Netherlands Bioinformatics Centre

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Netherlands Bioinformatics Centre
Typenot-for-profit organisation
Location
Website www.nbic.nl

The Netherlands Bioinformatics Centre or NBIC [1] (2003-2013) was a Dutch, government-funded organization, that coordinated all academic work on bioinformatics in the Netherlands. [2] 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.

Contents

History

In 2003 NBIC was launched [3] as a not-for-profit organization, to strengthen and organize the bioinformatics research in the Netherlands. NBIC is one of the four enabling technology centres that were initiated by the Netherlands Genomics Initiative (NGI) [4] to improve the genomics-based research in the Netherlands. The other three technology centres are: the Netherlands Proteomics Centre (NPC), [5] the Netherlands Metabolomics Centre (NMC) [6] and the Netherlands Consortium for Systems Biology (NCSB). [7] Most services moved to the Dutch Techcentre for Life Sciences in 2015. [8]

Funding

The Netherlands Bioinformatics Centre was funded by the Dutch government through the Netherlands Genomics Initiative (NGI) [9] and the BSIK [10] (knowledge infrastructures) programme.[ citation needed ]

Support

The support department of NBIC, BioAssist, consists of task forces that bring together experts in the different fields of Bioinformatics. Together, these people identify common problems in their field that they set out to solve in a collaborative way. BioAssist also has a group, BioInformatics Research Support (BRS), [11] [12] that helps biological and medical professionals with short bioinformatics projects.

Education

The education part of NBIC, BioWise, organizes courses and trainings at different levels. They provide awareness training at schools, [13] collaborate with the different bioinformatics education programs at the universities in the Netherlands, and organize trainings for PhD students. Also, subject-specific trainings and conferences are organized, either nationally or with other international partners like the Swiss Institute of Bioinformatics.

Achievements

Organising Bioinformatics research

So far, NBIC has achieved its goal of bringing together the different bioinformatics research groups in the Netherlands. It is now also partnering up with Dutch universities of Applied Sciences (UAS) in the LOBIN network. in July 2011, four UASes have joined. [14]

Bioinformatics software

A wide variety of bioinformatics software has been created by people involved in NBIC. [15] NBIC also hosts a service to coordinate software development (Trac server with software releases and project documentation). [16] Many tools are also made available through NBIC's own open Galaxy server [17]

First steps have been made to include commercial entities, among others, via the Bioinformatics Industrial Users Platform (BIUP). The BIUP, though still in its start-up phase in mid-2011, has already attracted partners such as DSM.

Community Building

A large part of NBIC's efforts focus on developing new or strengthening existing bio-informatics communities. For example, NBIC hosted the 2011 Galaxy Community Conference. [18] The Netherlands Bioinformatics for Proteomics Platform (for short NBPP) is a joint initiative of the Netherlands Bioinformatics Centre (NBIC) and the Netherlands Proteomics Centre (NPC).

The inaugural meeting of the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET) was held at NBIC in November 2012. [19]

Related Research Articles

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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 subsequent process of analyzing and interpreting data is referred to as computational biology.

<span class="mw-page-title-main">Swiss Institute of Bioinformatics</span>

The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.

<span class="mw-page-title-main">Biocomplexity Institute of Virginia Tech</span> Research organization for computational biology and related fields

The Biocomplexity Institute of Virginia Tech was a research institute specializing in bioinformatics, computational biology, and systems biology. The institute had more than 250 personnel, including over 50 tenured and research faculty. Research at the institute involved collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology and medicine. The institute developed -omic and bioinformatic tools and databases that can be applied to the study of human, animal and plant diseases as well as the discovery of new vaccine, drug and diagnostic targets.

The Spanish National Bioinformatics Institute is an academic service institution tasked with the coordination, integration and development of bioinformatics resources in Spain. Created in 2003, the INB is—since 2015—the main node through which the Carlos III Health Institute is connected to ELIXIR, a European-wide infrastructure of life science data, coordinating the other Spanish institutions partaking in the initiative such as the Spanish National Cancer Research Centre (CNIO), the Centre for Genomic Regulation (CRG), the Universitat Pompeu Fabra, the Institute for Research in Biomedicine (IRB) and the Barcelona's National Supercomputing Center.

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.

Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. The individual resources are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.

Integrative bioinformatics is a discipline of bioinformatics that focuses on problems of data integration for the life sciences.

<span class="mw-page-title-main">Galaxy (computational biology)</span>

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.

The Center for Molecular and Biomolecular Informatics (CMBI) is an academic computational biology (bioinformatics) research department based in Nijmegen, and is part of the Radboudumc University Medical Center.

<span class="mw-page-title-main">International Society for Computational Biology</span> Scholarly society

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.

The Netherlands Bioinformatics for Proteomics Platform (NBPP) is joint initiative of the Netherlands Bioinformatics Centre (NBIC) and the Netherlands Proteomics Centre (NPC).

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.

<span class="mw-page-title-main">BioMart</span>

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The Netherlands Proteomics Centre (NPC) is a Dutch research center in the field of proteomics. The research is focused on the proteome, the entire set of proteins expressed by a genome, cell, tissue or organism.

<span class="mw-page-title-main">Terri Attwood</span> British bioinformatics researcher

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<span class="mw-page-title-main">Eline Slagboom</span>

P. Eline Slagboom is a Dutch biologist specializing in the human familial longevity and ageing.

<span class="mw-page-title-main">Ron Appel</span> Swiss academic

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 '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.

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References

  1. NBIC Website
  2. van Gelder, Celia W. G.; Hooft, Rob W. W.; van Rijswijk, Merlijn N.; van den Berg, Linda; Kok, Ruben G.; Reinders, Marcel; Mons, Barend; Heringa, Jaap (15 September 2017). "Bioinformatics in the Netherlands: the value of a nationwide community". Briefings in Bioinformatics. 20 (2): 375–383. doi:10.1093/bib/bbx087. PMC   6433734 . PMID   28968694.
  3. Netherlands Genomics Initiative information on NBIC
  4. Overview NGI Genomics Centres
  5. Website Netherlands Proteomics Centre
  6. Website Netherlands Metabolomics Centre
  7. "Website Netherlands Consortium for Systems Biology". Archived from the original on 2012-01-25. Retrieved 2012-02-27.
  8. "NBIC: BioAssist activities moved to DTL Data programme". www.nbic.nl. Retrieved 2 March 2018.
  9. Website Netherlands Genomics Initiative
  10. Website BSIK: Besluit subsidies Investeringen Kennisinfrastructuur
  11. "Bioscience Omics Facility". 23 November 2012.
  12. "NBIC: Bioinformatics Research Support". www.nbic.nl. Archived from the original on 2010-10-31.
  13. Bioinformatica in de klas
  14. LOBIN members
  15. list of key software products of NBIC
  16. NBIC trac server
  17. NBIC Galaxy server
  18. Galaxy Community Conference 2011 homepage
  19. "BTN/GOBLET meeting | GOBLET". www.mygoblet.org. Retrieved 24 August 2016.