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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. [1] On 2011 EMBnet has 37 nodes spread over 32 countries. The nodes include bioinformatics related university departments, research institutes and national service providers.
The main task of most EMBnet nodes is to provide their national scientific community with access to bioinformatics databanks, specialised software and sufficient computing resources and expertise. EMBnet is also working in the fields of bioinformatics training and software development. Examples of software created by EMBnet members are: EMBOSS, wEMBOSS, [2] UTOPIA.
EMBnet represents a wide user group and works closely together with the database producers such as EMBL's European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (Swiss-Prot), the Munich Information Center for Protein Sequences (MIPS), in order to provide a uniform coverage of services throughout Europe. EMBnet is registered in the Netherlands as a public foundation (Stichting).
Since its creation in 1988, EMBnet has evolved from an informal network of individuals in charge of maintaining biological databases into the only worldwide organization bringing bioinformatics professionals to work together to serve the expanding fields of genetics and molecular biology. Although composed predominantly of academic nodes, EMBnet gains an important added dimension from its industrial members. The success of EMBnet is attracting increasing numbers of organizations outside Europe to join.
EMBnet has a tried-and-tested infrastructure to organise training courses, give technical help and help its members effectively interact and respond to the rapidly changing needs of biological research in a way no single institute is able to do.
In 2005 the organization created additional types of node to allow more than one member per country. The new category denomination is "associated node".
EMBnet is governed by the Annual General Meetings (AGM), and is coordinated by an executive board (EB) that oversees the activities of three project committees:
EMBnet had the first gopher and World Wide Web servers in biology (CSC BioBox)
EMBnet was the first to come up with solutions for daily database updates using Internet (NDT), distributed computing (HASSLE) and efficient database browsing and linking (Sequence Retrieval System, SRS).
The Ping project was created as a means to obtain continuous information about network efficiency across the whole of Europe.
EMBnet is committed to bringing the latest software algorithms to the user free of charge (Extended GCG or EGCG [3] ) and continues to develop state of the art public software (EMBOSS).
EMBER [ permanent dead link ]: a European Multimedia Bioinformatics Educational Resource. EMBER was a European Union (EU) funded project aiming to develop a suite of multimedia bioinformatics educational tools [4] . EMBER comprises a self-contained, interactive Web tutorial in bioinformatics, & the equivalent stand-alone course on CD-ROM.
The EMBnet community was involved in the creation of the peer reviewed journal Briefings in Bioinformatics (BiB). BiB was also supported by an educational grant from EMBnet.
The Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) was formed as a nonprofit foundation at the 2012 EMBnet annual meeting. [5] [6]
| Discipline | Bioinformatics |
|---|---|
| Language | English |
| Edited by | Erik Bongcam-Rudloff |
| Publication details | |
| History | 2010-present |
| Publisher | EMBnet |
| Frequency | Quarterly |
| Yes | |
| Standard abbreviations | |
| ISO 4 | EMBnet.journal |
| Indexing | |
| ISSN | 2226-6089 |
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Starting from 1994 and up to 2009 EMBnet published EMBnet.news. [7] Its primary goal was to bring information and report on the latest news and developments from the network to the user community.
Established in 2010 as the successor of the EMBnet.news (with volume numbering continuing uninterrupted), EMBnet.journal is a peer-reviewed open access scientific journal publishing original research and technical papers in bioinformatics. [8] [9] The journal contains two main sections, one for research articles, reviews, and technical notes, and one for non-peer-reviewed commentary, reportage, user-guides, training information, and news. EMBnet.journal publishes also conference proceedings and meeting abstracts as supplements.
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer science and engineering which uses bioengineering to build computers.
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
Erik Bongcam-Rudloff is a Chilean-born Swedish biologist and computer scientist. He received his doctorate in medical sciences from Uppsala University in 1994. He is Professor of Bioinformatics and the head of SLU-Global Bioinformatics Centre at the Swedish University of Agricultural Sciences. His main research deals with development of bioinformatics solutions for the Life Sciences community.
EMBOSS is a free c software analysis package developed for the needs of the molecular biology and bioinformatics 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.
The EB-eye, also known as EBI Search, is a search engine that provides uniform access to the biological data resources hosted at the European Bioinformatics Institute (EBI).
UTOPIA is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects. There are two major components, the protein analysis suite and UTOPIA documents.
The African Society for Bioinformatics and Computational Biology (ASBCB) is a non-profit professional association dedicated to the advancement of bioinformatics and computational biology in Africa. Transformed from the African Bioinformatics Network (ABioNET), ASBCB was established in February 2004 at a meeting in Cape Town, South Africa. The Society serves as an international forum and resource devoted to developing competence and expertise in bioinformatics and computational biology in Africa. It complements its activities with those of other international and national societies, associations and institutions, public and private, that have similar aims. It also promotes the standing of African bioinformatics and computational biology in the global arena through liaison and cooperation with other international bodies. It is an affiliated regional group of the International Society for Computational Biology (ISCB).
The International Society for Computational Biology (ISCB) is a scholarly society for researchers in computational biology and bioinformatics. The society was founded in 1997 to provide a stable financial home for the Intelligent Systems for Molecular Biology (ISMB) conference and has grown to become a larger society working towards advancing understanding of living systems through computation and for communicating scientific advances worldwide.
BioSLAX is a Live CD/Live DVD/Live USB comprising a suite of more than 300 bioinformatics tools and application suites. It has been released by the Bioinformatics Resource Unit of the Life Sciences Institute (LSI), National University of Singapore (NUS) and is bootable from any PC that allows a CD/DVD or USB boot option and runs the compressed Slackware flavour of the Linux Operating System (OS), also known as Slax. Slax was created by Tomáš Matějíček in the Czech Republic using the Linux Live Scripts which he also developed. The BioSLAX derivative was created by Mark De Silva, Lim Kuan Siong and Tan Tin Wee.
The clique percolation method is a popular approach for analyzing the overlapping community structure of networks. The term network community has no widely accepted unique definition and it is usually defined as a group of nodes that are more densely connected to each other than to other nodes in the network. There are numerous alternative methods for detecting communities in networks, for example, the Girvan–Newman algorithm, hierarchical clustering and modularity maximization.
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.
Teresa K. Attwood is a professor of Bioinformatics in the Department of Computer Science and School of Biological Sciences at the University of Manchester and a visiting fellow at the European Bioinformatics Institute (EMBL-EBI). She held a Royal Society University Research Fellowship at University College London (UCL) from 1993 to 1999 and at the University of Manchester from 1999 to 2002.
ELIXIR is an initiative that allows life science laboratories across Europe to share and store their research data as part of an organised network. Its goal is to bring together Europe's research organisations and data centres to help coordinate the collection, quality control and storage of large amounts of biological data produced by life science experiments. ELIXIR aims to ensure that biological data is integrated into a federated system easily accessible by the scientific community.
Alfonso Valencia is a Spanish biologist, ICREA Professor, current director of the Life Sciences department at Barcelona Supercomputing Center. and of Spanish National Bioinformatics Institute (INB-ISCIII). From 2015-2018, he was President of the International Society for Computational Biology. His research is focused on the study of biomedical systems with computational biology and bioinformatics approaches.
Georgios (George) V. Magklaras is a computer scientist working as a Senior Computer Systems Engineer at the Norwegian Meteorological Institute, in Norway. He also co-founded Steelcyber Scientific, an information security based consultancy specialising in digital forensics. He is a high-performance computing engineer and information security researcher. He developed methods in the field of insider IT misuse detection and prediction and digital forensics. He is the author of the LUARM and POFR tools for the Linux Operating System. He has been a strong advocate of Linux, open source tools and the Perl programming language and has given a series of lectures internationally in the fields of intrusion detection systems, digital forensics, bioinformatics, computer programming and systems administration.
Michal Linial is a Professor of Biochemistry and Bioinformatics at the Hebrew University of Jerusalem (HUJI). Linial is the Director of The Sudarsky Center for Computational Biology at HUJI. Since 2015, she is head of the ELIXIR-Israel node.
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.
Manuel Corpas is an Anglo-Spanish biologist and entrepreneur known primarily for his contributions to the field of Bioinformatics and Genomics. Currently Corpas is Chief Scientist of Cambridge startup Cambridge Precision Medicine, a tutor at the Institute for Continuing Education at the University of Cambridge and a lecturer at the Universidad Internacional de La Rioja. Manuel worked on the human genome from the beginning of his career, being one of the first consumers to sequence and his own genome and that of close relatives, which he published as the Corpasome. He has held positions at the Earlham Institute as Project Leader, and the Wellcome Sanger Institute, developing the DECIPHER database, a database that aids in the diagnosis of patients with rare genomic disorders.
Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.
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