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Ten Simple Rules for a Community Computational Challenge

Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac
2015 PLoS Computational Biology  
To help choose an appropriate method for a particular task, scientists often form community-based challenges for the unbiased evaluation of methods in a given field.  ...  These challenges help evaluate existing and novel methods, while helping to coalesce a community and leading to new ideas and collaborations.  ...  Brenner, Michal Linial, Christine Orengo, and Burkhard Rost for their service on the CAFA steering committee.  ... 
doi:10.1371/journal.pcbi.1004150 pmid:25906249 pmcid:PMC4408123 fatcat:vc4dv7cpxfgwhc4uoo3x7m5tp4

Ten simple rules for biologists learning to program

Maureen A. Carey, Jason A. Papin, Scott Markel
2018 PLoS Computational Biology  
Acknowledgments Thank you to Ed Hall, Pat Schloss, Matthew Jenior, Angela Zeigler, Jhansi Leslie, and Gregory Medlock for their feedback.  ...  For specific advice, see "Ten Simple Rules for a Computational Biologist's Laboratory Notebook" [13] , "Ten Simple Rules for Reproducible Computational Research" [14] , and "Ten Simple Rules for Taking  ...  ] , "Ten Simple Rules for Cultivating Open Science and Collaborative R&D" [11] , and "Ten Simple Rules To Combine Teaching and Research" [12] .  ... 
doi:10.1371/journal.pcbi.1005871 pmid:29300745 pmcid:PMC5754048 fatcat:vkxwxsp5xzevdak5s3hdkql4rq

Ten simple rules for doing a postdoc in pharma

Jitao David Zhang
2021 PLoS Computational Biology  
Postdoctoral programs in the pharmaceutical and life science industry offer opportunities for personal and professional development, if you know why to join, what to expect, and how to prepare.  ...  academia [2] , Ten simple rules for selecting a postdoctoral position [3] , and Ten simple rules for landing on the right job after your PhD or postdoc [4] .  ...  Meanwhile, great resources are available to help people make career decisions after PhD, among others pieces from the Ten Simple Rules series, including Ten simple rules for choosing between industry and  ... 
doi:10.1371/journal.pcbi.1008989 pmid:34081699 pmcid:PMC8174744 fatcat:hsimlpewgzdzvlf6ygp64jy5ci

One thousand simple rules

Philip E. Bourne, Fran Lewitter, Scott Markel, Jason A. Papin
2018 PLoS Computational Biology  
The definitive qualitative measure of success came with the "Ten Simple Rules for Writing Ten Simple Rules" [2] .  ...  Anonymous, Academic faculty "Ten Simple Rules for Reproducible Computational Research, and other articles related to computational biology, programming, etc.  ... 
doi:10.1371/journal.pcbi.1006670 pmid:30571692 pmcid:PMC6301566 fatcat:6awkh2wyujhm3ifrh3v5itpumm

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  
Many novel analytic and predictive computer programmes fully optimised for manipulating human genome sequence data have been developed, whereas considerably less effort has been invested in exploring the  ...  A helpful model, often used by the bioinformatics community, is the so-called hackathon. These are events when all stakeholders beyond their disciplines work together creatively to solve a problem.  ...  The hackathon team members gratefully acknowledge SARA for providing computer facilities and hosting one hackathon.  ... 
doi:10.14806/ej.26.0.983 fatcat:w3zxsxellzcyljbhdea5xiwobm

Identifying Transformative Scientific Research

Yi-Hung Huang, Chun-Nan Hsu, Kristina Lerman
2013 2013 IEEE 13th International Conference on Data Mining  
Such a disruption is visible soon after the challenger's introduction. We define a disruption score to quantify the disruption and develop an algorithm to compute it from a large citation network.  ...  This paper presents a datadriven approach where citation patterns of scientific papers are analyzed to quantify how much a potential challenger idea shifts an established paradigm.  ...  Table II lists the ten top-ranked challengers identified by the method proposed in this paper and the baseline. The disruption score of challengers was computed for a ten-year period (τ = 10).  ... 
doi:10.1109/icdm.2013.120 dblp:conf/icdm/HuangHL13 fatcat:hej6t7mbqjervbylxuxzmrfcei

Ten Simple Rules for Developing Usable Software in Computational Biology

Markus List, Peter Ebert, Felipe Albrecht, Scott Markel
2017 PLoS Computational Biology  
Acknowledgments We would like to thank Thomas Lengauer, Nico Pfeifer, and Fabian Müller for their critical reading of the manuscript and insightful comments.  ...  To alleviate this, several related challenges have been previously addressed in the Ten Simple Rules series, including reproducibility [1] , effectiveness [2] , and open-source development of software  ...  To this end, we propose ten simple rules that, in our experience, have a considerable impact on improving usability of scientific software.  ... 
doi:10.1371/journal.pcbi.1005265 pmid:28056032 pmcid:PMC5215831 fatcat:mkrwobit2jfcraap4xrrpxbmt4

Ten Simple Rules for a successful remote postdoc

Kevin R. Burgio, Caitlin McDonough MacKenzie, Stephanie B. Borrelle, S. K. Morgan Ernest, Jacquelyn L. Gill, Kurt E. Ingeman, Amy Teffer, Ethan P. White, Russell Schwartz
2020 PLoS Computational Biology  
Further, our rules can be useful for research labs generally and can help foster a more flexible and inclusive environment.  ...  With planning, communication, and creativity, remote postdocs can be a fully functioning and productive member of a research lab.  ...  Tonietto for their valuable feedback. KRB and CMM conceived of the concept. SBB and KEI made the figures. All authors contributed to the writing and editing of the manuscript.  ... 
doi:10.1371/journal.pcbi.1007809 pmid:32379759 fatcat:p6nbgxbuv5gfldl7mi2demuxvm

Ten Simple Rules for Cultivating Open Science and Collaborative RD

Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne, Fran Lewitter
2013 PLoS Computational Biology  
Acknowledgments We thank Jean Arkedis, Robert Hecht, and Paul Wilson for comments on early versions of this article.  ...  We suggest Ten Simple Rules for Cultivating Open Science and Collaborative R&D. We also offer eight conversational interviews exploring life experiences that led to these rules (Box 1).  ...  What Rule 8: Think Big For projects hoping to harness the power of mass collaboration, a major challenge can be attracting a large community of contributors.  ... 
doi:10.1371/journal.pcbi.1003244 pmid:24086123 pmcid:PMC3784487 fatcat:b6hqqv2h3jfv5d3onk3ln2z3ky

Ten simple rules for short and swift presentations

Christopher J. Lortie
2017 PLoS Computational Biology  
For instance, as a general rule-of-thumb, talks prepared for a more general public audience should emphasize the PLOS Computational Biology | https://doi.  ...  Succinct prose is thus a critical element in communicating science using these presentation formats.  ...  Lortie CJ (2017) Ten simple rules for short and swift presentations.  ... 
doi:10.1371/journal.pcbi.1005373 pmid:28358832 pmcid:PMC5373506 fatcat:pod24v4ddvhhzp6kimboeu6vbm

Ten Simple Rules for a Successful Collaboration

Quentin Vicens, Philip E. Bourne
2007 PLoS Computational Biology  
Acknowledgments We wish to thank Tom Cech for insightful discussions, and Chrysa Latrick, David Zappulla, Barbara Cohen, Emma Veitch, Catherine Nancarrow, and Hemai Parthasarathy for helpful suggestions  ...  The authors received no specific funding for this article. Competing interests. The authors have declared that no competing interests exist.  ...  As you can see, we have obeyed Rule 8. & Citation: Vicens Q, Bourne PE (2007) Ten simple rules for a successful collaboration.  ... 
doi:10.1371/journal.pcbi.0030044 pmid:17397252 pmcid:PMC1847992 fatcat:4suh4cztxjflbpyefl5wuurcua

Ten simple rules for making a vocabulary FAIR

Simon J. D. Cox, Alejandra N. Gonzalez-Beltran, Barbara Magagna, Maria-Cristina Marinescu, Scott Markel
2021 PLoS Computational Biology  
We present ten simple rules that support converting a legacy vocabulary—a list of terms available in a print-based glossary or in a table not accessible using web standards—into a FAIR vocabulary.  ...  The rules are arranged as a stepwise recipe for creating a FAIR vocabulary based on the legacy vocabulary.  ...  Acknowledgments We thank CODATA (https://codata.org) and the DDI Alliance (https://ddialliance.org/), who organised a Workshop on Cross-domain Metadata at Schloss Dagstuhl in October 2019, where this work  ... 
doi:10.1371/journal.pcbi.1009041 pmid:34133421 fatcat:nk543tvzjfggrijsjs7fvbkx3q

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article

Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne, Fran Lewitter
2014 PLoS Computational Biology  
This review article itself was inspired by a journal club meeting devoted to the Ten Simple Rules collection, and the authors would like to thank all the members of the Parkville Bioinformatics Journal  ...  Acknowledgments It's unlikely the advice you are dispensing has arisen in a vacuum. Give credit.  ...  If you are stumped, here are some suggestions: Ten Simple Rules for retiring when you know you should. Ten Simple Rules for winning a Nobel Prize. Ten Simple Rules for managing a scientific rivalry.  ... 
doi:10.1371/journal.pcbi.1003858 pmid:25340653 pmcid:PMC4207461 fatcat:ue3kcad5uzedhdg52f74oyhiye

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing

Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti
2017 PLoS Computational Biology  
Code can also be shared on Github with issue trackers for error detection. Modern life context for the ten simple rules.  ...  We describe these rules and highlight several successful multi-site collaborations. Fig 1 . 1 Fig 1. Modern life context for the ten simple rules.  ... 
doi:10.1371/journal.pcbi.1005278 pmid:28103227 pmcid:PMC5245793 fatcat:vubx7fcbv5fafpo3wxog2lvrdi

Ten Simple Rules for a Bioinformatics Journal Club

Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow, Fran Lewitter
2016 PLoS Computational Biology  
We would also like to thank Mina Stevenson and Alicia Oshlack for their feedback on the manuscript.  ...  The authors would like to thank the Dr Dax Kitchen for their coffee and great service (putting up with us).  ...  Ten Simple Rules collection itself!  ... 
doi:10.1371/journal.pcbi.1004526 pmid:26820645 pmcid:PMC4731213 fatcat:eaqpabppordc7e3bykwwexvtpy
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