Table 1.
Tools and databases for systems bioinformatics approaches in therapeutics, diagnostics, network visualization/analysis, integration and systems modelling
| Tool category/description | Publication year | Link | Reference |
|---|---|---|---|
| Network-based therapeutics | |||
| TCM-Mesh: The database and analytical system for network pharmacology analysis for TCM preparations | 2017 | http://mesh.tcm.microbioinformatics.org/ | [123] |
| SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug–target interactions and drug repositioning | 2017 | The program is available on request | [124] |
| A protein network descriptor server and its use in studying protein, disease, metabolic and drug-targeted networks | 2016 | http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi | [128] |
| systemsDock: a web server for network pharmacology-based prediction and analysis | 2016 | http://systemsdock.unit.oist.jp/iddp/home/index | [129] |
| BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology | 2016 | https://www.bindingdb.org/bind/index.jsp | [130] |
| NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning | 2015 | http://nffinder.cnb.csic.es/ | [131] |
| NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods | 2015 | http://sbb.hku.hk/services/NutriChem-2.0/FoodDisease.php | [132] |
| TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples | 2015 | https://cran.r-project.org/web/packages/timma/ | [133] |
| Network-based diagnostics | |||
| GWAB: a web server for the network-based boosting of human genome-wide association data | 2017 | http://www.inetbio.org/gwab/ | [113] |
| Netter: re-ranking gene network inference predictions using structural network properties | 2016 | https://github.com/JRuyssinck/netter | [134] |
| MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis | 2016 | https://github.com/NCBI-Hackathons/Network_SNPs | [135] |
| GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets | 2016 | http://www.integrativegenomics.org/ | [136] |
| NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities | 2016 | http://netdecoder.hms.harvard.edu/ | [137] |
| MUFFINN: cancer gene discovery via network analysis of somatic mutation data | 2016 | http://www.inetbio.org/muffinn/ | [138] |
| HitWalker2: visual analytics for precision medicine and beyond | 2016 | https://github.com/biodev/HitWalker2 | [139] |
| NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings | 2016 | http://ncg.kcl.ac.uk/ | [140] |
| dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation | 2015 | http://140.138.144.145/∼dbSNO/index.php | [141] |
| Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems | 2015 | http://causalbionet.com/ | [142] |
| Network reconstruction-visualization-analysis | |||
| MotifNet: a web-server for network motif analysis | 2017 | http://netbio.bgu.ac.il/motifnet/ | [143] |
| cMapper: gene-centric connectivity mapper for EBI-RDF platform | 2017 | http://cmapper.ewostech.net/ | [144] |
| BRANE Clust: Cluster-assisted gene regulatory network inference refinement | 2017 | http://www-syscom.univ-mlv.fr/∼pirayre/Codes-GRN-BRANE-clust.html | [145] |
| vcfr: a package to manipulate and visualize variant call format data in R | 2017 | https://cran.r-project.org/web/packages/vcfR/index.html | [146] |
| shinyheatmap: Ultra-fast low-memory heatmap web interface for big data genomics | 2017 | http://shinyheatmap.com/ | [147] |
| PROXiMATE: a database of mutant protein–protein complex thermodynamics and kinetics | 2017 | http://www.iitm.ac.in/bioinfo/PROXiMATE/ | [148] |
| Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks | 2017 | https://github.com/ibalaur/MetabolicFramework | [149] |
| RAIN: RNA–protein association and interaction networks | 2017 | http://rth.dk/resources/rain/ | [150] |
| Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data | 2017 | https://uclex.cs.ucl.ac.uk/ | [151] |
| Pheno4J: a gene to phenotype graph database | 2017 | https://github.com/phenopolis/pheno4j | [152] |
| SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network | 2017 | https://github.com/YuanlongLiu/SigMod | [153] |
| iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations | 2017 | http://iregnet3d.yulab.org/index/ | [154] |
| JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data | 2017 | https://github.com/jijiadong/JDINAC | [155] |
| SmartR: An open-source platform for interactive visual analytics for translational research data | 2017 | https://github.com/transmart/SmartR | [156] |
| D-Map: random walking on gene network inference maps towards differential avenue discovery | 2017 | http://bioserver-3.bioacademy.gr/Bioserver/DMap/index.php | [157] |
| TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments | 2016 | http://www.cabsel.ethz.ch/tools/trace.html | [158] |
| The Network Library: a framework to rapidly integrate network biology resources | 2016 | https://github.com/gsummer | |
| Web-based network analysis and visualization using CellMaps | 2016 | http://cellmaps.babelomics.org/ | [159] |
| PathwAX: a web server for network crosstalk based pathway annotation | 2016 | http://pathwax.sbc.su.se/ | [160] |
| Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology | 2016 | http://brg.ai.sri.com/ptools/ | [161] |
| NAPS: Network analysis of protein structures | 2016 | http://bioinf.iiit.ac.in/NAPS/ | [162] |
| UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation | 2016 | http://140.138.144.145/∼ubinet/index.php | [163] |
| MET network in PubMed: a text-mined network visualization and curation system | 2016 | http://btm.tmu.edu.tw/metastasisway | [164] |
| QuIN: a web server for querying and visualizing chromatin interaction networks | 2016 | https://quin.jax.org/ | [165] |
| NET-GE: a web server for NETwork-based human gene enrichment | 2016 | http://net-ge.biocomp.unibo.it/enrich | [166] |
| IIIDB: a database for isoform–isoform interactions and isoform network modules | 2015 | http://syslab.nchu.edu.tw/IIIDB/ | [167] |
| cyNeo4j: connecting Neo4j and Cytoscape | 2015 | http://apps.cytoscape.org/apps/cyneo4j | [168] |
| BRANE Cut: biologically related a priori network enhancement with graph cuts for gene regulatory network inference | 2015 | http://www-syscom.univ-mlv.fr/∼pirayre/Codes-GRN-BRANE-cut.html | [169] |
| NetExplore: a web server for modelling small network motifs | 2015 | http://line.bioinfolab.net/nex/NetExplore.htm | [170] |
| COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems | 2015 | http://coxpresdb.jp/ | [171] |
| NAIL: a software toolset for inferring, analysing and visualizing regulatory networks | 2015 | https://sourceforge.net/projects/nailsystemsbiology/ | [172] |
| LncReg: a reference resource for lncRNA-associated regulatory networks | 2015 | http://bioinformatics.ustc.edu.cn/lncreg/ | [173] |
| TeloPIN: a database of telomeric proteins interaction network in mammalian cells | 2015 | http://songyanglab.sysu.edu.cn/telopin/ | [174] |
| MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse | 2015 | http://guanlab.ccmb.med.umich.edu/misomine/ | [175] |
| CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization | 2015 | http://www.innatedb.ca/CerebralWeb/ | [176] |
| Network-based integration | |||
| NaviCom: a web application to create interactive molecular network portraits using multilevel omics data | 2017 | https://navicom.curie.fr/bridge.php | [177] |
| KeyPathwayMinerWeb: online multi-omics network enrichment | 2016 | https://keypathwayminer.compbio.sdu.dk/keypathwayminer/ | [178] |
| Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization | 2016 | http://bcil.github.io/VOE/ | [179] |
| ModuleAlign: module-based global alignment of PPI networks | 2016 | http://ttic.uchicago.edu/∼hashemifar/ModuleAlign.html | [180] |
| Fuse: multiple network alignment via data fusion | 2016 | http://www0.cs.ucl.ac.uk/staff/natasa/FUSE/index.html | [181] |
| The SMAL web server: global multiple network alignment from pairwise alignments | 2016 | http://haddock6.sfsu.edu/smal/ | [182] |
| Mergeomics: a web server for identifying pathological pathways, networks and key regulators via multidimensional data integration | 2016 | http://mergeomics.research.idre.ucla.edu/ | [183] |
| MAGNA ++: Maximizing accuracy in global network alignment via both node and edge conservation | 2015 | http://www3.nd.edu/∼cone/MAGNA±+/ | [184] |
| ZoomOut: analysing multiple networks as single nodes | 2015 | http://bioserver-3.bioacademy.gr/Bioserver/ZoomOut/ | [185] |
| RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse | 2015 | http://www.regnetworkweb.org/ | [186] |
| Systems biology and modelling | |||
| FAIRDOMHub: a repository and collaboration environment for sharing systems biology research | 2017 | https://fair-dom.org/publication/fairdomhub-a-repository-and-collaboration-environment-for-sharing-systems-biology-research/ | [187] |
| The systems biology format converter | 2016 | https://www.ebi.ac.uk/biomodels/tools/converters/ | [188] |
| SBtab: a flexible table format for data exchange in systems biology | 2016 | https://www.sbtab.net/ | |
| PeTTSy: a computational tool for perturbation analysis of complex systems biology models | 2016 | http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/ | [189] |
| AMIGO2: a toolbox for dynamic modelling, optimization and control in systems biology | 2016 | https://sites.google.com/site/amigo2toolbox/ | [190] |
| ComPPI: a cellular compartment-specific database for PPI network analysis | 2015 | http://comppi.linkgroup.hu/ | [191] |
| JSBML 1.0: providing a smorgasbord of options to encode systems biology models | 2015 | http://sbml.org/Software/JSBML | [192] |
| MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory | 2015 | http://mptheory.scienze.univr.it/ | [193] |
| SYSBIONS: nested sampling for systems biology | 2015 | http://www.theosysbio.bio.ic.ac.uk/resources/sysbions/ | [194] |
| Dizzy-Beats: a Bayesian evidence analysis tool for systems biology | 2015 | https://sourceforge.net/p/bayesevidence/home/Home/ | [195] |