Food safety bioinformatics hackathon

Lead Research Organisation: Quadram Institute
Department Name: Microbes in the Food Chain

Abstract

United Kingdom

Publications

10 25 50
 
Description This hackathon brought together food safety specialists from 12 countries around the world, leading to new collaborations and networks.
Exploitation Route Many of the attendees have gone on to be founding members of the Public Health Alliance for Genomic Epidemiology (funded by Gates) to bring about global standardisation of our field.
Sectors Agriculture

Food and Drink

Education

Healthcare

Pharmaceuticals and Medical Biotechnology

 
Description Public health alliance for genomic epidemiology (PHA4GE) - Founding member of Data Structures working group
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
URL https://pha4ge.github.io/
 
Title A set of curated AMR protocols for the community 
Description A website was developed by an international team at the Food Safety Bioinformatics Hackathon, aggregating multiple different competing anti-biotic resistance protocols and tools. This data was then presented in an easy to use website, allowing researchers to gain straightforward information about how anti-biotic resistance was called in different papers, and the tools involved. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Too early to have any impact 
URL https://food-safety-bioinformatics-hackathon.github.io/AMR-protocols/
 
Title Phage finding command line tool 
Description This is a commandline tool for detecting Phage. Most preexisting tools are on-line only (low throughput), are difficult to use, or provide inconsistent results. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact Too early yet 
URL https://github.com/tseemann/phastaf
 
Description Hackathon at Quadram Institute 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A 3 day hackathon was held at the Quadram Institute Bioscience with participants from Australia, Canada, Netherlands, Portugal, France, Scotland, Qatar, Germany and Scotland.
Year(s) Of Engagement Activity 2019
URL https://quadram.ac.uk/hackathon0619/
 
Description Virtual lab talk webcast with presenters from UKRI and BfD 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a webcast from the hackathon with 2 presenters: Dr Simon Tausch from the German Federal Institute for Risk Assessment (BfD) and Dr Will Rowe from the UKRI. It was streamed live on Zoom.us and a recording was uploaded to YouTube. There were questions from the international audience.
Year(s) Of Engagement Activity 2019
URL https://youtu.be/VFdZgliceRM
 
Description Webcast roundtable with international researchers 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was a roundtable with multiple different international researchers (about 25 in total), streamed on YouTube. It was presented by Dr Emma Griffiths from the British Columbia Centers for Disease Control in Canada during the Food Safety Bioinformatics Hackathon. The intention was to give other researchers (not at the hackathon) an idea of how the events work, what people are working on and insights into how diverse sets of scientists worked together.
Year(s) Of Engagement Activity 2019
URL https://youtu.be/gD13CnIy9cU