Food safety bioinformatics hackathon
Lead Research Organisation:
Quadram Institute
Department Name: Microbes in the Food Chain
Abstract
United Kingdom
| 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 |