Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning
- PathWhiz 1.0 - Pathway Drawing Web Server
- PaVESy 20060803 - Pathway Visualization Editing System
- Paxtools 5.1.0 / PaxtoolsR 1.26.0 - Accessing & Manipulating BioPAX Data
- Payao Uploader 1.0 - CellDesigner Plugin to Upload Model to Payao
- pDynamo 1.9.0 - Simulation of Molecular Systems
- Pepper 1.5.1 - Protein Complex Expansion using Protein-Protein intERaction networks
- PET 0.7.9 - Parameter Estimation Toolkit
- PetriScape 1.0 - Plugin for discrete Petri net simulations in Cytoscape
- PeTTSy 1.0 - Perturbation Theory Toolbox for Systems
- PEWCC - Identify Protein Complexes from PPI
- PheWAS-View / Phenogram - Visulation of PheWAS (Phenome-Wide Association Studies) Results
- PIANA 1.47 - Protein Interactions And Network Analysis tool
- PiiL - Pathway Interactive data Visualization tool
- PINA 3.0 - Protein Interaction Network Analysis platform
- PINALOG 1.0 - Protein Interaction Network Alignment
- PINBPA 1.1.9 - Cytoscape app for Network Analysis of GWAS data
- piNet - Modular Network Models of Plant Immune Reponse
- Pint 20190524 - Formal analysis of Dynamics for Large-scale Biological Networks
- PINTA - Gene Prioritization by Network Analysis
- PINV - Web-based Protein Interaction Network Visualizer
- PISwap - Protein Interaction Network Alignments
- PITUFO - Find minimal sets of Precursors of Target Compounds in a Metabolic Network
- PiType 2.0 - Protein Interaction Classifier
- pLasso - Incorporating Prior Knowledge into Gene Network Study
- PLW - Detecting Protein Complexes from Protein Interaction Networks
- PMAP II - Resolve pathway mapping problem with Operon and Regulon information
- PNK 2e - Modeling and Simulation of Biological Processes
- PNmerger 1.0 - Merge Biological Pathways and Protein Interaction Networks
- PNNS - Protein Network Neighbor Search
- Pointillist 2.1.2 - MATLAB Codes of Iterative Framework for Biological Modeling
- PolyFARM 0.3.4 - Data Mining software for Relational Data
- PottersWheel 4.0 - MatLab Toolbox of Mathematical Modeling of Dynamical Systems
- PPICompare 1.04 - Detection of Rewiring Events in Protein Interaction Networks
- PPIExtend 1.0 - Find Quasi-bicliques in PPI networks
- PPIXpress 1.23 - Specific Protein Interaction Networks from Transcript Expression
- Predictionet 1.36.0 - Inference for Predictive Networks designed for Genomic data
- PrePPItar 0.0.1 - Machine Learning Framework to Predict PPI Target for Drug
- PRIN - Predicted Rice Interactome Network
- PRINCESS - Protein Interaction Confidence Evaluation System with multiple data sources
- PRINCIPLE 1.0 - Associating Genes with Diseases via Network Propagation
- ProbTF - Transcription Factor Binding Prediction from multiple data sources
- Profppikernel 1.0.4 - Protein-protein Interaction Prediction
- PROM - Probabilistic Regulation of Metabolism
- ProMoT 0.8.5 - Process Modeling Tool
- ProRank 0.1 - Detection of Protein Complexes using a Protein Ranking algorithm.
- protein hypernetworks 1.0.2 - Logic Framework for Interaction Dependencies in Protein Networks
- ProteoLens 1.11 - A Visual Network Data Mining Tool
- PSN - Protein Pocket Similarity Networks
- PTHGRN - Post-translational Hierarchal Gene Regulatory Network
- pwOmics 1.24.0 - Pathway-based data integration of Omics data
- PyBioNetFit v1.1.2 - Fitting tool for Rule-based Models
- Pycellerator 1.0rc2 - Biological Simulation using Reaction-Like Arrows
- Pysces 0.9.6 - Python Simulator of Cellular Systems
- Qcut / HQcut - Finding Communities in Biology Networks
- Rast2Systrip 1.0.4 - Reconstruct and View Metabolic Networks
- RAVEN 2.5.1 - Reconstruction, Analysis, and Visualization of Metabolic Networks Toolbox
- RCytoscape 1.24.1 - Tools for Molecular Cartography
- ReactionFlow - Visualization tool for Causality Analysis in Biological Pathways
- Red - Inference of Epistatic Gene Networks
- REDEMPTION 20150708 – Reduced Dimension Ensemble Modeling and Parameter Estimation
- RedeR 1.34.0 - Interactive Visualization and Manipulation of Nested Networks
- Redi 1.0 - REaction-DIffusion simulator
- RedoxMech - Microscopic Kinetics Modeling framework for Oxidoreductases (EC 1)
- REDUCE 1.0 - Optimal Design of Gene Knock-out (KO) for the purpose of Gene Regulatory Network (GRN) Inference
- regEfmtool 3.3 - Regulatory Elementary Flux Mode Tool
- ReMoDiscovery - Inferring Transcriptional Module networks from ChIP-chip-, motif- and microarray data
- RENCO 0.3 - A Synthetic Regulatory Network Generator
- ReNE 1.95 - A Cytoscape Plugin for Regulatory Network Enhancement
- RenoDoI 1.1.0 - Visual Analysis of Biological Data-knowledge Networks
- Reposition 0.02 - Cytoscape Plugin for reuse of layouts
- ResponseNet v.3 - Revealing Signaling and Regulatory Networks linking Genetic and Transcriptomic Screening data
- RESQUE 1.0 - REduction-based scheme using Semi-Markov scores for networkQUEing
- ReTrace 1.03 - Infers Branching Metabolic Pathways
- RIDDLE - Network-assisted Gene Set Analysis
- RIMBANET - Reconstructing Integrative Molecular Bayesian Networks
- RINalyzer 2.0 - Cytoscape plugin of Visualization and Analysis of Biomolecular Networks
- RIP 1.1 - Predicting Target Genes of Transcription Factors
- RIPE 1.1 - Regulatory Network Inference
- RNAinteract 1.40.0 / RNAinteractMAPK 1.30.0 - Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi
- RobinViz 1.0 - Reliability Oriented Bioinformatic Networks Visualization
- RocketBugs / RocketBugsRender - Simulation of the Actin-based Motility of Listeria Monocytogenes
- RTN 2.10.1 - Reconstruction and Analysis of Transcriptional Networks
- RuleBender 2.3 - Biological Rule-based Modeling, Simulation, and Visualization
- runSBML 1.11 - Pathway Simulation Tool
- RXA 20100914 - Relative Expression Analysis of Gene Expession Profiles
- rxncon 2.0 - Reaction-contingency based bipartite Boolean modelling
- SAGPAR - StructurAl Grammar-based automated PAthway Reconstruction
- SAMNetWeb - Simultaneous Analysis of Multiple Networks
- SANTA 2.24.0 - Spatial ANalysis of NeTwork Associations
- SAPIN - Structural Analysis of Protein Interaction Networks
- SB.OS 1.4.1 - Systems Biology Operational Software DVD ISO Image
- SBEAMS 0.22.1 - Systems Biology Experiment Analysis Management System
- SBEToolbox 1.3.3 - MATLAB Systems Biology & Evolution Toolbox
- SBGN-ED 1.6 - Editing, Translating and Validating of SBGN Maps
- SBML Converters 20100413 - Conversions to & from SBML
- SBML Reaction Finder 1.2.1 - Extracts Chemical Reactions from SBML models
- SBML-PET-MPI 1.2 - Parallel Parameter Estimation Tool for SBML based Models
- SBML2SMW 1.0 - Extract Celldesigner Model to Semantic Mediawiki
- SBMLeditor 2.0-b1 - SBML File Editor
- SBMLsimulator 1.2.1 - Java Solver Implementation for SBML
- SBMLsqueezer 2.1 - Generate Kinetic Equations for Biochemical Networks
- SBMLToolbox 4.1.0 - SBML models toolbox for MATLAB users
- SBRT 2.0.0 - The Systems Biology Research Tool
- SBSI 1.4.5 - Systems Biology Software Infrastructure
- SBSI CellDesigner Plugin 20111025 - Bridge Functionalities of CellDesigner & SBSI
- SBW 2.12.2 - Systems Biology Workbench
- ScanToolBox 1.0 - Structural Cobra Add-oN for Metabolic Networks
- SDREM 1.2 - Signaling and Dynamic Regulatory Events Miner
- SEAS 1.0 - System for SEED-based Pathway Enrichment Analysis
- SemanticSBML 2.0 - Annotation Checking& Merging of Systems Biology Models
- SemanticSimilarity - Bien's measure of Semantic Similarity for Gene Ontology
- SemGen 4.2.3 - Semantics of Biological Processes
- SensA - Web-based Sensitivity Analysis of SBML models
- SensiPath 2.1.2 - Computer-aided Design of Sensing-enabling Metabolic Pathways
- SensSB 20120926 - Development and Sensitivity Analysis of Systems Biology Models
- SEPARATOR - Decompose Large Biochemical Networks into Smaller Subsystems
- Seq2pathway 1.25.1 - Pathway analysis of Next-generation Sequencing data
- SEREND 1.1 - SEmi-supervised REgulatory Network Discoverer
- Sets2Networks - Network Inference from Repeated Observations of Sets
- setsApp 2.2.0 - Save and Manipulate Sets of Nodes and Edges
- SGD-RJ - Stochastic Gradient Descent based on Reversible jump MCMC
- SGN Sim / SGNS2 2.1.170 - Stochastic Genetic Networks Simulator
- SiGN-SSM 1.3.0 / SiGN-L1 1.1.0 - Gene Network Estimation Software
- SigTran 3.0.4 - Cell Signaling Simulation Software
- SIM - Cell- and Gene-based Computer Model for Mammalian Somitogenesis
- SIMBA - Organization of the Yeast Molecular Network by Integrated Analysis of Genome-wide Data
- SimBioNeT 1.2.16 - Simulator of Biological Network Topology
- SimBoolNet 1.0 - Simulate the Dynamics of Signaling Transduction using Boolean networks
- simbTUM 3.0a - Simulation of Stochastic processes and ODE models in Biology
- SimCell 1.8.0b - DCA Cell simulator
- SIMCOMP 2.1.4 / SUBCOMP - Chemical Structure Similarity / Chemical Substructure Search
- Simmune v.2.3.1 - Generation of Comprehensive Models
- SimPheny to SBML l2v1 - Convert SimPheny output to SBML
- SimTrek 2.0 - Cytoscape plugin for Ontology-based Similarity Assessment of Biological Networks
- Simulac - Simulator for Complex Gene Expression Circuits
- SIREN 1.0 - Signing of Regulatory Networks
- SIRENE 1.1 - Supervised Inference of REgulatory NEtworks
- sLDA - Sparse Linear Discriminant Analysis
- SLIPPER - SeLf-Interacting Protein PrEdictoR
- SLML Tools v1.5.2 - Implement Generative Models of Subcellular Location
- SloppyCell - system for Modeling Biochemical Reaction Networks
- SmartCell v4.3 Beta3 - A Cell Network Simulation Program
- SME 1.8 - Sigmoid Model Explorer
- SMETANA 1.0 - Semi-Markov random walk scores Enhanced by consistency Transformation for Accurate Network Alignment
- Smoldyn 2.61 - Cell-scale Biochemical Simulator
- SNAVI 20081120 - Analysis and Visualization of Large-Scale Cell Signaling Networks
- SNPLS - Identifying Joint Modular Patterns of Gene-expression and Drug-response data
- Sorad 20130721 - Infer and Analyze Dynamic Signaling Pathways
- SOSlib 1.7.0 - ODE Solver for SBML
- Spartan 3.0.2 - Understanding Uncertainty in Simulations of Biological Systems
- SPECifIC - Sub-Pathway Extractor and Enricher
- SpectralNET 1.0 - Analyze Networks of Interactions
- SPEDRE - Systematic Parameter Estimation in Data-Rich Environments for Cell Signaling Dynamics
- SPEED 20110708 - Signaling Pathway Enrichment using Experimental Datasets
- SPEM 1.32.0 - S-system Parameter Estimation Method for Biological Networks.
- SPIA 2.44.0 - Signaling Pathway Impact Analysis
- SPiM 0.05 / SPiM Player 1.13 - Programming Language for Designing and Simulating Computer Models of Biological Processes
- spinal 2 - Scalable Protein Interaction Network Alignment
- SpotXplore 20100804 - Cytoscape plugin for Visual Exploration of Hotspot Expression in Gene Regulatory Networks
- SPSens 3.4 - Stochastic Parameter Sensitivity Analysis for Biochemical Networks
- SRSim 2.0.8 - Rule Based Modelling in 3d Space
- SSC 0.6 - Stochastic Simulation Compiler
- StemCellNet 1.3.3 - Network-oriented Investigations in Stem Cell Biology
- STEPP - Search Tool for Exploration of Petri net Paths
- STITCH 5.0 - Search Tool for Interactions of Chemicals and proteins
- StochDecomp 20131028 - Noise Decomposition in Stochastic Biochemical Systems
- STOCHSIM 1.4 - Stochastic Simulator for Biochemical Reactions
- STOCKS 2.0 - STOChastic Kinetic Simulation of Biochemical Processes
- STRING 11.0 - Search Tool for the Retrieval of Interacting Genes/Proteins
- stringgaussnet 1.1 - PPI and Gaussian Network Construction from Transcriptomic Analysis Results Integrating a Multilevel Factor
- Struct2Net 1.0 - Structure-based Computational Predictions of Protein-protein interactions
- structureViz - Link Visualization of Biological Networks in Cytoscape
- STSE - Spatio-Temporal Simulation Environment
- SubNet 2.0 - Subnetwork Extraction
- SubSeqer - Detection and Identification of Repetitive Elements in low-complexity Sequences
- SyBiL 2.1.5 / sybilSBML 3.0.5 / sybilFCF 0.2.1 - Systems Biology Library for R
- SYCAMORE 2016 - Systems Biology Computational Analysis and Modeling Research Environment
- symsim 0.1 - Sympatric Speciation Simulation for Recombining Microbial Populations
- SynTReN 1.2 - Generator of Synthetic Gene Expression data for Design and Analysis of Structure Learning algorithms
- SYSBIONS 04 - Nested Sampling for Systems Biology
- SysGenSim 1.2 - Simulation software for Systems Genetics
- Systems Biology Toolbox for MATLAB 1.8
- Systrip 1.0 - Investigation of Time-series data in the context of Metabolic Networks
- T7 v2.5 - Simulator for the intracellular Infection Kinetics of phage T7
- Tav4SB 0.2.2 - Web service operations for analysis of the Kinetic models of Biological Systems
- tDBN 0.1.4 - Polynomial-time algorithm for Learning optimal Tree-augmented Dynamic Bayesian Networks
- TEAK 20130207 - Topology Enrichment Analysis frameworK
- tEFMA 1.2 - Calculates Thermodynamically Feasible Elementary Flux Modes
- TENET V.1 - Topological Feature-based Target Characterization in Signaling Networks
- TIGER 1.2.0-beta - Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation
- TIGRESS 2.1 - Trustful Inference of Gene REgulation using Stability Selection
- TINGe 1.062 / GeNA 0.1 - Gene Networks Inference and Analysis
- TINKER - Design Metabolic Paths using the Known Universe of Enzymes and Reactions
- TinkerCell 20120703 - CAD Software for Synthetic Biology
- TissueNet v.2 - Human Tissue Protein-protein Interactions
- TopoGSA - Network Topological Gene Set Analysis
- TORQUE - Topology-Free Querying of Protein Interaction Networks
- TRaCE 0.1 - Transitive Reduction and Closure Ensemble
- TSN 1.0 - Expression Classification method from Small numbers of Biomolecules
- TSN-PCD / DFM-CIN - Identify Protein Complexes / Functional Modules from these TSNs
- TSNI / TSNI-integral - Time Series Network Identification
- TSP/TST (GPU) 1.1 - Top-Scoring Pair and Top-Scoring Triple on the GPU
- TST 1.4.3 - Tissue Simulation Toolkit
- TuRF-E 1.0 - Gene-gene Interaction Giltering with Ensemble of Filters
- Twixtrix r4 - Context-specific Transcriptional Regulatory Network Inference
- tYNA - Tool for Managing, Comparing and Mining Multiple Networks
- UBViz 0.9R04- Explore Metabolic Pathways in 3D
- VANESA 0.3 - Visualization and Analysis of Networks in System Biology
- VANTED 2.6.5 - Visualization and Analysis of Networks containing Experimental Data
- VCell 7.2 - Environment for Modeling & Simulation of Cell Biology
- Vernan - Specification, Construction, and Exact Reduction of State Transition System models of Biochemical Processes
- Vesimulus 2.1 - Molecular Stochastic Simulations of Metabolic or Signaling Systems
- vExplorer 2.0 - Function Explorer
- VirHostNet 2.0 - Knowledgebase for the management and analysis of Proteome Wide Virus-host Interaction Networks
- VirtualLeaf 1.0.2 - Plant Tissue Simulation
- visANT 5.53 - Integrative Visual Analysis Tool for Biological Networks & Pathways
- ViSEN 1.0beta0.3 - Visualization tool for Statistical Epistasis Networks
- VISIBIOweb 1.1 - pathway visualization software for BioPAX
- Visualisation tools - Display 2-loop & 3-loop Arabidopsis Clock Models
- VitaPad 0.6.1c - Visualize and Analyze Biological Pathways
- VLAD 1.5.1 - Visualize GO Annotations
- VToD - Voting based Cancer module Identification by combining Topological and Data-driven Properties
- WaRSwap - Network Motif Discovery
- WebPropagate - Web Server for Network Propagation
- WinSAAM 3.0 - The Simulation, Analysis and Modeling Software
- WordCloud 3.1.3 - Cytoscape plugin to Generate a Visual Summary of a Network
- Workflow4Metabolomics 4.0 - Metabolomics data Processing, Analysis and Annotation
- Wormpath 1.0.4 - Searching for Molecular Interaction Networks in Caenorhabditis Elegans
- X2K 1.6.1207 - mRNA Profiling Linked to Multiple Upstream Regulatory Layers
- xCellerator 0.91 - Mathematica Package for Biological Modeling
- XlinkCyNET 1.4.3 - Generate Residue-to-residue connections provided by XL-MS in PIN
- XTMS - Pathway Design in an eXTended Metabolic Space
- YANAsquare 201212 / YANAvergence - Integrated Network Reconstruction, Visualization and Analysis
- yasimSBML 1.0.1 - Simulate Metabolic Network depending on the Flux Distribution
- ZOOMA 1.0-beta - Discover Optimal Ontology Mappings
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