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Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
ExPASy is a bioinformatics resource portal operated by the SIB Swiss Institute of Bioinformatics and in particular the SIB Web Team. It is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can access a wide range of resources in many different domains, such as proteomics, genomics, phylogenetics/evolution, systems biology, population genetics, and transcriptomics. The individual resources are hosted in a decentralised way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by many different SIB groups and external institutions. The portal features a search function across selected resources. Internally, the availability and usage of resources are monitored. The portal is aimed for both expert users and for people who are not familiar with a specific domain in life sciences: in particular, the new web interface provides visual guidance for newcomers to ExPASy.
GenePattern is a freely available computational biology open-source software package originally created and developed at the Broad Institute for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. GenePattern is currently developed at the University of California, San Diego.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
Genedata provides bioinformatics enterprise software solutions and a variety of software-related services that support large-scale, experimental processes in life science research - with a focus on automating data rich, highly complex data workflows. Genedata solutions are used in R&D laboratories primarily in biopharmaceutical but also in industrial and agro-biotech, nutrition, and health industries as well as in contract research organizations (CROs) and academic research institutions. The world's top 25 pharmaceutical companies license one or more of Genedata products or services, and the firm has relationships with more than 40 of the top 50 pharmaceutical companies. The company is headquartered in Basel, Switzerland with subsidiaries and offices in Boston, London, Munich, San Francisco, Singapore, and Tokyo.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
OpenMS is an open-source project for data analysis and processing in protein mass spectrometry and is released under the 3-clause BSD licence. It supports most common operating systems including Microsoft Windows, OS X and Linux.
The LONI Pipeline is a free distributed system for designing, executing, monitoring and sharing scientific workflows on grid computing architectures. Pipeline allows users to connect and run any number of different software tools, and conveniently visualize and download the results.
Discovery Net is one of the earliest examples of a scientific workflow system allowing users to coordinate the execution of remote services based on Web service and Grid Services standards. The system was designed and implemented at Imperial College London as part of the Discovery Net pilot project funded by the UK e-Science Programme. Many of the concepts pioneered by Discovery Net have been later incorporated into a variety of other scientific workflow systems.
A scientific workflow system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or workflow, in a scientific application.
LabKey Server is a software suite available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources. Specific scientific applications and workflows can be added on top of the basic platform and leverage a data processing pipeline.
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.
Anduril is an open source component-based workflow framework for scientific data analysis developed at the Systems Biology Laboratory, University of Helsinki.
Integromics is a global bioinformatics company headquartered in Granada, Spain, with a second office in Madrid and subsidiaries in the US and UK and distributors in 10 countries. Integromics S.L. provides bioinformatics software for data management and data analysis in genomics and proteomics. The company provides a line of products that serve the gene expression, sequencing and proteomics markets. Customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations and biotechnology companies.
A bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, that relate to bioinformatics.
ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses. It provides a framework for unified mass spectrometry data file access and performs standard chemistry and LCMS dataset computations. Specifically, it is able to read many of the vendor-specific, proprietary formats and converting the data into an open data format.
The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing 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.