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Ten simple rules to run a successful BioHackathon

Leyla Garcia, Erick Antezana, Alexander Garcia, Evan Bolton, Rafael Jimenez, Pjotr Prins, Juan M. Banda, Toshiaki Katayama, Scott Markel
2020 PLoS Computational Biology  
Acknowledgments We want to thank the participants of the NBDC/DBCLS and ELIXIR Europe BioHackathons. Special thanks to the organizing committees.  ...  To structure our suggestions as a "Ten simple rules" manuscript, we followed the recommended approach for writing this kind of paper [13] .  ...  We have focused on and extended those that we see as more relevant for BioHackathons. Fig 1 . 1 A graphical overview of 10 simple rules to successfully run a BioHackathon.  ... 
doi:10.1371/journal.pcbi.1007808 pmid:32379758 pmcid:PMC7205200 fatcat:gn4fceegkffozewo4wfuezvux4

Ten Simples Rules on How to Organise a Bioinformatics Hackathon

Susanne Hollmann, Babette Regierer, Teresa K. Attwood, Andreas Gisel, Jacques Van Helden, Gregoire Rossier, Paul J. Kersey, Eija Korpelainen, Gert Vriend, Erik Bongcam-Rudloff
2020 Zenodo  
A hackathon is an event in which bioinformatics developers convene to work together to produce new software tools and webservices as solutions to the challenges provided.  ...  The AllBio consortium developed 10 Rules as recommendations how to organise hackathons in the life sciences based on the experience in AllBio to make the information available to the life science communities  ...  gratefully acknowledge SARA for providing computer facilities, and SARA for hosting one hackathon. 327 We thank NBIC's BioAssist programme for helping us find excellent programmers and for allowing 328 them to  ... 
doi:10.5281/zenodo.3695002 fatcat:p7sl2jfpxvgehcwndgm7inas44

Ten Simples Rules on How to Organise a Bioinformatics Hackathon

Susanne Hollmann, Babette Regierer, Teresa K Attwood, Andreas Gisel, Jacques Van Helden, Gregoire Rossier, Paul J Kersey, Eija Korpelainen, Gert Vriend, Erik Bongcam-Rudloff
2021 EMBnet journal  
The completion of the human genome sequence triggered worldwide efforts to unravel the secrets hidden in its deceptively simple code.  ...  Based on this experience, in the following, the authors present a step-by-step and standardised workflow explaining how to organise a bioinformatics hackathon to develop software solutions to biological  ...  We thank NBIC's BioAssist programme for helping us find excellent programmers and allow them to spend adequate time on the projects.  ... 
doi:10.14806/ej.26.0.983 fatcat:w3zxsxellzcyljbhdea5xiwobm

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz (+65 others)
2020 F1000Research  
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote  ...  We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics  ...  We thank Yuji Kohara, the director of DBCLS, for his support of the BioHackathons. Page 24 of 34 F1000Research 2020, 9:136 Last updated: 29 JUN 2020  ... 
doi:10.12688/f1000research.18236.1 pmid:32308977 pmcid:PMC7141167 fatcat:oaglnztjrrhpvgluujl3reudoe

Ten simple rules for making training materials FAIR

Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K. Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C. Dimopoulos, Victoria Dominguez del Angel, Michel Dumontier (+12 others)
2020 PLoS Computational Biology  
The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects  ...  Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.  ...  Special thanks to Luc Wiegers who codesigned the figure summarizing the rules described in this paper.  ... 
doi:10.1371/journal.pcbi.1007854 pmid:32437350 fatcat:6buhtk5w5ratzbwzpzzylnyl2y

D5.1 Interoperability Implementation Regulations

Carol Goble, Chris Evelo, Helen Parkinson, ELIXIR Interoperability Community
2018 Zenodo  
This deliverable originally aimed to present "Interoperability Implementation Regulations" as "a set of standards, rules, controlled vocabularies, authorized unique identifiers and interoperable service  ...  This deliverable does not seek to dictate or prescribe the rules, regulations or vocabularies.  ...  Events are being run to encourage further adoption, e.g. tutorials at ECCB 2018, NETTAB 2018, and SWAT4HCLS 2018, as well as a hackathon topic at the ELIXIR-sponsored Biohackathon 2018 to further enhance  ... 
doi:10.5281/zenodo.1452414 fatcat:j6bod5nlinadhl623uez7x46m4

Perspectives on automated composition of workflows in the life sciences

Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil (+20 others)
2021 F1000Research  
This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences.  ...  Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation  ...  BioHackathon Japan, European Biohackathon 2020). Establish a regular dedicated hackathon on the theme of automated workflow composition.  ... 
doi:10.12688/f1000research.54159.1 pmid:34804501 pmcid:PMC8573700 fatcat:ht57fgnzwbbmdmkazs7wi7r5s4

ELIXIR Annual Report 2020 [article]

ELIXIR
2021
Ten simple rules for making training materials FAIR.  ...  rules for making training materials FAIRAdapted illustration from Luc Wiegers and Celia van Gelder (https://doi.org/10.5281/zenodo.3593257) published in the article 'Ten simple rules for making training  ...  The difference between the value of these contributions valued in Euros at the date of payment and the date of the approval of the 2020 budget was a loss of €36k (2019: loss of €68k).  ... 
doi:10.7490/f1000research.1118580.1 fatcat:saezbeodv5cpxoxfbh55pxjvwa

Graphical Pangenomics

Erik Garrison, Richard Durbin
2018 Zenodo  
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large.  ...  I validate that the variation graph model can be applied to align RNA sequencing data to a splicing graph.  ...  However, such approaches became completely inconceivable as new sequencing technologies allowed the generation of tens and then hundreds of gigabytes of data in a single run.  ... 
doi:10.5281/zenodo.1463032 fatcat:e65awps6hbav5gczb3ubrf65oi

Graphical pangenomics

Erik Garrison, Richard Durbin
2018 Zenodo  
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large.  ...  I validate that the variation graph model can be applied to align RNA sequencing data to a splicing graph.  ...  However, such approaches became too expensive as new sequencing technologies allowed the generation of tens and then hundreds of gigabytes of data in a single run.  ... 
doi:10.5281/zenodo.3269840 fatcat:glracsk2jvgb3lehvepq2jl5l4

Feuille de route IFB 2021-2028: MUDIS4LS [article]

Jacques Van Helden, Julien Seiler, Gildas Le Corguillé, Claudine Médigue, IFB Teams
2021 Zenodo  
The main goal of MuDiS4LS (Mutualized Digital Space for FAIR data in Life and Health Sciences) is to develop a framework that will rely on the national and regional data centers to enable scientists controlling  ...  Our objective is for the 21 member platforms of the IFB to collaborate in the operation of the NNCR, making it possible to extend its scope of action to 9 regions of France.  ...  Ten simple rules for making training materials FAIR. PLoS Comput Biol 16 : e1007854. Ison, J., et al. 2013.  ... 
doi:10.5281/zenodo.5229330 fatcat:speqf7rjcjc5hiaqeemlmvjg7m

Referee report. For: Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved]

Rafael Ferreira Da Silva
2021
This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences.  ...  Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation  ...  Action Examples Community Use hackathons to bring the community together, e.g. propose topics in established building Hackathons (e.g. BioHackathon Japan, European Biohackathon 2020).  ... 
doi:10.5256/f1000research.57615.r96797 fatcat:4d7itrpe65e3zcg5e5wsf7hpo4

Graphical pangenomics

Erik Garrison, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Richard Durbin
2019
To do so I formalize the concept of a variation graph to link genomes to a graphical model of their mutual alignment that is capable of representing any kind of genomic variation, both small and large.  ...  I validate that the variation graph model can be applied to align RNA sequencing data to a splicing graph.  ...  However, such approaches became too expensive as new sequencing technologies allowed the generation of tens and then hundreds of gigabytes of data in a single run.  ... 
doi:10.17863/cam.41621 fatcat:azz437j74jfr5dqsywt3u36tni

Computational methods for the identification and quantification of transcript isoforms from next generation sequencing data

Foivos Gypas, Mihaela Zavolan, Petr Svoboda
2019 unpublished
Expecting that most users would -at least initially -run the methods 'out-of-the-box', we sought to apply the surveyed methods with default settings, and departed from this general rule only to test the  ...  Although IsoEM seems to trade off a relatively large memory footprint (from <10 to >30 GB) for extremely short running times, we did not observe a general inverse correlation between the running time and  ...  I further contributed to writing the manuscript. • Travel grand to attend and lead a project in the Biohackathon in Paris November 2018. • Marie Curie PhD Fellow (project number 607720) from January 2014  ... 
doi:10.5451/unibas-007110711 fatcat:tcsb54ppgbahdfgcf6f62gqs4i

Heterogeneous Data Processing for Information and Knowledge Management in Glycomics and Glycoproteomics

Julien Mariethoz, Frédérique Lisacek
2022
During the multiple projects related to this thesis, I was also privileged to collaborate and learn from many individuals and groups. There are too many people to name them all.  ...  individuals from SIB's internal teams such as NextProt, ViralZone, Cellosaurus, and Uniprot and external organizations or projects including Cermav, MatrixDB, Göteborg University, Beilstein Institute, and BioHackathon  ...  Sriram Neelamegham (State University of New York at Buffalo, Buffalo, USA) for supporting our contribution to the SNFG nomenclature and turning our suggestion into a fruitful discussion in the SNFG group  ... 
doi:10.13097/archive-ouverte/unige:159753 fatcat:uadamnb5yrhgfmcess2ukrh3n4