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Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives

Thomas Schmutzer, Marie E. Bolger, Stephen Rudd, Jinbo Chen, Heidrun Gundlach, Daniel Arend, Markus Oppermann, Stephan Weise, Matthias Lange, Manuel Spannagl, Björn Usadel, Klaus F.X. Mayer (+1 others)
2017 Journal of Biotechnology  
This review introduces the GCBN's spectrum of web-services and integrated data resources that address common research problems in the plant genomics community.  ...  As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure  ...  Mayer and Björn Usadel acknowledge support from the German Ministry of Education and Research (BMBF) for grant 031A536 "de.NBI". Uwe Scholz and Klaus F.X.  ... 
doi:10.1016/j.jbiotec.2017.07.006 pmid:28698099 fatcat:mvlhv6xkevdy5bz4zknuo436oa

The International Virus Bioinformatics Meeting 2020

Franziska Hufsky, Niko Beerenwinkel, Irmtraud M. Meyer, Simon Roux, Georgia May Cook, Cormac M. Kinsella, Kevin Lamkiewicz, Mike Marquet, David F. Nieuwenhuijse, Ingrida Olendraite, Sofia Paraskevopoulou, Francesca Young (+7 others)
2020 Viruses  
The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting.  ...  On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics.  ...  Acknowledgments: The conference organisers acknowledge sponsorship from the Swiss Institute of Bioinformatics (SIB), the Swiss Society for Microbiology (SSM), Novartis, Boehringer Ingelheim, the Vetsuisse  ... 
doi:10.3390/v12121398 pmid:33291220 pmcid:PMC7762161 fatcat:73puf5gx2bcjplldfm7mryez7m

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs

C. Durrant, M. A. Swertz, R. Alberts, D. Arends, S. Moller, R. Mott, P. Prins, K. J. van der Velde, R. C. Jansen, K. Schughart
2011 Briefings in Bioinformatics  
During a meeting of the SYSGENETworking group 'Bioinformatics', currently available software tools and databases for systems genetics in mice were reviewed and the needs for future developments discussed  ...  R should be used as the principal computer language for QTL data analysis in all platforms and a 'cloud' should be used for software dissemination to the community.  ...  FUNDING SYSGENET is funded through the COST framework, an intergovernmental framework for European Cooperation in Science and Technology (http://www.cost.eu/about_cost) and is coordinated by Klaus Schughart  ... 
doi:10.1093/bib/bbr026 pmid:22396485 pmcid:PMC3294237 fatcat:hplbo5ks4fhwtbmtl2louquhg4

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology

Joanna Friesner, Sarah M. Assmann, Ruth Bastow, Julia Bailey-Serres, Jim Beynon, Volker Brendel, C. Robin Buell, Alexander Bucksch, Wolfgang Busch, Taku Demura, Jose R. Dinneny, Colleen J. Doherty (+27 others)
2017 Plant Physiology  
These include the Course Source Bioinformatics Learning framework, which has been developed and reviewed by members of the Genomics Education Partnership, the Network for Integrating Bioinformatics into  ...  As a community, developing a portal that provides reviews and ratings of these programs would be a valuable resource (Searls, 2012) .  ... 
doi:10.1104/pp.17.01490 pmid:29208732 pmcid:PMC5717721 fatcat:diocyqmgbvdm7dpoanfwxnlc4y

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2019 F1000Research  
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF).  ...  The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR network.  ...  of a web service in the cloud for other researchers.  ... 
doi:10.12688/f1000research.20244.1 pmid:33163154 pmcid:PMC7607484 fatcat:g4gztfjahrbkdepxw6rgkjfhjy

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2020 F1000Research  
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF).  ...  for quality assessment on both the technical and administrative levels.  ...  of a web service in the cloud for other researchers.  ... 
doi:10.12688/f1000research.20244.2 fatcat:io4rgsengvddhlhwjgpqv5livu

Community-driven roadmap for integrated disease maps

Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M T Fleming, Nicolas Le Novère, Piotr Gawron, Thomas Ligon, Anna Niarakis (+6 others)
2018 Briefings in Bioinformatics  
The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge.  ...  Reinhard Schneider is the Head of the Bioinformatics Core facility at the Luxembourg Centre for Systems Biomedicine (LCSB).  ...  Acknowledgements The authors would like to thank the DMC members, whose participation in the discussions in the meeting helped greatly to shape the contents of this article:  ... 
doi:10.1093/bib/bby024 pmid:29688273 fatcat:evg6lluamfg2tn5ygblmxsznea

SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei
2013 Nucleic Acids Research  
Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads.  ...  Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource.  ...  The authors particularly thank Mathias Walter, Helmholtz-Center Munich, for many helpful discussions and suggestions.  ... 
doi:10.1093/nar/gkt970 pmid:24165881 pmcid:PMC3965014 fatcat:nxbvchfugjd6pa7u7whwbn7idq

Bioinformatics Web Portals [chapter]

Mario Cannataro
Encyclopedia of Portal Technologies and Applications  
The Helmholtz Network for Bioinformatics (HNB, n.d.) offers access to numerous bioinformatics resources provided by many German bioinformatics research groups through a single Web portal.  ...  The grid protein sequence analysis (GPSA) is an integrated grid portal devoted to molecular bioinformatics and offers a user-friendly interface for the grid genomic resources on the EGEE grid.  ... 
doi:10.4018/978-1-59140-989-2.ch013 fatcat:z7atnj4j6zbhvmt36y3k7oxgnm

Combined C&D Group Publication on INFRAFRONTIER and IMPC Globally Available and Shared Resources

Asrar Ali Khan, Michael Raess
2020 Zenodo  
This deliverable was submitted to AMRC Open Research for publication as a 'document' article on 18 August 2020. At the time of submission of this deliverable, the article was not published.  ...  This deliverable is a publication on globally available and shared resources available from INFRAFRONTIER and IMPC.  ...  TCP is an integral networking partner in several INFRAFRONTIER EC-grants but does not offer any services directly.  ... 
doi:10.5281/zenodo.5833762 fatcat:dep7yddhmjfz5dv5ci5t5w63ki

FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum

U. Guldener
2006 Nucleic Acids Research  
The comprehensive set of gene calls was also used for the design of an Affymetrix GeneChip. The resource is accessible on  ...  The database can be accessed to retrieve information from bioinformatics analyses and functional classifications of the proteins.  ...  This work was supported by the Austrian genome programme GEN-AU (bm:bwk-Federal Ministry for Education, Science and Culture, GZ 200.051/6-VI/1/2001), the Impuls-und Vernetzungsfonds der Helmholtz-Gemeinschaft  ... 
doi:10.1093/nar/gkj026 pmid:16381910 pmcid:PMC1347389 fatcat:3b2fyo6iozc5litkfdj25a7ihu

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
Our team maintains the Enzyme portal, a resource that integrates enzyme-related data for all EMBL-EBI enzyme resources as well as the underlying functional and genomic data.  ...  a clan. http://merops.sanger.ac.uk Enzyme Portal The Enzyme Portal provides integrated enzyme-related data for all EMBL-EBI enzyme resources as well as the underlying functional and genomic data. •  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

transPLANT Resources for Triticeae Genomic Data

Manuel Spannagl, Michael Alaux, Matthias Lange, Daniel M. Bolser, Kai C. Bader, Thomas Letellier, Erik Kimmel, Raphael Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer (+17 others)
2016 The Plant Genome  
integration of data from distributed resources.  ...  Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting  ...  The IPK resources Barley Blast Server, BARLEX, and Kmasker e!  ... 
doi:10.3835/plantgenome2015.06.0038 pmid:27898761 fatcat:qbt3ggpfgvbz3okorau7zvsnca

Digital services for science – where is the journey heading? [article]

Uwe Konrad, Konrad Förstner, Johannes Reetz, Klaus Wannemacher, Jürgen Kett, Florian Mannseicher
2021 Zenodo  
Due to advances in information technology, ever-increasing cross-domain networking in science and research and the need to share services and resources, distributed digital services are being increasingly  ...  them fully available for use.  ...  System) portal at the Swiss Bioinformatics Institute (SIB, Lausanne).  ... 
doi:10.5281/zenodo.4301946 fatcat:waha7fedmnbzfktd4jbftv7hse

NFDI4BioDiversity - A Consortium for the National Research Data Infrastructure (NFDI)

Frank Oliver Glöckner, Michael Diepenbroek, Janine Felden, Anton Güntsch, Jens Stoye, Jörg Overmann, Klaus Wimmers, Ivaylo Kostadinov, Ramin Yahyapour, Wolfgang Müller, Uwe Scholz, Dagmar Triebel (+6 others)
2020 Zenodo  
for mankind.  ...  To foster access to interoperable data, NFDI4BioDiversity focuses on the following six objectives: 1) Promoting research data management as an integral part of biodiversity research, 2) Enabling FAIRness  ...  naturgucker web portal.  ... 
doi:10.5281/zenodo.3943644 fatcat:lltfs5w6y5hn3ixe5bw2sitoa4
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