German Network for Bioinformatics Infrastructure: Difference between revisions

Revision as of 12:14, 15 June 2020

Revision as of 21:24, 23 June 2020

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**Members: [[Bielefeld University]], [[University of Gießen]] and [[Otto von Guericke University Magdeburg]]

**Topic: Microbial Bioinformatics, e.g. [[Genomics]], [[Transcriptomics]], [[Metagenomics]], [[Proteomics]], [[Metaproteomics]], [[Metabolomics]] and [[Cloud Computing]]

*Bioinformatics for Proteomics (BioInfra.Prot):<ref name="autogenerated1">{{cite journal| pmid=28606611 | doi=10.1016/j.jbiotec.2017.06.005 | volume=261 | title=BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication | year=2017 | journal=J Biotechnol | pages=116–125 | last1 = Turewicz | first1 = M | last2 = Kohl | first2 = M | last3 = Ahrens | first3 = M | last4 = Mayer | first4 = G | last5 = Uszkoreit | first5 = J | last6 = Naboulsi | first6 = W | last7 = Bracht | first7 = T | last8 = Megger | first8 = DA | last9 = Sitek | first9 = B | last10 = Marcus | first10 = K | last11 = Eisenacher | first11 = M| doi-access = free }}</ref>

**Members: [[Ruhr University Bochum]] ("Medical Bioinformatics" research unit of the Medizinisches Proteom-Center), Leibniz Institute for Analytical Sciences ISAS e.v. [[Dortmund]] ("Department of Bioanalytics"), [[Research Center Borstel]] and [[Max Planck Institute of Molecular Cell Biology and Genetics]]

**Topic: [[Proteomics]] and [[Lipidomics]]

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=== Databases ===

de.NBI develops and maintains the five large databases [[SILVA]],<ref>{{cite journal| pmid=28648396 | doi=10.1016/j.jbiotec.2017.06.1198 | volume=261 | title=25 years of serving the community with ribosomal RNA gene reference databases and tools | year=2017 | journal=J Biotechnol | pages=169–176 | last1 = Glöckner | first1 = FO | last2 = Yilmaz | first2 = P | last3 = Quast | first3 = C | last4 = Gerken | first4 = J | last5 = Beccati | first5 = A | last6 = Ciuprina | first6 = A | last7 = Bruns | first7 = G | last8 = Yarza | first8 = P | last9 = Peplies | first9 = J | last10 = Westram | first10 = R | last11 = Ludwig | first11 = W| doi-access = free }}</ref> [[PANGAEA]],<ref>{{cite journal| pmid=28743591 | doi=10.1016/j.jbiotec.2017.07.016 | volume=261 | title=Terminology supported archiving and publication of environmental science data in PANGAEA | year=2017 | journal=J Biotechnol | pages=177–186 | last1 = Diepenbroek | first1 = M | last2 = Schindler | first2 = U | last3 = Huber | first3 = R | last4 = Pesant | first4 = S | last5 = Stocker | first5 = M | last6 = Felden | first6 = J | last7 = Buss | first7 = M | last8 = Weinrebe | first8 = M| doi-access = free }}</ref> [[BacDive]],<ref>{{cite journal| pmid=28487186 | doi=10.1016/j.jbiotec.2017.05.004 | volume=261 | title=Mobilization and integration of bacterial phenotypic data-Enabling next generation biodiversity analysis through the BacDive metadatabase | year=2017 | journal=J Biotechnol | pages=187–193 | last1 = Reimer | first1 = LC | last2 = Söhngen | first2 = C | last3 = Vetcininova | first3 = A | last4 = Overmann | first4 = J| doi-access = free }}</ref> [[ProteinPlus]]<ref>{{cite journal| pmid=28610996 | doi=10.1016/j.jbiotec.2017.06.004 | volume=261 | title=From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library | year=2017 | journal=J Biotechnol | pages=207–214 | last1 = Bietz | first1 = S | last2 = Inhester | first2 = T | last3 = Lauck | first3 = F | last4 = Sommer | first4 = K | last5 = von Behren | first5 = MM | last6 = Fährrolfes | first6 = R | last7 = Flachsenberg | first7 = F | last8 = Meyder | first8 = A | last9 = Nittinger | first9 = E | last10 = Otto | first10 = T | last11 = Hilbig | first11 = M | last12 = Schomburg | first12 = KT | last13 = Volkamer | first13 = A | last14 = Rarey | first14 = M| doi-access = free }}</ref> and [[BRENDA]].<ref>{{cite journal| pmid=28438579 | doi=10.1016/j.jbiotec.2017.04.020 | volume=261 | title=The BRENDA enzyme information system-From a database to an expert system | year=2017 | journal=J Biotechnol | pages=194–206 | last1 = Schomburg | first1 = I | last2 = Jeske | first2 = L | last3 = Ulbrich | first3 = M | last4 = Placzek | first4 = S | last5 = Chang | first5 = A | last6 = Schomburg | first6 = D| doi-access = free }}</ref> They provide access to ribosomal RNA genes from all three domains of life (SILVA), georeferenced data from earth system research (PANGAEA), strain-linked information on the different aspects of bacterial and archaeal biodiversity (BacDive), protein structures (ProteinPlus) and to comprehensive enzyme information (BRENDA).

=== Tools ===

de.NBI develops and supplies about 100 bioinformatics tools for the German and global life sciences community, e.g. [[Galaxy (computational biology)]]/useGalaxy.eu (Workflow engine for all Freiburg RNA Tools),<ref>{{cite journal| pmid=28554830 | doi=10.1016/j.jbiotec.2017.05.019 | volume=261 | title=RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation | year=2017 | journal=J Biotechnol | pages=76–84 | last1 = Backofen | first1 = R | last2 = Engelhardt | first2 = J | last3 = Erxleben | first3 = A | last4 = Fallmann | first4 = J | last5 = Grüning | first5 = B | last6 = Ohler | first6 = U | last7 = Rajewsky | first7 = N | last8 = Stadler | first8 = PF| doi-access = free }}</ref> EDGAR (Comparative Genome Analyses Plattform),<ref>{{cite journal| pmid=28705636 | doi=10.1016/j.jbiotec.2017.07.010 | volume=261 | title=A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies | year=2017 | journal=J Biotechnol | pages=2–9 | last1 = Yu | first1 = J | last2 = Blom | first2 = J | last3 = Glaeser | first3 = SP | last4 = Jaenicke | first4 = S | last5 = Juhre | first5 = T | last6 = Rupp | first6 = O | last7 = Schwengers | first7 = O | last8 = Spänig | first8 = S | last9 = Goesmann | first9 = A| doi-access = free }}</ref> [[KNIME]] (Workflow engine),<ref>{{cite journal| pmid=28757290 | doi=10.1016/j.jbiotec.2017.07.028 | volume=261 | title=KNIME for reproducible cross-___domain analysis of life science data | year=2017 | journal=J Biotechnol | pages=149–156 | last1 = Fillbrunn | first1 = A | last2 = Dietz | first2 = C | last3 = Pfeuffer | first3 = J | last4 = Rahn | first4 = R | last5 = Landrum | first5 = GA | last6 = Berthold | first6 = MR| doi-access = free }}</ref> [[OpenMS]] (Open-source software C++ library for LC/MS data management and analyses),<ref>{{cite journal| pmid=28559010 | doi=10.1016/j.jbiotec.2017.05.016 | volume=261 | title=OpenMS - A platform for reproducible analysis of mass spectrometry data | year=2017 | journal=J Biotechnol | pages=142–148 | last1 = Pfeuffer | first1 = J | last2 = Sachsenberg | first2 = T | last3 = Alka | first3 = O | last4 = Walzer | first4 = M | last5 = Fillbrunn | first5 = A | last6 = Nilse | first6 = L | last7 = Schilling | first7 = O | last8 = Reinert | first8 = K | last9 = Kohlbacher | first9 = O| doi-access = free }}</ref> [[SeqAN]] (Open source [[C++]] library of efficient algorithms and data structures),<ref>{{cite journal| pmid=28888961 | doi=10.1016/j.jbiotec.2017.07.017 | volume=261 | title=The SeqAn C++ template library for efficient sequence analysis: A resource for programmers | year=2017 | journal=J Biotechnol | pages=157–168 | last1 = Reinert | first1 = K | last2 = Dadi | first2 = TH | last3 = Ehrhardt | first3 = M | last4 = Hauswedell | first4 = H | last5 = Mehringer | first5 = S | last6 = Rahn | first6 = R | last7 = Kim | first7 = J | last8 = Pockrandt | first8 = C | last9 = Winkler | first9 = J | last10 = Siragusa | first10 = E | last11 = Urgese | first11 = G | last12 = Weese | first12 = D| doi-access = free }}</ref> PIA (toolbox for MS based protein inference and identification analysis),<ref name="autogenerated1" /> [[Fiji (software)]] (Image processing package), [[MetFrag]] (in silico fragmenter combines compound database searching and fragmentation prediction for small molecule identification from tandem [[mass spectrometry]] data),<ref>{{cite journal| pmid=28554829 | doi=10.1016/j.jbiotec.2017.05.018 | volume=261 | title=Bioinformatics can boost metabolomics research | year=2017 | journal=J Biotechnol | pages=137–141 | last1 = Meier | first1 = R | last2 = Ruttkies | first2 = C | last3 = Treutler | first3 = H | last4 = Neumann | first4 = S| doi-access = free }}</ref> [[COPASI]] ([[Open-source software|Open source]] software application for creating and solving [[mathematical models]] of [[biological processes]]),<ref>{{cite journal| pmid=28655634 | doi=10.1016/j.jbiotec.2017.06.1200 | pmc=5623632 | volume=261 | title=COPASI and its applications in biotechnology | year=2017 | journal=J Biotechnol | pages=215–220 | last1 = Bergmann | first1 = FT | last2 = Hoops | first2 = S | last3 = Klahn | first3 = B | last4 = Kummer | first4 = U | last5 = Mendes | first5 = P | last6 = Pahle | first6 = J | last7 = Sahle | first7 = S}}</ref> [[SIAMCAT]] (Framework for the statistical inference of associations between [[microbial communities]] and host [[phenotypes]]), [[The e!DAL Plant Phenomics and Genomics Research Data Repository|e!DAL - PGP]] (Open source software framework to publish and share research data), MGX ([[Metagenome]] analysis)<ref>{{cite journal| pmid=29690922 | doi=10.1186/s40168-018-0460-1 | pmc=5937802 | volume=6 | title=Flexible metagenome analysis using the MGX framework | year=2018 | journal=Microbiome | page=76 | last1 = Jaenicke | first1 = S | last2 = Albaum | first2 = SP | last3 = Blumenkamp | first3 = P | last4 = Linke | first4 = B | last5 = Stoye | first5 = J | last6 = Goesmann | first6 = A}}</ref> and many more.

de.NBI tools are also registered and searchable in the ELIXIR Tools and Data Services Registry that provides more information in a standardized format.