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Bio-Linux as a tool for bioinformatics training

Timothy Booth, Mesude Bicak, Hyun Soon Gweon, Dawn Field, Enis Afgan
2012 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)  
Bio-Linux helps on both counts by offering well over one hundred bioinformatics tools packaged into a single distribution, easily accessible and readily usable.  ...  Furthermore this paper discusses how bioinformatics training on Bio-Linux is helping to bridge the data production and analysis gap.  ...  ACKNOWLEDGMENT The authors acknowledge the many past Bio-Linux developers, as well as CloudBioLinux developers Ntino Krampis and Brad Chapman, the Galaxy Team (http://wiki.g2.bx.psu.edu/Galaxy Team), the  ... 
doi:10.1109/bibe.2012.6399736 dblp:conf/bibe/BoothBGFA12 fatcat:kjovdrrs2bhq3dntjaeo7xsnua

The Art of Bioinformatics Learning in Our Arabic World

Alsamman M. Alsamman
2019 Highlights in BioScience  
Besides the regular education system, few bioinformatics training courses are offered and less are affordable to fresh graduates in countries most of which are categorized as developing countries.  ...  Teaching bioinformatics is very challenging since it is a multidisciplinary field, where most of the undergraduate programs in colleges provide only one area required for bioinformatics.  ...  Morad Mokhtar (Molecular Genetics and Genome Mapping Lab Agricultural The Art of Bioinformatics Learning in Our Arabic World  ... 
doi:10.36462/h.biosci.20193 fatcat:wxeu4gxk7bh35fqnhqshrvfad4

Bioinformatics and Data Management Support for Environmental Genomics

Dawn Field, Bela Tiwari, Jason Snape
2005 PLoS Biology  
The Bio-Linux Computing Platform (A) Bio-Linux is a Linux distribution customized to be user-friendly that contains approximately 60 popular bioinformatics packages.  ...  As part of the Environmental Genomics initiative, NERC funded the creation of a dedicated bioinformatics centre with a remit to provide bioinformatics consultation, training, and data management.  ... 
doi:10.1371/journal.pbio.0030297 pmid:16089508 pmcid:PMC1187860 fatcat:gk4xrntzl5gwrhiyekgduu6fba

Desktop as a Service Supporting Environmental 'omics

David C. H. Wallom, Timothy Booth, Andy Bowery, Ben Collier, Phillip Kershaw, Anurag Priyam, Yannick Wurm, Dawn Field
2015 2015 IEEE 11th International Conference on e-Science  
Desktop-aaS is a paradigm where specific user environments, in our case personal Linux virtual machine instances, are operated as Software as a Service solutions.  ...  This experience paper describes the development of a new Desktop as a Service (Desktop-aaS) system to support the deployment and utilisation of tools for researchers who are working on Environmental 'omics  ...  Bio-Linux has traditionally been installed onto bare-metal, possibly on a dualboot workstation, or run directly from a USB stick for training and demo purposes.  ... 
doi:10.1109/escience.2015.53 dblp:conf/eScience/WallomBBCKPWF15 fatcat:4oyc2ru43ff3bi42nd6k753kdu

Training workshop on Mycobacterium whole genome sequence data analysis

Yonas Kassahun Hirutu, Mesert D Bayeleygne, Adey F Desta, Tewodros Tariku, Markos Abebe
2019 EMBnet journal  
This report describes a bioinformatics training initiative started at AHRI aiming to support life science researchers and postgraduates in handling next-generation sequencing data.  ...  Basic bioinformatics training workshop conducted at Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia.  ...  Acknowledgements The workshop was supported by training and research directorate at AHRI with a funding source from the Swedish International Development Cooperation Agency (SIDA).  ... 
doi:10.14806/ej.24.0.920 fatcat:rcvwql3t2nczfkvm677yaunx7e

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján (+16 others)
2014 BMC Bioinformatics  
, as well as providing an opportunity for new participants to get involved in collaborative projects.  ...  Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus.  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the  ... 
doi:10.1186/1471-2105-15-s14-s7 pmid:25472764 pmcid:PMC4255748 fatcat:p7jbtuipnbdafo3zauaqrhu5sq

Sprints, Hackathons and Codefests as community gluons in computational biology

Steffen Möller, Enis Afgan, Michael Banck, Peter J. A. Cock, Matus Kalas, Laszlo Kajan, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Andreas Tille (+3 others)
2013 EMBnet journal  
The events' hosting institutions and funding agencies are thanked for providing facilities and support.  ...  O'Reilly, Electric Genetics, Apple Asia, the Debian project and the employing institutions are thanked for contributing to the travel costs of the events.  ...  To help achieve these goals, the Bioinformatics Open Source Conference (BOSC) was established in 2000 by the Open Bioinformatics Foundation Bio* project members as an international venue for showcasing  ... 
doi:10.14806/ej.19.b.726 fatcat:n7hmrivnpfekzgrdcj4f5tpndq

Broader incorporation of bioinformatics in education: opportunities and challenges

M. P. Cummings, G. G. Temple
2010 Briefings in Bioinformatics  
kept up-to-date as the field and tools change.  ...  The major opportunities for broader incorporation of bioinformatics in education can be placed into three general categories: general applicability of bioinformatics in life science and related curricula  ...  As a field, we cannot rely solely on separate courses in bioinformatics to train our current students.  ... 
doi:10.1093/bib/bbq058 pmid:20798182 fatcat:o6p4gzvgpfe4lidhdsvfnyjyx4

Russian EMBnet node: AGM2011 report

Sergei Alexandrovich Spirin
2011 EMBnet journal  
Bioengineering and Bioinformatics of MSU.  ...  The Russian EMBnet node is based on the Belozersky Institute of Physical-Chemical Biology, which is a scientific department of Moscow State University (MSU) and is closely connected with the Faculty of  ...  p 9 : a tool for phylogenetic tree prediction; DotHeli d. x 10 : local similarity map for two biological sequences; SVETK e.  ... 
doi:10.14806/ej.17.a.219 fatcat:2f4nt7reazdjvdpdkyftpvkoaa

BioRuby: bioinformatics software for the Ruby programming language

N. Goto, P. Prins, M. Nakao, R. Bonnal, J. Aerts, T. Katayama
2010 Bioinformatics  
The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language.  ...  Funding: Information-technology Promotion Agency Japan (IPA); Database Center for Life Science (DBCLS) Japan; Human Genome Center, Institute of Medical Science, University of Tokyo; Open Bioinformatics  ...  We thank Hilmar Lapp and Chris Fields for comments and review of the manuscript.  ... 
doi:10.1093/bioinformatics/btq475 pmid:20739307 pmcid:PMC2951089 fatcat:cdodnzoxhvgijjuvexzsl73gla

Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau (+57 others)
2015 Nucleic Acids Research  
sequences as well as tools for sequence analysis, phylogenetics, structure analysis, chemioinformatics and network analysis.  ...  Sapienza University Biocomputing group resources and tools http://www.biocomputing.it/index.php/About-us/tools A collection of 19 resources and tools for structural bioinformatics, immunoinformatics and  ...  ACKNOWLEDGEMENTS The authors would like to thank Steve Pettifer and Dave Thorne for the initial discussions and ideas founding the registry effort.  ... 
doi:10.1093/nar/gkv1116 pmid:26538599 pmcid:PMC4702812 fatcat:npzer6xh7fezlbcamfmdvv552m

Survey of Bioinformatics and Computational Needs in Australia 2016.pdf

Maria Victoria Schneider, MADISON FLANNERY, PHILIPPA GRIFFIN
2016 Figshare  
In order to gain a snapshot of the bioinformatics and computational biology needs among life scientists and medical researchers, EMBL-ABR Hub conducted a survey (July-Sep 2016) across Australia.  ...  In total 123 responses were received from around Australia, distributed across all states and this document summarises the results and provides a link to the collected survey results.  ...  One respondent requested less training -"Less training, more resource funding and allocation" -which may indicate a frustration with general under-resourcing for bioinformatics as a whole.  ... 
doi:10.6084/m9.figshare.4307768.v1 fatcat:qbw7kcgxujc2dj3ms5wwsfwfqu

So you want to be a computational biologist?

Nick Loman, Mick Watson
2013 Nature Biotechnology  
Software tools are often implementations of a particular algorithm that may be well-suited for particular types of data; for example, in de novo assembly, an Overlap-Layout-Consensus assembler is optimized  ...  Understanding the underlying methods and algorithms gives you the tools to interpret the results.  ...  The right tool for the job Become comfortable working from the UNIX/Linux command line.  ... 
doi:10.1038/nbt.2740 pmid:24213777 fatcat:hyee753ejvdg7irqs6h3ls3t2u

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
EDAM can be helpful in documenting and categorising bioinformatics resources using a standard "vocabulary", enabling users to find respective resources and choose the right tools.  ...  data format compatible with Web services and programmatic libraries, that is expressive enough to be usable as a common, canonical data model that serves tools, libraries, and users with convenient data  ...  a substantial portion of contemporary bioinformatics tools via integration from various repositories including Bio-Linux, Bio*, and Bioconductor.  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

EMBnet.journal 17 Suppl. A

EMBnet Journal
2011 EMBnet journal  
tools and/or bioinformatics training.  ...  server to a new Linux server in Norway.  ...  AliBee 8 : an original program for multiple alignment; c. TreeTop 9 : a tool for phylogenetic tree prediction; d. DotHelix 10 : local similarity map for two biological sequences; e.  ... 
doi:10.14806/ej.17.a.261 fatcat:yofrffbhlrhfhdhqzxghsxyhn4
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