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Best practices in bioinformatics training for life scientists

A. Via, T. Blicher, E. Bongcam-Rudloff, M. D. Brazas, C. Brooksbank, A. Budd, J. De Las Rivas, J. Dreyer, P. L. Fernandes, C. van Gelder, J. Jacob, R. C. Jimenez (+7 others)
2013 Briefings in Bioinformatics  
possible thanks to EMBnet and SeqAhead (COST Action, BM1006), to The Genome Analysis Centre (TGAC, Norwich, UK), the Biotechnology and Biological Sciences Research Council (BBSRC, UK), and the SLU-Global Bioinformatics  ...  This article summarizes the key discussion points from a more extensive best-practice document on bioinformatics training for life scientists.  ...  CONCLUDING REMARKS Demand for bioinformatics training is increasing as more and more life scientists, working in diverse research areas, are generating and using data produced by high-throughput methodologies  ... 
doi:10.1093/bib/bbt043 pmid:23803301 pmcid:PMC3771230 fatcat:i5ljsmqxxjah5bfy75ebfb5dku

A global perspective on evolving bioinformatics and data science training needs

Teresa K. Attwood, Sarah Blackford, Michelle D. Brazas, Angela Davies, Maria Victoria Schneider
2017 Briefings in Bioinformatics  
Basic data stewardship is still taught relatively rarely in life science education programmes, creating a chasm between theory and practice, and fuelling demand for bioinformatics training across all educational  ...  Concerned by this, surveys have been conducted in recent years to monitor bioinformatics and computational training needs worldwide.  ...  Acknowledgements The authors thank all the participants of the SEB Bioinformatics Workshop, held in Manchester (2014), and GOBLET 2014 AGM, held in Toronto, who contributed to wide-ranging discussions  ... 
doi:10.1093/bib/bbx100 pmid:28968751 fatcat:vl2jt4n3evb3nd735ikx7huxr4

Scientific Meeting 2014 "NGS Data after the Gold Rush" & "Management Committee" Meeting, Norwich, UK

Vicky Schneider, Erik Bongcam-Rudloff
2014 EMBnet journal  
training life scientists to make the most of existing solutions, and ensuring best practice in experimental design, in data quality control, analysis and storage, and in facilitating interoperability  ...  practices both in the lab and in bioinformatics to do the best possible research.  ... 
doi:10.14806/ej.20.a.794 fatcat:6x5wbvdowja4tciboi2cgnnkbq

A Vision for Collaborative Training Infrastructure for Bioinformatics

Jason Williams
2016 Figshare  
and existing life scientists.  ...  While college curricula are slower to adapt, grassroots, startup-spirited organizations such as Software and Data Carpentry have made impressive inroads in training on the best practices of software use  ...  ACKNOWLEDGMENTS The authors thank Lindsay Barone, Jonah Duckles and Greg Wilson for helpful comments and corrections.  ... 
doi:10.6084/m9.figshare.3807723 fatcat:hdvs4p6mdnaxdg567x57qj7v4e

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 de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.  ...  The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics  ...  Nanopore best practice workshop.  ... 
doi:10.12688/f1000research.20244.1 pmid:33163154 pmcid:PMC7607484 fatcat:g4gztfjahrbkdepxw6rgkjfhjy

NIBLSE: A Network for Integrating Bioinformatics into Life Sciences Education

Elizabeth Dinsdale, Sarah C. R. Elgin, Neal Grandgenett, William Morgan, Anne Rosenwald, William Tapprich, Eric W. Triplett, Mark A. Pauley
2015 CBE - Life Sciences Education  
ACKNOWLEDGMENTS The authors thank the members of NIBLSE for their contributions to the network and for their participation in the April 2014 conference.  ...  how best to integrate bioinformatics into life sciences curricula.  ...  Challenges • Many current faculty were trained before the widespread use of bioinformatics in research and thus need training in this area themselves in order to teach bioinformatics to their students.  ... 
doi:10.1187/cbe.15-06-0123 pmid:26466989 pmcid:PMC4710410 fatcat:z6xzliiybrc5fjc3s5fcfpmroa

Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

Brendan Lawlor, Paul Walsh
2015 Bioengineered  
engineering best practices in that field.  ...  Life scientists show no such consensus.  ... 
doi:10.1080/21655979.2015.1050162 pmid:25996054 pmcid:PMC4601517 fatcat:pk34huwztzaxdain5dwzgwvi2a

FAIR Training in ELIXIR Europe

Mateusz Kuzak, Leyla García Castro, Bérénice Batut, Ricardo Arcila, Niall Beard, Melissa Burke, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Kim Gurwitz, Pascal Kahlem, Paula Martinez, Sarah Morgan (+5 others)
2019 Zenodo  
This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices, such as best practices for developing and sharing training materials.  ...  The ELIXIR Training Platform coordinates training activities, trains life-science researchers, and helps scientists and developers to find the training they need.  ...  a lized registry, e.g., Host it in a public repository Or make the use rules public in your metadata (e.g., membership or subscription) 10 recommendations to make your training materials FAIRer  ... 
doi:10.5281/zenodo.3349846 fatcat:z67seyd445crteupitx6h275ry

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

Teresa K. Atwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder, Lonnie Welch
2015 PLoS Computational Biology  
training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.  ...  In recent years, high-throughput technologies have brought big data to the life sciences.  ...  Acknowledgments We would like to thank Barbara van Kampen for providing administrative support.  ... 
doi:10.1371/journal.pcbi.1004143 pmid:25856076 pmcid:PMC4391932 fatcat:yeudcjpdkjgl3idlaksgy2ljd4

The application of project-based learning in bioinformatics training

Laura R. Emery, Sarah L. Morgan, Francis Ouellette
2017 PLoS Computational Biology  
., and many other members of the EBI user-training-working group for their ideas and Twells, R. for being open-minded about reshaping an already successful formula.  ...  audience of life scientists.  ...  bioinformatics training practice.  ... 
doi:10.1371/journal.pcbi.1005620 pmid:28817584 pmcid:PMC5560525 fatcat:zpveh42cibeqfa5gqqgocbbocm

e-infrastructures from the viewpoint of bioinformatics [article]

Fotis Psomopoulos
2018 Figshare  
Slides presented during the 2nd EOSC Stakeholders Forum in Vienna (https://www.eoscpilot.eu/events/second-eosc-stakeholders-forum) 21-22 Nov 2018, during the session "Users meet the service providers:  ...  data Point researchers to the best solutions based on their requirements  EOSC-Lifetraining Data Experts, to be embedded in each RI and provide support to the various user groups.  ...  / optimal solution, instead of what colleagues are using  Training  30/10/2018 Open Access Week 2018 6 Thank you for your attention!  ... 
doi:10.6084/m9.figshare.7375916 fatcat:3dcyds7i7ze2xezwtrle67x3ny

Putting the Life Science RDM support landscape in context with RDMkit

Pinar Alper, Carole Goble
2021 Zenodo  
For researchers, RDMkit is a one stop shop of information, advice and signposting to research data management know-how, tools, examples and best practice, written by life scientists for life scientists  ...  RDMkit is recommended in the European Commission's Horizon Europe Program Guide as the "resource for Data Management guidelines and good practices for the Life Sciences."  ...  RDM support throughout the entire life cycle of projects as outlined in DMPs Website focal point for guidance, information, best practice, examples Putting the Life Science RDM support landscape in context  ... 
doi:10.5281/zenodo.5541423 fatcat:l24iprvzofg2flupobte2gejnu

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

J.-W. Li, D. Bolser, M. Manske, F. M. Giorgi, N. Vyahhi, B. Usadel, B. J. Clavijo, T.-F. Chan, N. Wong, D. Zerbino, M. V. Schneider
2013 Briefings in Bioinformatics  
He is involved in SEQanswers, an online community for next-generation sequencing technology.  ...  Each chapter comes with practical exercises so readers may Jing-Woei Li is a postdoctoral fellow at The Chinese University of Hong Kong.  ...  ACKNOWLEDGMENTS We thank Darren Logan for his advice and encouragement.  ... 
doi:10.1093/bib/bbt045 pmid:23793381 pmcid:PMC3771235 fatcat:dvrfsizvcbblhn2e5yfrils5ya

Building a local community of practice in scientific programming for life scientists

Sarah L. R. Stevens, Mateusz Kuzak, Carlos Martinez, Aurelia Moser, Petra Bleeker, Marc Galland
2018 PLoS Biology  
In this paper, we describe why and how to build a local community of practice in scientific programming for life scientists who use computers and programming in their research.  ...  While most life scientists are well trained in the laboratory to conduct experiments, good practices with (big) data sets and their analysis are often missing.  ...  Acknowledgments We are thankful to the Carpentries Foundation for assistance in workshop organization.  ... 
doi:10.1371/journal.pbio.2005561 pmid:30485260 pmcid:PMC6287879 fatcat:77nf6eoctrhkbnfz5lgybusxte
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