New scheme available on PubMLST. 👇

A new database has been set up for Lactococcus garvieae to support the MLST scheme described in pubmed.ncbi.nlm.nih.gov/24391975/. The database is curated by Guilherme Campos, Universidade Federal de Minas Gerais, Brazil. pubmlst.org/organisms/lact…

BIGSdb v1.41.2 has been released. This introduces a choice of 26 colour palettes for use on front-end and query dashboards that can be selected by users. BIGSdb powers all the databases on PubMLST. github.com/kjolley/BIGSdb.

pubmlst.org/organisms/bact… 👇

Presenting one of my DPhil projects at Maiden Lab group: Development and Validation of Haemophilus influenzae core genome MLST scheme at Microbiology Society Annual Conference today as a Society Conference Grants recipient. P.S. The scheme has been implemented at PubMLST too 😉

Come and see the latest visual analytic developments on the PubMLST website at the #ABPHM23 bioinformatics showcase. youtu.be/mC22A4WYmhA

Had an amazing session at EduCon 2023 which was all about diversity and inclusivity in teaching. Had the honour to deliver a bioinformatics worship for beginners for implementation in undergraduate courses. #educon2023 #ASM2023

Short-term opportunity to work with me and amazing people in our Gastro Bioinfo Team at UK Health Security Agency. Come join us for sequencing bacterial pathogens and diving into the world of gastro illness investigation. tinyurl.com/BioinfoGastro

PubMLST now incorporates serotype identification using results from hicap (Stephen Watts & @DrKatHolt) in H. influenzae genome records. Example at pubmlst.org/bigsdb?page=in…. Overseen by Made Krisna.

I’d like to think PubMLST as a hub for data AND bioinformatic tools integration. This is one of the many examples. For my thesis, I found hicap very useful for Hinf serotype identification, and asked Keith’s help to do his magic so other users can easily access the tool ✨

BIGSdb v1.42.5 has been released. This introduces a new plugin that provides a wrapper for ReporTree (pubmed.ncbi.nlm.nih.gov/37322495/) – a tool for the automated identification of genetic clusters. BIGSdb powers all the databases on PubMLST. github.com/kjolley/BIGSdb.

We have had to implement rate-limiting on the PubMLST API. We have always requested that API calls are limited to no more than 4 concurrent connections. This is now enforced due to abuse and additional connections will automatically be rejected. pubmlst.org/api

Come and do a PhD with me and Tim. It'll be fun, I promise! Tim Overton ChemEng Bham IMIBirmingham

BIGSdb v.1.42.6 has been released. This version expands list query functionality to every table in the database – previously it was only possible to use lists to search by attribute values for isolates, profiles and alleles for single loci.

Yesterdays viva celebrations after completing my PhD with no corrections! #PhDone

My first PhD paper is out - exploring mosaicism in the 𝑁𝑒𝑖𝑠𝑠𝑒𝑟𝑖𝑎 𝑝𝑒𝑛𝐴 gene at the population level! Very excited to share this work. Thanks are in order to Odile Harrison and Martin Maiden Maiden Lab for their excellent supervision. microbiologyresearch.org/content/journa…

Please note that PubMLST will be unavailable from Thursday 21 - Monday 25 March due to essential data centre maintenance. Normal service should resume on Tuesday 26 March.

1st year PhD student Priyanshu Singh Raikwar with Sam Sheppard attended The 2nd IOI Oxbridge Cohort conference at Selwyn College, Cambridge Cambridge University Priyanshu Singh Raikwar talked about exploring Ribosomal protein as a plausible drug target. Ineos Oxford Institute for Antimicrobial Research University of Oxford Oxford Biology

Our 2018 paper describing PubMLST, the BIGSdb platform, and their applications has just reached 2000 citations on Google Scholar. ncbi.nlm.nih.gov/pmc/articles/P…

BIGSdb v1.47.0 has been released and is now live on PubMLST. This introduces an embargo system for isolate submissions. If enabled, submitters will now see an option to request an embargo when they submit isolates.