Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.
The National Center for Biotechnology Information (NCBI) is part of the (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
A sequence profiling tool in bioinformatics is a type of software that presents information related to a genetic sequence, gene name, or keyword input. Such tools generally take a query such as a DNA, RNA, or protein sequence or ‘keyword’ and search one or more databases for information related to that sequence. Summaries and aggregate results are provided in standardized format describing the information that would otherwise have required visits to many smaller sites or direct literature searches to compile. Many sequence profiling tools are software portals or gateways that simplify the process of finding information about a query in the large and growing number of bioinformatics databases. The access to these kinds of tools is either web based or locally downloadable executables.
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
The GFP-cDNA project documents the localisation of proteins to subcellular compartments of the eukaryotic cell applying fluorescence microscopy. Experimental data are complemented with bioinformatic analyses and published online in a database. A search function allows the finding of proteins containing features or motifs of particular interest. The project is a collaboration of the research groups of Rainer Pepperkok at the European Molecular Biology Laboratory (EMBL) and Stefan Wiemann at the German Cancer Research Centre (DKFZ).
The European Molecular Biology network (EMBnet) is an international scientific network and interest group that aims to enhance bioinformatics services by bringing together bioinformatics expertises and capacities. On 2011 EMBnet has 37 nodes spread over 32 countries. The nodes include bioinformatics related university departments, research institutes and national service providers.
Biomax Informatics is a Munich-based software company specializing in research software for bioinformatics. Biomax was founded in 1997 and has its roots in the Munich Information Center for Protein Sequences (MIPS). The company's customer base consists of companies and research organizations in the areas of drug discovery, diagnostics, fine chemicals, food and plant production. In addition to exclusive software tools, Biomax Informatics provides services and curated knowledge bases.
DAVID is a free online bioinformatics resource developed by the Laboratory of Human Retrovirology and Immunoinformatics. All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. DAVID can be found at https://david.ncifcrf.gov/
AstridBio Ltd. is a privately held biotechnology company based in Szeged, Hungary. Started in 2003, AstridBio's focus is in biobanking software development, data management and analysis for genomics research. Its clients include academic research institutes, pharmaceutical and biotech companies.
The Netherlands Bioinformatics Centre or NBIC (2003–2013) was a Dutch, government-funded organization, that coordinated all academic work on bioinformatics in the Netherlands. NBIC consisted of programs for research (BioRange), for education (BioWise), and for support (BioAssist). NBIC partners are all Dutch universities and university hospitals, and some commercial entities. The NBIC central office was hosted by the Center for Molecular and Biomolecular Informatics (CMBI) at the Radboud University Nijmegen Medical Centre.
Melbourne Bioinformatics is a centre for computational life science expertise. It provides bioinformatics support for all researchers and students in a wide range of projects and services of local and national significance. Researchers can engage with Melbourne Bioinformatics through training and consulting with experts which can lead to project collaborations with academic staff within the University of Melbourne.
BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. Although the BioMart software is primarily used by the biomedical research community, it is designed in such a way that any type of data can be incorporated into the BioMart framework. The BioMart project originated at the European Bioinformatics Institute as a data management solution for the Human Genome Project. Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents.
Ron David Appel is a Swiss bioinformatician, professor of proteomics and bioinformatics at the University of Geneva and executive director of the Swiss Institute of Bioinformatics.
The Australia Bioinformatics Resource (EMBL-ABR) was a significant initiative under the associate membership to EMBL.
ATUM is an American biotechnology company. ATUM provides tools for the design and synthesis of optimized DNA, as well as protein production and GMP cell line development.
The Centre for Genomic Regulation is a biomedical and genomics research centre based in Barcelona. Most of its facilities and laboratories are located in the Barcelona Biomedical Research Park, in front of Somorrostro beach.
The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure initiated by the Federal Ministry of Education and Research funding 2015-2021. The network provides bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data. From 2022, the network will be integrated into Forschungszentrum Jülich.