GPAS Philip Fowler, 17th May 202113th October 2021 I’ve been working on this for the last few months and very happy that we can now share our plans. Through a very generous donation by ORACLE, a group of researchers led by ModMedMicro at Oxford, are developing a cloud-based clinical microbiology genetics processing service, called the Global Pathogen Analysis System (GPAS). GPAS is still in development and and uses the Scalable Pathogen Processing Pipeline to run a range of bioinformatic workflows on the ORACLE Cloud. For SARS-CoV-2, the idea is you’ll be able to upload SARS-CoV-2 genetic reads* to the ORACLE cloud which will then produce a consensus genome and associated relevant information, for example what lineage does this sample belong to and what mutations are there in the Spike protein? A key principle is that the data is owned by the submitter and therefore submitters will be able to request that their consensus sequence is automatically deposited in a public archive or that their genetic reads are deleted from the cloud following processing. Looking forward to sharing more on this soon. after personal identifiable information has been removed, as is standard. To begin with we will focussing on the ARTIC protocols and Illumina and ONT sequencing. Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance clinical microbiology computing distributed computing grants
antimicrobial resistance Updated preprint: predicting pyrazinamide resistance 21st November 20238th December 2023 This study was performed by Josh Carter back in 2019 and we uploaded a preprint… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
distributed computing Read Ellen’s Azure post 26th January 201814th March 2018 As I’ve described here, here and here, I ran a Hackathon instead of the more… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance Research position advertised 26th January 202126th January 2021 Come and work with me on antimicrobial resistance! Advert here. Broadly the idea is to… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More