Harnessing the power of PHE GitLab
Author(s): ,
Paul Cleary
Affiliations:
Field Epidemiology Service, Public Health England
,
Julian Flowers
Affiliations:
Public Health England Knowledge and Intelligence
,
Sebastian Fox
Affiliations:
Public Health England Knowledge and Intelligence
,
Francesco Giannocaro
Affiliations:
Public Health England HPC & Infrastructure Services, ICT
,
Thomas Inns
Affiliations:
Public Health England Field Epidemiology Service
,
Amy Mikhail
Affiliations:
Public Health England Gastrointestinal, Emerging and Zoonoses Infections
,
Sam Morris
Affiliations:
Public Health England HPC & Infrastructure Services, ICT
,
Sam Organ
Affiliations:
Public Health England Field Epidemiology Service
,
Simon Thelwall
Affiliations:
Public Health England Healthcare Associated Infection and Antimicrobial Resistance
Edwin Tye
Affiliations:
Public Health England Emergency Response Department
PHE ePoster Library. Cleary P. Mar 21, 2018; 205910; 12566
Paul Cleary
Paul Cleary
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Abstract
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Abstract In Public Health England, projects involving epidemiology, statistics, public health data analysis, research, modelling, bioinformatics or software development increasingly require development of code internally, often in collaboration with others. We describe the implementation of a powerful Web-based platform in PHE to facilitate code sharing and the collaborative development and quality assurance of coding projects, and provide examples of its use. The PHE GitLab platform (https://gitlab.phe.gov.uk) allows users to discover and contribute to projects that other users have created. It is available to all users of the PHE network. Using a software tool called Git, the leading tool for managing code, users can track changes to their work and synchronise it with one another. This reduces the duplication of effort that occurs when users would otherwise work independently from one another. GitLab provides a user-friendly Web interface for users to report issues, provide technical documentation for code and plan project development processes. GitLab also facilitates code review, where contributors can give feedback and help detect errors in code. GitLab and Git are open source projects that are free for anyone to use. GitLab has been developed by the open source community since 2011 and has over 100,000 users worldwide. PHE GitLab currently hosts over 450 projects by 273 PHE users working in communicable and non-communicable disease epidemiology, bioinformatics, knowledge and information, digital and other areas, and is maintained by the ICT HPC & Infrastructure team. We provide examples of the current use of PHE GitLab in outbreak investigation, surveillance, standardising reporting, whole genome sequencing, development of teaching materials, research paper writing, software development and development of data analysis tools. Funding N/A
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