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A Quick Guide for Building a Successful Bioinformatics Community

Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg, Amarda Shehu
2015 PLoS Computational Biology  
We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities.  ...  Such communities play a key role in many bioinformatics activities.  ...  A Quick Guide to Building a Successful Bioinformatics Community Analyses of successful, high-impact collaborations, organizations, networks, and communities have identified several common features of such  ... 
doi:10.1371/journal.pcbi.1003972 pmid:25654371 pmcid:PMC4318577 fatcat:g24ki4asi5a2xfo4r3lra3nolm

Executive Board: AGM2011 report

Teresa K Attwood
2011 EMBnet journal  
for its "rebirth"; updating the content of the EMBnet.journal website; and developing new Quick Guides, etc., as time permits.  ...  the EMBnet community.  ... 
doi:10.14806/ej.17.a.221 fatcat:dwjlgexmyvf3bhbivzpflv2xma

Making training materials FAIR experiences, challenges, solutions

Saskia Hiltemann, Anna Swan, Verena Ras, Maria Doyle, Melissa Burke, Patricia M. Palagi, Celia W.G. van Gelder
2021 Zenodo  
The WEB (Workshop on Education for Bioinformatics) 2021 was a dedicated forum for training providers, trainers and trainees to share their experiences of making training materials FAIR.  ...  registries Life/Success is a journey, not a destination• Open and FAIR is a journey and a destination  ...  others Australian BioCommons Melissa Burke Australian BioCommons is building digital capability for the life science communities Support volunteer trainers to deliver events nationally tinyurl.  ... 
doi:10.5281/zenodo.5820221 fatcat:quakdtmyxjg7vik5zkv5ogpuna

Coordinating SARS-CoV-2 Genomic Surveillance in the United States

Martha I Nelson, Peter Thielen
2021 Virus Evolution  
Building a Research Network for Genomic Epidemiology.  ...  High throughput bioinformatic pipelines allow state and local public health labs to flag new VOCs emerging in communities (Hadfield et al., 2018) .  ... 
doi:10.1093/ve/veab053 pmid:34527283 pmcid:PMC8195028 fatcat:d6wnpottdjgk7imhlfq6dzhry4

EMBnet.journal 17 Suppl. A

EMBnet Journal
2011 EMBnet journal  
Quick Guides A survey is under preparation to probe for interest in new Quick Guides. The level of response is still low but there is a clear incidence in "R", "Bioconductor" and "Primer design".  ...  The activities of the Portuguese node contribute to the integration of users, and communities of users, in global communities and activities; EMBnet-originated software, Quick Guides, newsletter articles  ...  Research Some directions of research in bioinformatics provided in our Institute (those that are not reflected in the above list of new software) are as follows: a. comparative structural description of  ... 
doi:10.14806/ej.17.a.261 fatcat:yofrffbhlrhfhdhqzxghsxyhn4

Elixir Advanced Workshops On Genome Annotation

Henrik Lantz, Bengt Persson
2017 Zenodo  
There are no golden standards, and the technology is rapidly advancing with new sequence technologies becoming available at a quick pace.  ...  Genome assembly and genome annotation constitute areas where significant resources, both manpower and computational resources, are needed to come to the successful conclusion of a project.  ...  ELIXIR is looking to establish such Communities of Practice of bioinformatics experts different levels of maturity, ranging from national infrastructures that have existed for over a involved in advanced  ... 
doi:10.5281/zenodo.557060 fatcat:jwg3axhhx5btvadfqandsblnoe

A Quick Guide for Developing Effective Bioinformatics Programming Skills

Joel T. Dudley, Atul J. Butte, Fran Lewitter
2009 PLoS Computational Biology  
JTD would also like to thank Shirley Wu for early feedback on the manuscript concepts and for demonstrating the value of these concepts to the broader bioinformatics community.  ...  Altman for the opportunity to present to his biomedical informatics students the lecture from which much of this manuscript has been derived.  ...  Java, for example, which is popular in both academic curriculum and industry, has served as the basis for many successful bioinformatics projects.  ... 
doi:10.1371/journal.pcbi.1000589 pmid:20041221 pmcid:PMC2791169 fatcat:vmfuql454zcdflra62zr7bkevi

Bioinformatics Workflow Management With The Wobidisco Ecosystem [article]

Sebastien Mondet, Bulent Arman Aksoy, Leonid Rozenberg, Isaac Hodes, Jeffrey Hammerbacher
2017 bioRxiv   pre-print
To conduct our computational experiments, our team developed a set of workflow-management-related projects: Ketrew, Biokepi, and Coclobas.  ...  The family of tools and libraries are designed with reliability and flexibility as main guiding principles. We describe the components of the software stack and explain the choices we made.  ...  The community includes very successful industrial users for whom safety and security matter [24] , [25] , and has contributed great tooling.  ... 
doi:10.1101/213884 fatcat:mualajjtcbh5bhq4kbmmi7p6au

Reliable Phylogenetic Trees Building: A New Web Interface for FIGENIX

Julien Paganini, Philippe Gouret
2012 Evolutionary Bioinformatics  
The community needed a reliable and user friendly tool to quickly produce robust phylogenetic trees which are crucial in evolutionary studies and genomes' functional annotation.  ...  Several laboratories around the world use it in their research, but it was difficult to use for non-expert users, thus we developed a new graphical user interface for the benefit of all biologists.  ...  Hemalatha for biological discussions, tests of the tool and for manuscript reading and corrections.  ... 
doi:10.4137/ebo.s9179 pmid:22844195 pmcid:PMC3399708 fatcat:lnoio5uy55cqfkpvhhinczpini

A quick guide for student-driven community genome annotation [article]

Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, Mirella Flores, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'elia, Susan J. Brown, Surya Saha
2018 arXiv   pre-print
Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for  ...  We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators.  ...  These results demonstrate that the student-driven community model is fully capable of producing high quality gene models while providing a supportive and valuable educational experience for undergraduate  ... 
arXiv:1805.03602v2 fatcat:ykgc4tzxfnhyhgy7ixt365mn6y

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Benjamin Moore, Patricia Carvajal-López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L. Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L. Morgan, Guilherme Oliveira (+5 others)
2021 PLoS Computational Biology  
Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program  ...  Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region.  ...  We would also like to thank Cath Brooksbank and Emily Perry for their insightful ideas and feedback during the writing process.  ... 
doi:10.1371/journal.pcbi.1009218 pmid:34411091 pmcid:PMC8375989 fatcat:gzj7vsv2wfgo3p45cnpdmo65re

Nine quick tips for efficient bioinformatics curriculum development and training

Susan McClatchy, Kristin M. Bass, Daniel M. Gatti, Adam Moylan, Gary Churchill, Russell Schwartz
2020 PLoS Computational Biology  
As a result, there is a concurrent need for training researchers to use and understand new computational tools.  ...  Here we describe an efficient and effective approach to developing curriculum materials that can be deployed in a research environment to meet this need.  ...  Acknowledgments The authors thank Karl Broman for providing a software user guide and other key materials, Tim Stearns and Georgi Kolishovski for contributing to experimental design and statistics curricula  ... 
doi:10.1371/journal.pcbi.1008007 pmid:32702019 fatcat:xqolsc2yqnf6vc4a4ljg7oo2na

Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program

Diane C Rein
2006 Journal of the Medical Library Association  
bioinformatics support services for the Purdue community.  ...  Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing  ...  ''proof of concept'' for developing new in-house bioinformatics services. • The success of the evaluation and assessment program, combined with the knowledge that bioinformatics information needs are  ... 
pmid:16888666 pmcid:PMC1525331 fatcat:n7bpa3hxo5cj5o7xzybuwfa2by

A quick guide for student-driven community genome annotation

Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, Mirella Flores-Gonzalez, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown, Surya Saha, Francis Ouellette
2019 PLoS Computational Biology  
Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for  ...  We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators.  ...  Poelchau from USDA-ARS, NAL for useful suggestions on the manuscript.  ... 
doi:10.1371/journal.pcbi.1006682 pmid:30943207 pmcid:PMC6447164 fatcat:brg35r3tu5grvnqgxz63qyd72u

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists

Hamza Mbareche, Nathan Dumont-Leblond, Guillaume J. Bilodeau, Caroline Duchaine
2020 Life  
The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols.  ...  Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities  ...  Acknowledgments: H.M. is a recipient of the FRQNT Ph.D. scholarship as well as a scholarship for a short internship from the Quebec Respiratory Health Network, and is the recipient of the Lab Exchange  ... 
doi:10.3390/life10090185 pmid:32911871 fatcat:ccm7ddmqmfe5lbnsx6u5rzfsme
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