Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Busby, Ben; Dillman, Allissa; Cl, Simpson; Fingerman, Ian M.; Yun, Sijung; Dm, Kristensen; Federer, Lisa; Shah, Nidhi; LaFave, Matthew C.; Jiménez-Barrón, Laura T.; Pande, Manjusha; Luo, W.; Miller, Bret; Mayden, C; Chandramohan, Dhruva; Fletez-Brant, Kipper; Pw, Bible; Nowoshilow, Sergej; Chan, Ada J.S.; Ej, Galvez; Chignell, Jeremy; Jn, Paulson; Kandpal, Manoj; Yoon, Seungtai; Asaki, Esther; Nellore, Abhinav; Stine, Adam; Sanders, Robert; Becker, Julia Powers; Lesko, Matthew; Abzug, Mordechai; Yaschenko, Eugene

doi:10.1101/018085

Cited by 3 publications

(4 citation statements)

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“…Research staff are less likely to be able to participate in posthackathon commitments after the hackathon is over because of their busier schedules; they are also less likely to generate a career benefit from a product. Conversely, postdocs and students may be able to engage more fully, including in the preparatory and follow-up stages, but will benefit from the presence of more senior faculty that might provide informal mentoring opportunities 2,42,44 . Hence, like others (e.g.…”

Section: Lessons Learnedmentioning

confidence: 99%

“…Since the early 2000s, hackathons have become increasingly popular ( Figure 1) -including across academic, non-profit, corporate, and government sectors -with events focused on a variety of topics, such as bioinformatics 2 , promoting open data 3 , medical education 4 , and healthcare informatics 5 .…”

Section: Introductionmentioning

confidence: 99%

“…Of the small amount of published work available, most consists of reports on specific hackathon events, some of which are short 4 , while others go into depth about the technical products of the event rather than the process 2,[8][9][10][11] . Others are news and opinion pieces [12][13][14][15] .…”

Section: Introductionmentioning

confidence: 99%

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Community and Code: Nine Lessons from Nine NESCent Hackathons

et al. 2017

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In recent years, there has been an explosion in the popularity of hackathonscreative, participant-driven meetings at which software developers gather for an intensive bout of programming, often organized in teams. Hackathons have tangible and intangible outcomes, such as code, excitement, learning, networking, and so on, whose relative merits are unclear. For example, a frequent complaint is that code is abandoned when the hackathon ends, and questions like, "which outcomes are produced most reliably?" and, "how valuable are they for participants, organizers, and sponsors?" remain open. As a first step in giving "hackology" a more rigorous footing, this paper describes the NESCent hackathon model, developed over the course of a decade to serve the academic discipline of evolutionary biology, with the dual goals of augmenting the community's shared software infrastructure, and fostering a diverse community of practice in open scientific software development. The paper presents a detailed guide to staging a NESCent-style hackathon, along with a structured information set on nine events involving 54 team projects. NESCent hackathons have produced tangible products with downstream impacts, including prototypes that were leveraged for major funding, incremental additions to production code bases, and creative drafts (designs, standards, and proofs-of-concept) that contributed to further work. The impacts of intangible outcomes could not be assessed objectively, but the subjective experience suggests that hackathons have a positive impact by (1) providing individuals with valuable experiences, networking, and training, and (2) fostering a more cohesive community of practice by enhancing awareness of challenges and best practices and by building links of familiarity between and among resources and people. Future research that recognizes the diverse outcomes of hackathons might enable evidence-based decisions about how to design hackathons for effectiveness.

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Section: Lessons Learnedmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Community and Code: Nine Lessons from Nine NESCent Hackathons

et al. 2017

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“…The first three events were held at the National Institutes of Health (NIH) in January 2015, August 2015, and January 2016, and attended by over 110 participants from 5 countries. The results of the groups participating in the January 2015 hackathon were collected in a single paper and have been posted to bioRxiv 4 . For subsequent hackathons, groups have reported their findings individually; discussions of their results are available in this channel, as well as in other forthcoming publications.…”

Section: Introductionmentioning

confidence: 99%

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping

Busby

Lesko

August³

et al. 2016

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Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping

2016

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In genomics, bioinformatics and other areas of data science, gaps exist between extant public datasets and the open-source software tools built by the community to analyze similar data types. The purpose of biological data science hackathons is to assemble groups of genomics or bioinformatics professionals and software developers to rapidly prototype software to address these gaps. The only two rules for the NCBI-assisted hackathons run so far are that 1) data either must be housed in public data repositories or be deposited to such repositories shortly after the hackathon’s conclusion, and 2) all software comprising the final pipeline must be open-source or open-use. Proposed topics, as well as suggested tools and approaches, are distributed to participants at the beginning of each hackathon and refined during the event. Software, scripts, and pipelines are developed and published on GitHub, a web service providing publicly available, free-usage tiers for collaborative software development. The code resulting from each hackathon is published at https://github.com/NCBI-Hackathons/ with separate directories or repositories for each team.

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Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Cited by 3 publications

References 38 publications

Community and Code: Nine Lessons from Nine NESCent Hackathons

Community and Code: Nine Lessons from Nine NESCent Hackathons

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping

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