| CBS Prediction Servers |
| http://www.cbs.dtu.dk/biotools |
| A collection of on-line prediction services from CBS-DTU. The resource contains 75 tools for gene finding and splice sites, post-translational protein modification, immunological features, protein function and structure, protein sorting, genomic epidemiology and more. The tools can be used via interactive input forms, with many available as software packages and SOAP Web services. |
| DRCAT resource catalogue |
| http://drcat.sourceforge.net |
| The data resource catalogue is a collection of metadata on bioinformatics Web-based data resources. The catalog contains over 600 resources including bioinformatics and biomedical databases, ontologies, taxonomies and catalogues. |
| BiBiServ |
| http://bibiserv.cebitec.uni-bielefeld.de |
| BiBiServ is a collection of bioinformatics tools that emerged from the research at Bielefeld University. It contains over 40 mainly analysis and utility tools, including RNA structure prediction, metagenomics, genome rearrangement, alignments, evolutionary relationships, primer design and suffix trees. These are available as interactive web applications, HTTP Web services and downloadable software. |
| BINF.KU.DK Services and Software |
| http://www.binf.ku.dk/services |
| A collection of over 20 web services, databases and software packages from The Bioinformatics Centre at The University of Copenhagen. The resource covers sequence and structure analysis, prediction and modeling, gene regulation, population genetics and more. |
| ELIXIR-CZ Services collection |
| https://www.elixir-czech.cz/services |
| The Czech Bioinformatics Services resource is provided by members of ELIXIR CZ node. It contains over 30 bioinformatics tools and databases for analysis of sequence, topology and structure of nucleic acids and proteins to genomics, proteomics and benchmarks for small molecule interactions. The databases can be accessed via web GUIs while tools are available as web, standalone and command-line applications. |
| ELIXIR eLearning Platform |
| https://elixir.mf.uni-lj.si |
| Orange |
| http://orange.biolab.si/ |
| Orange data mining suite is an open source data visualization and analysis software for data mining through visual programming or Python scripting. It consists of over 100 components for machine learning and add-ons for bioinformatics and text mining. |
| GoMapMan |
| http://www.gomapman.org |
| GoMapMan is a database of gene functional annotations in the plant sciences based on the plant-specific MapMan ontology. |
| ELIXIR-ITA Services collection |
| A collection of services provided by research institutions members of the ELIXIR Italian node. The resource includes databases and analysis tools developed and maintained by Italian bioinformatics groups and institutions. |
| University of Padova ELIXIR-ITA-PADOVA |
| http://protein.bio.unipd.it/ |
| A collection of 60 bioinformatics tools from the University of Padova.It includes databases for structural bioinformatics and genome sequences as well as tools for sequence analysis, phylogenetics, structure analysis, chemioinformatics and network analysis. |
| Bologna Biocomputing group predictors and services |
| http://biocomp.unibo.it/predictors.html |
| A collection of 22 predictors for subcellular localization, disease-related mutations and protein sequences annotation from Bologna Biocomputing Group. Most tools are accessible using a Web UI while some offer a command line interface. |
| Sapienza University Biocomputing group resources and tools |
| http://www.biocomputing.it/index.php/About-us/tools |
| A collection of 19 resources and tools for structural bioinformatics, immunoinformatics and genomics from the Sapienza University Biocomputing Group. |
| Molecular Genetics Group ELIXIR-ITA-TORVERGATA |
| http://moleculargenetics.uniroma2.it |
| A collection of 7 databases and portals linking physically and functionally gene products. All databases and portals data can be searched, visualized and downloaded through Web UI interfaces. |
| Molecular Bioinformatics Group ELIXIR-ITA-TORVERGATA |
| A collection of tools dedicated to the analysis of protein structures, the identification of structure motifs and the comparison of RNA secondary structure. |
| Milano-Bicocca Resources and Tools ELIXIR-ITA-BICOCCA |
| Online services and open source software, mainly for NGS and EST analysis or to infer evolutionary histories in tumors. The majority of tools are used via a command line interface while the rest offer a graphical interface. |
| Mobyle@Pasteur |
| http://mobyle.pasteur.fr |
| A collection of 300 bioinformatics tools covering various topics such as sequence analysis, phylogeny, integrated in an online workbench. The suite is a combination of tools developed at the Institut Pasteur and/or tools used by it, for research and education. |
| Galaxy@Institut Pasteur |
| https://galaxy.web.pasteur.fr |
| A collection of 260 bioinformatics tools, mainly dedicated to NGS analysis, and integrated into the Galaxy instance available at the Institut Pasteur. This instance is only available to Pasteur researchers and collaborators. |
| GenOuest |
| http://www.genouest.org |
| A collection of tools dedicated to the analyses of NGS data along with bioinformatics genomic databases hosted by GenOuest. Most tools can be used via command line, while the databases and some of the tools are available through a web interface. |
| IFB ELIXIR-FR |
| http://www.france-bioinformatique.fr/?q=en/services |
| The French Institute of Bioinformatics (IFB) is a national service infrastructure in bioinformatics that gathers together the bioinformatics platforms of the main French research organizations, CNRS, INRA, INRIA, CEA and INSERM, as well as CIRAD, the Pasteur and Curie Institutes and the French universities. IFB's principal mission is to provide basic services and resources in bioinformatics for scientists and engineers working in the life sciences. IFB is the French node of ELIXIR. |
| Loschmidt laboratories software resources |
| http://loschmidt.chemi.muni.cz/peg/software/ |
| A collection of tools developed at Loschmidt Laboratories for protein design, engineering and analysis. The tools are mostly available via web interface or as command line application. |
|
Identifiers.org
Registry
|
| http://identifiers.org/registry/ |
| The core of the Identifiers.org Registry is a catalogue of data collections—corresponding to controlled vocabularies, databases and more—along with their URIs and the associated physical URLs. |
| INB Services |
| http://www.inab.org/resources/list-of-all-systems-and-tools/ |
| The catalog of Spanish National Bioinformatics Institute. INB Services develops and provides software tools and web servers for the global life sciences research community. |
| PSB resources |
| http://bioinformatics.psb.ugent.be/software |
| A collection of tools developed at the department of Plant Systems Biology (VIB,Gent University). The tools cover topics such as comparative genomics, network analysis, genome prediction, annotation and visualization. The tools are available as web UI or command line applications. |
| CRS4 resources |
| http://orione.crs4.it |
| Biocomputing infrastructure to primarily support analysis of data produced by the CRS4 NGS facility. The system integrates hundreds of tools into a web-based traceability framework that can handle the whole transformation process from raw data to downstream analysis. |
| CCP4 |
| http://www.ccp4.ac.uk |
| A collection of computational tools for macromolecular X-ray crystallography, and other biophysical techniques. |
| Instruct |
| https://www.structuralbiology.eu/update/toolbox |
| A collection of computational tools for structural biology from Instruct. Instruct is a pan-European research infrastructure in structural biology, making high-end technologies and methods available to users. |
| University of Tartu bioinformatics resources |
|
http://biit.cs.ut.ee, http://bioinfo.ut.ee
|
| Estonian bioinformatics services, tools and databases provided by ELIXIR-Estonia contain almost 20 tools and databases for several high-throughput analyses, enrichment analysis, network dissection, primer design approaches, as well as data visualisation applications. The resources are mainly available as interactive web applications and R packages. |
| ExPASy/SIB resources |
| http://www.expasy.org |
| ExPASy is the SIB bioinformatics resources portal which provides access to scientific databases and software tools (i.e. resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics. |
| SEQanswers wiki |
| http://seqanswers.com/wiki/Software |
| The SEQanswers wiki (SEQwiki) is a wiki database that is actively edited and updated by the members of the SEQanswers community (http://seqanswers.com). The wiki provides an extensive catalogue of tools, technologies and tutorials for high-throughput sequencing. |
| USMI Cell Line Databases and Analysis Tools |
| http://bioinformatics.hsanmartino.it |
| The resource is devoted to management and distribution on information on human and animal cell lines and other biological resources. The tools are usually available as a web interface or as REST and SOAP Web Services. |
| BioCatalogue |
| http://biocatalogue.org |
| The BioCatalogue is a curated catalogue of 369 life science Web Services. Users and curators register metadata about Web Services. Web Services in the catalogue can be either SOAP or REST APIs. |
| SDU bioinformatics tools collection |
|
http://www.sdu.dk/en/Om_SDU/Institutter_centre/Bmb_biokemi_og_molekylaer_biologi/Forskning/Forskningsgrupper/Protein/Bioinformatics or https://elixir-registry.cbs.dtu.dk/?q=bmb.sdu.dk
|
| Collection of tools and services developed and maintained at the University of Southern Denmark currently comprising 13 applications. Covered topics are cluster validation, proteomics, pathway and network processing, and omics analyses. |
| University of Bergen and ELIXIR-NO tools |
| http://www.bioinfo.no/applications |
| A list of over 30 tools, including web applications and Web services, provided by the universities in Norway affiliated with ELIXIR-NO. |
| Tools@EBI |
| http://www.ebi.ac.uk/services |
| A portfolio of bioinformatics tools to facilitate scientific discovery within the life sciences, provided by EMBL-EBI. |
| GO tools registry |
| http://geneontology.org |
| A collection of resources to perform data analysis using Gene Ontology (GO). Includes tools developed by GO Consortium members as well as some third-party resources. |
| EMBOSS |
| http://emboss.sf.net |
| EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. |
| WHAT-IF |
| http://swift.cmbi.ru.nl/whatif |
| A versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc. |
| Bio-Linux |
| http://environmentalomics.org/bio-linux |
| Bio-Linux is an Ubuntu Linux-based distribution that adds more than 250 bioinformatics packages, providing around 50 graphical applications and several hundred command line tools, as well as the Galaxy environment for browser-based data analysis and workflow construction. |
| Debian Med |
| https://www.debian.org/devel/debian-med/ |
| Debian Med is a project that aims at developing Debian into an operating system that is particularly well fit for the requirements for medical and biological research. The goal of Debian Med is a complete free and open-source system for all tasks in life-scientific research. To achieve this goal Debian Med integrates applicable software into Debian. |
| Rostlab |
| http://rostlab.org |
| A collection of bioinformatics tools for the prediction and analysis of the aspects of protein structure and function, provided by the Rost lab at the Technical University of Munich and Columbia University of New York. |
| BioJS |
| http://biojs.net |
| A registry and open-source library of JavaScript components to visualise biological data. |
