PubMLST

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.

1st year PhD student @emPriyanshu with Sam Sheppard attended The 2nd IOI Oxbridge Cohort conference at Selwyn College, Cambridge @Cambridge_Uni @emPriyanshu talked about exploring Ribosomal protein as a plausible drug target. @IneosOxford @UniofOxford @OxfordBiology

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…

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.

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 @OdileHarrison and Martin Maiden @MaidenLab for their excellent supervision. microbiologyresearch.org/content/journa…

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

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.

Come and do a PhD with me and Tim. It'll be fun, I promise! @Overtonlab @ChemEngBham @IMIBirmingham

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

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.

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 ✨

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.

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

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

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

@AntiMicroBio Sorry, yes it is. The university departmental network we're hosted on (not NCBI) went down on Saturday. No IT response due to it being a public holiday here in the UK. Hope to be up and running again tomorrow.

Is #pubmlst down ? I can't access it for some reason. Other ncbi sites are working well. @PubMLST

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

pubmlst.org/organisms/bact… 👇

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.

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…