Groups working on networks and complex systems

• Luigi F. Agnati:
  http://www.cibiotech.it/asp/dtglresponsabile.asp?ID_socio=77
• Reka Albert:
  http://www.phys.psu.edu/~ralbert/
• László A. Barabási:
  www.BarabasiLab.com
• Adam P. Arkin:
  http://gobi.lbl.gov/~aparkin/People/TheBoss.html
• György Buzsáki:
  http://osiris.rutgers.edu/frontmid/indexmid.html
• Cambridge Networks Network
  http://www.cnn.group.cam.ac.uk/
• Luciano Costa
  http://cyvision.ifsc.usp.br/Cyvision/
  
• Murray Gell-Mann:
  http://www.santafe.edu/sfi/People/mgm/
• Mark Granovetter:
  http://www.stanford.edu/
  dept/soc/people/faculty/granovetter/granovet.html
• Balázs Gulyás:
  http://www.cns.ki.se/en/research/
  balazs_gulyas/balazs_gulyas/description.html
• Stuart A. Kaufmann:
  https://en.wikipedia.org/wiki/Stuart_Kauffman
• Jose Fernando Mendes, GNET:  http://www2.fis.ua.pt/grupoteorico/gteorico.htm
• Mark J. Newman:
  http://www.santafe.edu/~mark/
• Csaba Pléh:
  http://www.itm.bme.hu/ktk/csaba/
• Sándor Pongor:
  http://www.icgeb.trieste.it/RESEARCH/TS/Pongor.htm
• Ricard V. Solé:
  http://complex.upf.es/~ricard/
• Steven H. Strogatz:
  http://tam.cornell.edu/Strogatz.html
• Eörs Szathmáry:
  http://www.colbud.hu/main/FellowSection/permanentfellows.html
• Tamás Vicsek:
  http://angel.elte.hu/~vicsek/
  http://www.angel.elte.hu/clustering
• Duncan J. Watts:
  http://smallworld.columbia.edu/watts.html
• Peter Wolynes:
  http://www-chem.ucsd.edu/Faculty/bios/wolynes.html
• EmergeNet Group
  http://www.emergenet.org
  
• Cellular Network Biology Group:
  http://www.linkgroup.hu/links.php

Groups working with signaling networks

• Marc Vidal
  interactome modeling, molecular networks (C. elegans, Human)
  http://vidal.dfci.harvard.edu/
• Mark Gerstein
  tYNA Network Analyzer, literature-derived networks, predicting protein-protein interactions
  http://networks.gersteinlab.org/
• Sarah Teichmann
  organisation of protein domains in genome sequences, in metabolic pathways and in protein-protein interactions
  http://www.mrc-lmb.cam.ac.uk/genomes/Sarah/
• Tony Pawson
  mechanisms that underlie intracellular signal transduction, modular protein domains, synthetic biology
  http://pawsonlab.mshri.on.ca/
• Jason A. Papin
  signaling networks, cell-cell signaling, pathogen-host interactions
  http://www.bme.virginia.edu/csbl/
• Ravi Iyengar
  cellular signaling, heterotrimeric G proteins, dynamics of network topology
  http://www.mssm.edu/labs/iyengar/
• Harel Weinstein
  biomedicine, multidisciplinary approach, systems biology
  http://icb.med.cornell.edu/index.xml
• Trey G. Ideker
  comparative network science, DNA damage
  http://chianti.ucsd.edu/idekerlab/
  
• Hiroaki Kitano
  robustness of biological systems, metabolic pathways, protein-protein interactions
  http://www.symbio.jst.go.jp/symbio2/index.html http://www.systems-biology.org/
• Edda Klipp
  signal transduction, stress, yeast, systems biology
  http://www.molgen.mpg.de/~ag_klipp/
• Andre Levchenko
  bioinformatics, systems modelling
  http://www.icm.jhu.edu/
• Boris N. Kholodenko
  systems biology of cellular signaling, metabolic and gene networks
  http://cellnetworks.org/
• Upinder Bhalla
  quantitative cellular signaling, programing signaling pathways (MAPK)
  http://www.ncbs.res.in
• Bernhard O. Palsson
  metabolic and signaling networks, mathematical analysis
  http://gcrg.ucsd.edu/
• Wendell Lim
  protein-protein recognition, protein switches and networks, network evolution, synthetic biology
  http://www.ucsf.edu/limlab/
  
• Cellular Network Biology Group:
  http://www.linkgroup.hu/links.php

Biological science links

Aging databases

• AgeID: aging genes database http://uwaging.org/genesdb/index.php
• AnAge: Animal aging and longevity database http://genomics.senescence.info/species/
• GenAge: aging genes database http://genomics.senescence.info/genes/
• MatrixDB: extracellular aging-related PPI network http://matrixdb.ibcp.fr/
• NetAge: gene sets and microRNA-regulated PPI networks for longevity www.netage-project.org

Chemical compound similarity networks

• ChemProt: http://www.cbs.dtu.dk/services/ChemProt a database of more than 700,000 chemicals, 30,000 proteins and their over 2 million interactions integrated to a human protein-protein interaction network having over 400,000 interactions
• Connectivity Map http://www.broadinstitute.org/cmap similarity of mRNA expression profiles extended with disease mRNA expression profiles
• iCTNet Cytoscape plug-in, http://flux.cs.queensu.ca/ictnetphenotype/single-nucleotide polymorphism (SNP) associations, protein-protein interactions, disease-tissue, tissue-gene and drug-gene relationships: integrated Complex Traits Networks
• IMID, http://integrativebiology.org protein-protein interactions, protein-small molecule interactions, associations of interactions with pathways, species, diseases and Gene Ontology terms with the user-selected integration of manually curated and/or automatically extracted data: integrated molecular interaction database
• SARANEA: http://www.limes.uni-bonn.de/forschung/abteilungen/Bajorath/labwebsite/downloads/saranea/view a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets

Disease related web-resources

• CIPHER: http://rulai.cshl.edu/tools/cipher closeness of unrelated proteins is calculated in the interactome from protein products of disease-related genes, and compared with phenotype similarity profile: large closeness marks a potential new disease-related gene
• DADA: http://compbio.case.edu/dada statistically corrects random walk-based prediction with the degree distribution of the network
• DisGeNET Cytoscape plug-in: http://ibi.imim.es/DisGeNET/DisGeNETweb.html, human disease network
• Endeavour: http://esat.kuleuven.be/endeavour integrative method using similarities of neighbors or shortest paths in multiple data sources including interactomes
• Genes2Networks: http://actin.pharm.mssm.edu/genes2networks, new disease-related genes are predicted by their interactome closeness to known disease-related proteins
• GPEC Cytoscape plug-in: http://sourceforge.net/p/gpec random walks in the interactome are started from protein products of disease-related genes: frequent visits of a previously unrelated protein mark a potential new disease-related gene
• iCTNet: a Cytoscape plug-in to construct an integrative network of diseases, associated genes, drugs and tissues (http://www.cs.queensu.ca/ictnet)
• Phenopred: http://www.phenopred.org integrative method using similarities of neighbors or shortest paths in multiple data sources including interactomes
• PRINCIPLE/PRINCE Cytoscape plug-in http://www.cs.tau.ac.il/~bnet/software/PrincePlugin iterative steps of information flow from disease-related and between interacting proteins: after convergence a large flow of a previously unrelated protein marks potential new disease-related gene
• Prioritizer: http://129.125.135.180/prioritizer, constructs an integrative network and predicts candidate genes by their network closeness to known disease-related genes
• rcNet: http://phegenex.cs.umn.edu/Nano calculates rank coherences between the integrated network characteristic to the target disease and unrelated diseases
• VAVIEN: http://diseasegenes.org calculates neighborhood similarity in the interactome and prioritizes candidate genes

Drug-target related resources

• Integrated drug and drug target information resource
  • Balestraweb: Predicts the interactions of drugs with their potential targets (by providing only a drug identifier) or targets with their potential drugs (by providing only a target identifier)and any drug-target pair (by providing both a drug and a target identifier). http://balestra.csb.pitt.edu/
  • DrugBank: http://www.drugbank.ca
  • PharmGKB: http://www.pharmgkb.org
  • Therapeutic Target Database: http://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp
  • MATADOR: http://matador.embl.de/
  • Supertarget: http://insilico.charite.de/supertarget/
• Drug targets of neglected tropical diseases
  • TDR: http://tdrtargets.org/
• Drug – drug target docking information resource
  • BindingDB: http://www.bindingdb.org
  • BioDrugScreen: http://www.biodrugscreen.org
• Information on drug targets
  • PDTD - Potential Drug Target Database: http://www.dddc.ac.cn/pdtd
• Integrated network resource of chemical-protein interactions
  • STITCH 3: http://stitch.embl.de
  • Dr. PIAS - Druggable Protein-protein Interaction Assessment System: http://www.drpias.net/pias_top.php
• Drug combination database:
  • DCDB: http://www.cls.zju.edu.cn/dcdb
• Drug side-effect resource:
  • SIDER: http://sideeffects.embl.de
• Drug-induced toxicity related protein database
  • DITOP: http://bioinf.xmu.edu.cn/databases/ADR/index.html

Gene databases, List of E. coli gene database resources

• The yeast genome database: http://www.yeastgenome.org/
• The C. elegans knowledgebase: http://www.wormbase.org
• The Drosophila knowledgebase: http://www.flybase.org
• The database of selected eukaryotic genomes: http://www.ensembl.org

Genetic networks

• Gene interactions and pathways (genetic networks): http://www.biocarta.com/genes/allpathways.asp
  http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm
  http://www.its.caltech.edu/~mirsky/endomes.htm
  http://www.cifn.unam.mx/Computational_Genomics/regulondb
  http://strc.herts.ac.uk/bio/maria/NetBuilder/
  http://www.genome.jp/kegg/
• Genetic Interaction Predictor for C. elegans: http://tenaya.caltech.edu:8000/predict/
• Yeast sporulation network http://cmgm.stanford.edu/pbrown/sporulation
• Gene expression databases:
  http://www.ncbi.nlm.nih.gov/geo/
  http://www.mged.org/
  http://expression.gnf.org/
  http://genome-www5.stanford.edu/
• OpenStemCellWiki, a Differentially Expressed Connected Subnetwork (DECS) found to be active in human embryonic stem cells: http://www.openstemcellwiki.org

Protein databases

• BioGrid http://thebiogrid.org/
• IntAct experimentally verified, curated data  http://www.ebi.ac.uk/intact/main.xhtml
• MINT experimentally verified, curated data  http://160.80.34.4/mint/Welcome.do 
• STRING http://string-db.org/
• NetAge: Protein identifiers across multiple source databases, http://netage-project.org/
• http://www.ebi.ac.uk/Tools/picr/
• Yeast: http://www.proteome.com/YPDhome.html
• Human: http://www.hprd.org/
• Universal Protein Resource (UniProt): http://www.ebi.uniprot.org

Protein structure tools and networks

• Prediction of protein binding regions in disordered proteins http://anchor.enzim.hu
• Prediction of intrinsically unstructured proteins http://iupred.enzim.hu/
• RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape http://protein.bio.unipd.it/ring/

Protein networks

• 3did
  domain-domain interaction with 3D data
  http://3did.irbbarcelona.org
• APID
  interactome exploration
  http://bioinfow.dep.usal.es/apid/index.htm
• BioGRID
  integrated protein-protein interaction data
  http://thebiogrid.org
• BioProfiling
  inference of network data from expression patterns
  http://www.bioprofiling.de
• C. elegans: http://vidal.dfci.harvard.edu/interactomedb/i-View/interactomeCurrent.pl
• DIP
  experimental protein-protein interaction data
  http://dip.doe-mbi.ucla.edu
• DomainGraph
• Drosophila: http://proteome.wayne.edu/PIMdb.html
• Cytoscape plug-in for domain-domain interaction analysis
  http://domaingraph.bioinf.mpi-inf.mpg.de
• DOMINE
  domain-domain interaction data
  http://domine.utdallas.edu
• Estrella
  detection of mutually exclusive protein-protein interactions
  http://bl210.caspur.it/ESTRELLA/help.php
• Filtered high throughput database of yeast, worm, fly and human PIN: http://helix.protein.osaka-u.ac.jp/htp/htp.php
• HAPPI
  human protein-protein interaction data
  http://discern.uits.iu.edu:8340/HAPPI
• HPRD
  human protein-protein interaction data
  http://www.hprd.org
• Hubba
  identification of hubs (potentially essential proteins)
  http://hub.iis.sinica.edu.tw/Hubba
• IntAct
  curated protein-protein interaction data
  http://www.ebi.ac.uk/intact/main.xhtml
• IntNetDB
  human protein-protein interaction data
  http://hanlab.genetics.ac.cn/sys
• IRView
  protein interacting regions
  http://ir.hgc.jp
• MEGADOCK
  protein 3D structure docking algorithm for large scale PPI-s
  http://www.bi.cs.titech.ac.jp/megadock/
• MiMI
  protein interaction information
  http://mimi.ncibi.org
• MINT
  protein-protein interactions in refereed journals
  http://mint.bio.uniroma2.it/mint
• Mitochondrial interactome: http://mitointeractome.kobic.kr
• MOPED:
  multi-omics profiling expression database
  https://www.proteinspire.org/MOPED/mopedviews/proteinExpressionDatabase.jsf
• NetAligner
  interactome comparison
  http://netaligner.irbbarcelona.org
• Pathwaylinker
  combines protein-protein interaction and signaling data
  http://PathwayLinker.org
• PINA
  interactome analysis
  http://cbg.garvan.unsw.edu.au/pina
• PIPs
  human protein-protein interaction prediction
  http://www.compbio.dundee.ac.uk/www-pips
• PPISearch
  search of homologous protein-protein interactions across many species
  http://gemdock.life.nctu.edu.tw/ppisearch
• STRING
  integrated protein-protein interaction data
  http://string.embl.de
• UniHI
  human protein-protein interaction and drug target data
  http://www.unihi.org
• Yeast:
  http://yeast.cellzome.com
  http://www.bind.ca
  http://dip.doe-mbi.ucla.edu/
  http://vidal.dfci.harvard.edu/fyi/
• TISSUES:
  tissue expression database
  http://tissues.jensenlab.org/Search

Text search engines for extracting information on bionetwork

• Text mining: www.textrend.org
• iHOP provides the network of genes and proteins as a natural way of accessing the millions of abstracts in PubMed. By employing genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed becomes bound together into one navigable resource. : http://www.ihop-net.org/UniPub/iHOP/
• Arrowsmith: a tool for identifying links between two sets of Medline articles: http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/start.cgi
• Connect-Molecules Query: will attempt to find a sequence of interactions that connect two or more given molecules: http://cmap.nci.nih.gov/PW/Connect
• A Compendium of Free, Public Biomedical Text Mining Tools Available on the Web: http://arrowsmith.psych.uic.edu/arrowsmith_uic/tools.html
• Textpresso: http://www.textpresso.org/
• GoPubMed - Ontology based literature search: http://www.gopubmed.org/

Datamining sites for network buildings

• A rich collection of different pathway websites: http://www.pathguide.org
• MultiParanoid A database of multi-species clusters of orthologs: http://multiparanoid.cgb.ki.se
• MINT database for functional interactions between biological molecules (proteins, RNA, DNA): http://mint.bio.uniroma2.it/mint/Welcome.do
• pSTIING: knowledgebase about protein-protein, ligand-receptor interactions, receptor-cell type information and signal transduction pathways: http://pstiing.licr.org/
• BioGRID
  a database of physical and genetic interactions for model organisms including Homo sapiens, Saccharomyces cerevisiae, Mus musculus, C. elegans, and Drosophila melanogaster: http://www.thebiogrid.org/
• List of databases of interactions: http://www.biodirectory.com/directory/
  Molecular_interactions/Databases_of_interactions_394.html
• Functional annotation site: http://david.abcc.ncifcrf.gov/

Chemical reactions, metabolic networks

• BRENDA: Comprehensive enzyme data resource, http://www.brenda-enzymes.info
• HMDB: Human Metabolome Database, http://www.hmdb.ca
• Metabolic networks
  • yeast: http://systemsbiology.ucsd.edu/organisms/yeast.html
  • E. coli: http://gcrg.ucsd.edu/organisms/ecoli.html
• Metabolic pathway resource
  • HumanCyc: http://www.humancyc.org
  • KEGG: http://www.genome.jp/kegg
  • MetaCyc: http://www.metacyc.org
• Modeling of biochemical reactions: http://www.gepasi.org/
• Red blood cell: http://systemsbiology.ucsd.edu/organisms/rbc.html
• SMPDB: Small Molecule (e.g., drug) Pathway Database, http://www.smpdb.ca
• Whole cell simulation:
  • http://www.e-cell.org/
  • http://www.nrcam.uchc.edu/
• YeastNet: Yeast metabolic network, http://www.comp-sys-bio.org/yeastnet

Signaling pathway analyzer tools

• Signaling pathway resources
  • IPAVS: http://ipavs.cidms.org
  • NCI Nature – Pathway Interaction Database: http://pid.nci.nih.gov
  • NetPath: http://netpath.org
  • Reactome: http://www.reactome.org
• Transcription factor – transcription factor binding information
  • JASPAR: http://jaspar.genereg.net
  • MPromDB: http://bioinformatics.wistar.upenn.edu/MPromDb
  • OregAnno: http://oreganno.org
  • PAZAR: http://www.pazar.info
  • TFe: http://www.cisreg.ca/cgi-bin/tfe
• mRNA-miRNA target information
  • PicTar: http://pictar.mdc-berlin.de
  • TarBase: http://diana.cslab.ece.ntua.gr/tarbase
  • TargetScan: http://www.targetscan.org
• Integrated resource of miRNA target information
  • miRecords: http://mirecords.umn.edu
  • miRGen: http://diana.cslab.ece.ntua.gr/mirgen
• Regulatory information of miRNAs
  • PutMir: http://www.isical.ac.in/~bioinfo_miu/TF-miRNA.php
  • TransMir: http://cmbi.bjmu.edu.cn/transmir
• Integrated signaling network resources
  • IntegromeDB: http://www.integromedb.org
  • SignaLink 2.0: http://signalink.org
  • TranscriptomeBrowser 3.0: http://tagc.univ-mrs.fr/tbrowser

• Biological Networks: http://brak.sdsc.edu/pub/BiologicalNetworks/reg.php
• Hippron: Dynamic Signaling Maps: http://www.hippron.com/hippron/
• Ingenuity Pathway Analyser: https://analysis.ingenuity.com/
• SiTNA: http://www.eco.ethz.ch/SITNA/

Social networks

• Social network analysis software: http://en.wikipedia.org/wiki/Social_network_analysis_software
• Menopause and Black Cohosh Information center
• small world home

Complex system evolution

• NetLogo: a cross-platform multi-agent programmable modeling environment: http://ccl.northwestern.edu/netlogo/
• Physis - software tool for studying the evolution of self-replcating  machine-code  computer programs: http://physis.sourceforge.net
• Starlogo: Complex system modelling program: http://education.mit.edu/starlogo/

Network analysis

• BIANA - http://sbi.imim.es/web/BIANA.php - a software framework for compiling biological interactions and analyzing networks
• BiMat: bipartite network modularity and nestedness analysis - http://www.mathworks.com/matlabcentral/fileexchange/47008-bimat
• BisoGenet - http://bio.cigb.edu.cu/bisogenet - Bioinformatic tool for searching, visualizing and analyzing molecular interactions information around a set of genes/proteins
• Boolean Network Modeling - http://code.google.com/p/booleannet/ - Intuitive and accessible tools for simulating biological regulatory networks in a boolean formalism. Using this simulator biologist and bioinformaticians can specify their system in a simple textual language then explore various dynamic behaviors via a web interface or an application programming interface (API).
• Centrality measures toolbox - http://www.network-centrality.com/
• CitNetExplorer is a software tool for visualizing and analyzing citation networks of scientific publications. The tool allows citation networks to be imported directly from the Web of Science database. Citation networks can be explored interactively, for instance by drilling down into a network and by identifying clusters of closely related publications. http://www.citnetexplorer.nl
• Conan: a platform for complex network analysis (network reverse engineering, topological entropy, fractal dimension, modularization, etc.) http://github.com/rhz/conan/
• Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data, http://www.cytoscape.org/
• CerebraL: it uses subcellular localization annotation to create a layered view of a cell, a Cytospace plugin http://www.pathogenomics.ca/cerebral/
• Dynamic multi-level network analysis http://www.dynanets.org/
• Game theoretic centrality - http://www.game-theoretic-centrality.com/
• Gephi: visualization and exploration platform for networks and complex systems http://gephi.org/
• Graph partitioning algorithms and test graphs:
  http://staffweb.cms.gre.ac.uk/~c.walshaw/partition/
• GraphCrunch 2 - http://bio-nets.doc.ic.ac.uk/graphcrunch2 - An open source, multi-platform (Windows and Linux) software tool for network modeling, alignment and clustering that parallelizes computationally intensive tasks.
• GUESS, a network visualization and analysis tool, http://graphexploration.cond.org/index.html
• KNIME [naim] (www.knime.org) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network.
• MuxViz: visualization of multilayer networks https://github.com/manlius/muxViz
• Network modularization tools
• Agarwal method http://www-scf.usc.edu/~gaurava/
• Caflish method http://www.biochem-caflisch.uzh.ch/public/5/network-clusterization-algorithm.html
• CFinder for overlapping modules http://cfinder.org
• COS: parallel algorithm to find k-cliques
• Clauset algorithms http://cs.unm.edu/~aaron/research/fastmodularity.htm http://tuvalu.santafe.edu/~aaronc/hierarchy/
• Gregory’s methods like CONGA http://www.cs.bris.ac.uk/~steve/networks/index.html
• Jerarca hierarchical clustering method, http://jerarca.sourceforge.net/
• Latapy-Pons Walktrap http://www-rp.lip6.fr/~latapy/PP/walktrap.html
• Louvain method http://sites.google.com/site/findcommunities/
• Lumped Markov-chain community finding method (http://home.dei.polimi.it/piccardi/FTNCbyLMC.html)
• MCL, Markov Cluster Algorithm http://www.micans.org/mcl/
• ModuLand for pervasively overlapping modules www.linkgroup.hu/modules.php
• Nepusz method for overlapping modules http://www.cs.rhul.ac.uk/home/tamas/assets/files/fuzzyclust-static.tar.gz
• Radicchi method http://filrad.homelinux.org/Data/
• Rosvall – Bergstom Infomap http://www.tp.umu.se/~rosvall/code.html 
• Wakita method http://ken-wakita.net/research/en/community-structure-analysis/
• Wiggins methods http://www.columbia.edu/~chw2/code.html
• NetworKit: a complex network analysis tool to assess degree distribution, connected components, clustering coefficients, community detection, k-core decomposition, degree assortativity and centrality. http://parco.iti.kit.edu Download it!
• Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research. http://nwb.slis.indiana.edu/
• PyNetMet -- a Python program package for network (especially metabolic network) analysis, http://pypi.python.org/pypi/PyNetMet
• Pyunicorn: a time-series + network analysis tool package: https://github.com/pik-copan/pyunicorn
• RINalyzer - http://www.rinalyzer.de/ - A Cytoscape plugin to link Cytoscape with UCSF Chimera and thus to analyze and visualize residue interaction networks (RINs).
• RING - http://protein.bio.unipd.it/ring/ - RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape.
• Social network analysis software http://en.wikipedia.org/wiki/Social_network_analysis_software
• tnet - analysis of weighted, two-mode and longitudinal networks: http://opsahl.co.uk/tnet/content/view/15/27/
• UCSF Chimera - http://www.cgl.ucsf.edu/chimera/ - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
  • VisANT: a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways http://visant.bu.edu/
• Wordom - http://wordom.sf.net - Wordom is a command line utility for molecular structure and dynamics analysis. It is also able to manipulate and convert dcd, xtc, pdb, crd and xyz files and can be used in shell scripts or in custom modules.

Network comparison methods

• AlignNemo:
  Uncovers subnetworks of proteins and uses an expansion process, which gradually explores the network beyond the direct neighborhood. http://sourceforge.net/p/alignnemo
• Differential dependency network analysis
  A set of conditional probabilities is proposed as a local dependency model, and a learning algorithm is developed to show the statistical significance of the local structures. http://www.cbil.ece.vt.edu/software.htm
• Graphcrunch2, C-GRAAL, MI-GRAAL
  Compares networks with random networks. Additionally, clusters nodes based on their topological similarities in the compared networks. http://bio-nets.doc.ic.ac.uk/graphcrunch2; http://bio-nets.doc.ic.ac.uk/MI-GRAAL
• IsoRankN (IsoRank Nibble)
  Uses spectral clustering on the induced graph of pair-wise alignment scores. http://isorank.csail.mit.edu
• MetaPathway-Hunter
  Finds tree-like pathways in metabolic networks. http://www.cs.technion.ac.il/~olegro/metapathwayhunter
• MNAligner
  Combines molecular and topological similarity using integer quadratic programming, enabling the comparison of weighted and directed networks and finding cycles beyond tree-like structures. http://doc.aporc.org/wiki/MNAligner
• Module Preservation
  Uses several module comparison statistics based on the adjacency matrix, or on the basis of pair-wise correlations between numeric variables. http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ModulePreservation
• NeMo
  Detects frequent co-expression modules among gene co-expression networks across various conditions. http://zhoulab.usc.edu/NeMo
  
• NetAlign
  Aligns conserved network substructures. http://netalign.ustc.edu.cn/NetAlign
  
• NetAligner
  Compares whole interactomes, pathways and protein complexes of 7 organisms. http://netaligner.irbbarcelona.org
• NetMatch
  Finds subgraphs of the original network connected in the same way as the querying network. Can also handle multiple edges, multiple attributes per node and missing nodes. http://baderlab.org/Software/NetMatch
  
• PathBLAST
  Finds smaller linear pathways in protein-protein interaction networks. http://www.pathblast.org
  
• PINALOG
  Combines information from protein sequence, function and network topology. http://www.sbg.bio.ic.ac.uk/~pinalog
  
• Rahnuma
  Represents metabolic networks as hypergraphs and computes all possible pathways between two or more metabolites. http://portal.stats.ox.ac.uk:8080/rahnuma

Network datasets

• Alex Arenas datasets: http://deim.urv.cat/~aarenas/data/welcome.htm
• Barabasi network data: http://www.barabasilab.com/rs-netdb.php http://www.nd.edu/~networks/resources.htm
• Benchmark graphs of Santo Fortunato: http://sites.google.com/site/santofortunato/inthepress2
• Connectome, human cortex (96 people, 1015 nodes) http://pitgroup.org/connectome/
• Ecological networks: a compehensive map of many datasets http://www.web-of-life.es/map.php
• FunCoup: genome-wide functional coupling of 11 organisms http://funcoup.sbc.su.se/help/
• Gephi datasets: http://wiki.gephi.org/index.php/Datasets
• Indiana University datasets: http://iv.slis.indiana.edu/db/index.html
• International network archive http://www.princeton.edu/~ina/data/index.html
• Mark Newman network data: http://www-personal.umich.edu/~mejn/netdata/
• Mouse cortical connectivity: http://www.mouseconnectome.org
• Network time series data-sources http://www.stanford.edu/group/sonia/dataSources/index.html
• Pajek datasets: http://vlado.fmf.uni-lj.si/pub/networks/data/
• RINdata - http://rinalyzer.de/rindata.php - 3D protein structure dataset created with RINalyzer/RINerator from Protein Data Bank.
• RING - http://protein.bio.unipd.it/ring/ - RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape.
• Social network datasets: http://datamob.org/datasets/tag/social-networks
• Stanford large network datasets: http://snap.stanford.edu/data/
• Thesaurus of synonym words:
  http://www.visualthesaurus.com/landing/?ad=cdo&utm_medium=default
  &utm_campaign=VT&utm_source=cdo&word=functionality
• Trust network datasets: http://www.trustlet.org/wiki/Trust_network_datasets
• UciNet datasets: http://vlado.fmf.uni-lj.si/pub/networks/data/UciNet/UciData.htm

Network visualization

• Arena 3D: visualizes biological networks in 3D: http://arena3d.org/
  
• ArrayXPath : http://www.snubi.org/software/ArrayXPath
• AVIS: viewer of signaling networks, http://actin.pharm.mssm.edu/AVIS2
• BioLayout Express 3D: general network visualization and analysis tool, http://www.biolayout.org
  A Chopin nocturne in a network sense: http://www.youtube.com/watch?v=asDXpfFMKNA
• BiologicalNetworks: http://biologicalnetworks.net
• BioTapestry: http://www.biotapestry.org
• BisoGenet - http://bio.cigb.edu.cu/bisogenet - Bioinformatic tool for searching, visualizing and analyzing molecular interactions information around a set of genes/proteins
• CellDesigner: biochemical network drawing tool, http://www.celldesigner.org
• Cell Illustrator: http://www.cellillustrator.com
• CFinder: visualization of densely overlapping groups, http://www.cfinder.org/
• Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data, http://www.cytoscape.org/
• DIMES: internet visualization, http://www.netdimes.org/new/?q=node/17
• Gephi: visualization and exploration platform for networks and complex systems http://gephi.org/
• GenePro: interactome Cytoscape plug-in, http://wodaklab.org/genepro
• GeneWays: http://anya.igsb.anl.gov/Geneways/GeneWays.html
• GEOMIi: http://sydney.edu.au/engineering/it/~visual/valacon/geomi/
• Gephi: general network visualization tool, http://gephi.org
• Graphviz: general network visualization tool, http://www.graphviz.org
• Gridlayout: http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm
• GUESS, a network visualization and analysis tool, http://graphexploration.cond.org/index.html
• Hive Plots: general network visualization tool, http://www.hiveplot.com
• Hybridlayout: http://www.cadlive.jp/hybridlayout/hybridlayout.html
• Hyperdraw: R package, hypergraph visualization, http://www.bioconductor.org/packages/release/bioc/html/hyperdraw.html
• IM Browser: http://proteome.wayne.edu/PIMdb.html
• IPath: metabolic pathway visualizer, http://pathways.embl.de
• KGML-ED: http://kgml-ed.ipk-gatersleben.de
• LEDA: general network analysis and visualization tool, http://www.algorithmic-solutions.com/leda/about/index.htm
• MAVisto: http://mavisto.ipk-gatersleben.de
• Medusa: interactome visualizer, http://coot.embl.de/medusa
• ModuLand: Cytoscape plug-in for visualization of hierarchical modules, www.linkgroup.hu/modules.php
• Multilevel Layout: Cytoscape plug-in for visualization of hierarchical modules, http://code.google.com/p/multilevellayout
• MuxViz: visualization of multilayer networks https://github.com/manlius/muxViz
• NAViGaTOR: http://ophid.utoronto.ca/navigator
• NetMiner: general network analysis and visualization tool, http://www.netminer.com/index.php
• Network Workbench: A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research. http://nwb.slis.indiana.edu/
• Ondex: data visualization and integration, http://www.ondex.org
• Osprey is a software platform for visualization of complex interaction networks: http://biodata.mshri.on.ca/osprey/servlet/Index
• Pajek: http://pajek.imfm.si/doku.php
• PathDraw: http://rospath.ewha.ac.kr/toolbox/PathwayViewerFrm.jsp
• Pathway Tools: metabolic and transcription regulatory networks, http://bioinformatics.ai.sri.com/ptools
• PATIKA: pathway analyzer, http://www.patika.org
• Paup for phylogenetic trees: http://paup.csit.fsu.edu
• PaVESy: http://pavesy.mpimp-golm.mpg.de/PaVESy.htm
• PhyloGrapher: http://www.atgc.org/PhyloGrapher
• PIMWalker, protein-protein interaction network visualizer, http://pimr.hybrigenics.com 
• PIVOT: protein interaction visualization, http://acgt.cs.tau.ac.il/pivot
• PolarMapper: protein interaction + mRNA networks, http://kdbio.inesc-id.pt/software/polarmapper
• ProteinNetVis, protein network visualizer, http://graphics.cs.brown.edu/research/sciviz/proteins/home.htm
• ProteoLens, general network analysis and visualization tool, http://bio.informatics.iupui.edu/proteolens
• RedeR: R and Bioconductor package for visualization of hierachical modules, http://bioconductor.org/packages/release/bioc/html/RedeR.html
• RING - http://protein.bio.unipd.it/ring/ - RING is a web server that can be used to derive protein residue interaction networks, i.e. different physical/chemical interactions at atomic level, to be visualized with Cytoscape.
• SoNIA: network image animator, http://www.stanford.edu/group/sonia
• Text visual representation: http://www.textarc.org/
• Transcriptome-Browser, gene transcription and interactome networks, http://tagc.univ-mrs.fr/tbrowser
• UCSF StructureViz - http://www.cgl.ucsf.edu/cytoscape/structureViz/ - UCSF structureViz is a Cytoscape plugin that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera.
• VANTED: http://vanted.ipk-gatersleben.de
• VisANT: a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways http://visant.bu.edu/
• VitaPad: http://sourceforge.net/projects/vitapad
• WebInterViewer: http://interviewer.inha.ac.kr
• Web-site graphs: http://www.aharef.info/2006/05/websites_as_graphs.htm http://www.aharef.info/static/htmlgraph/
• yFiles: http://www.yworks.com/en/index.html
• yWays: http://www.yworks.com/en/products_yfiles_extensionpackages_ep2.htm

Other mathematical tools

• The database of useful biological numbers: http://bionumbers.hms.harvard.edu/default.aspx
• Differential equation solvers:
  http://www.berkeleymadonna.com
  http://www.math.pitt.edu/~bard/xpp/whatis.html

• NIH-Image, an image analysis software: http://rsb.info.nih.gov/nih-image/Default.html
• R statistical computing and graphics http://www.r-project.org/
• StochSim: stochastical simulation of biochemical reactions: http://www.ebi.ac.uk/~lenov/stochsim.html
• Text mining www.textrend.org

Related organizations

• Hungarian Cell Stress Society
  (an affiliate of Cell Stress Society International)
  • Annual report 2005.
  • Annual report 2006.
  • Annual report 2007.
  • Annual report 2008.
  • Annual report 2009.
  • Annual report 2010.