@SimonBray18

Research software engineer / computational chemist at Gain Therapeutics.

 UK
orcid.org/0000-0002-0621-6705
Joined July 2018
  • Tweets74
  • Following204
  • Followers88
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New paper: Accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy #usegalaxy academic.oup.com/gigascience…

An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

AbstractBackground. Artificial intelligence (AI) programs that train on large datasets require powerful compute infrastructure consisting of several CPU co

academic.oup.com
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It took almost 4 years since the defence, but finally my master's thesis has appeared in article form. :) Thanks Steffen for providing a great project and supervision, and to Victor for extending the work to the trypsin-benzamidine system!
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Job alert: Galaxy EU @UniFreiburg has open positions for DevOps Engineers. uni-freiburg.de/universitaet… #DevOps #Germany #freiburg #Bioinformatics #usegalaxy #galaxyproject #opensource
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My master's thesis in preprint form - we present some methods for identifying and classifying pathways in ensembles of non-equilibrium ligand unbinding simulations. Thanks @Herr_Flow and @MolDynFR for providing the cool project and supervision! 😀
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Hey #bioconda users: if you experience cases where apparently a wrong dependency is selected by conda or mamba (maybe because of insufficient constraints on the version of the dependency), please file an issue here github.com/bioconda/bioconda… and add the label "update-pinnings"

Issues · bioconda/bioconda-recipes

Conda recipes for the bioconda channel. Contribute to bioconda/bioconda-recipes development by creating an account on GitHub.

github.com
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Our latest paper demonstrating how @galaxyproject can be used as a workflow management system for docking and free energy calculations is out! Thanks to Tim, @rachaelskyner and @FrankvonDelft for the collaboration 😀
Journal of Cheminformatics@jcheminf13 Apr 2022
Another article for our Special Collection on Data Analysis is published: "Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease" jcheminf.biomedcentral.com/a…
Fig. 1: Schematic of the docking and scoring workflow

ALT Fig. 1: Schematic of the docking and scoring workflow

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Another nice piece of work coming from the Mpro data @XChem_DLS @covid_moonshot through a collaboration with @galaxyproject @bjoerngruening @FrankvonDelft jcheminf.biomedcentral.com/a…

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease

Journal of Cheminformatics - We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of...

link.springer.com
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Simon Bray retweeted
Jaime R.@jaime_rgp12 Apr 2022
Honored to share some of the key figures that show the raw scale that @condaforge deals with daily. Look at those numbers! Oh, and happy birthday! 🎂
✨Tania Allard 💀🇲🇽 🇬🇧@ixek12 Apr 2022
Replying to @ixek
Some supporting data on the status of conda-forge. Not only it has standardised the build environment and workflows but led to the emergence of a bigger, healthier community
Slideck with a number of community, technical and usage stats from conda forge

ALT Slideck with a number of community, technical and usage stats from conda forge

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Simon Bray retweeted
Jaime R.@jaime_rgp16 Mar 2022
Heyyyyy! It's finally out! Share it, try it out and give us feedback! ❤️
conda@condaproject16 Mar 2022
Replying to @condaproject
The #conda 4.12.0 release includes support for a new (and very fast) dependency solver based on @quantstack's libmamba. Learn how to enable the libmamba solver here: github.com/conda/conda/relea…

Release 4.12.0 · conda/conda

Enhancements Add support for libmamba integrations. (#11193) This is a new experimental and opt-in feature that allows use of the new conda-libmamba-solver for an improved user experience, based ...

github.com
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On the #European #usegalaxy server you will find more than 2700 tools that everyone can use. All of them are unit-tested and have been developed with this Galaxy #SDK - planemo! Thanks to @jmchilton @SimonBray18 and all others!
bioRxiv@biorxivpreprint15 Mar 2022
Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses biorxiv.org/cgi/content/shor… #bioRxiv
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for designing, testing and executing #usealaxy tools, workflows and training material
bioRxiv@biorxivpreprint15 Mar 2022
Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses biorxiv.org/cgi/content/shor… #bioRxiv
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#AlphaFold2 now available in @galaxyproject @GalaxyAustralia @AusBiocommons #Protein3D biocommons.org.au/news/alpha…

AlphaFold now available in Galaxy — Australian BioCommons

Galaxy Australia provides Australian researchers access to a rich catalogue of computational resources - now including the GPU clusters required to power AlphaFold. Seizing the opportunity to further...

biocommons.org.au
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Replying to @JCIM_JCTC @JianyuLi8
ePharmaLib target prediction of bioactive compounds can now be performed within the Galaxy platform, from a web browser without requiring any programming experience. usegalaxy-eu.github.io/posts… #UseGalaxy @SimonBray18 @JianyuLi8
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Is today black-Thursday? Really? Awesome! Thanks to @SirYoplait @mariusvdbeek and @NicolaSoranzo the #usegalaxy codebase is not #Python black formatted. github.com/galaxyproject/gal… If you need help to rebase your branch, please ping us!

Python code formatting standard, automatic. by dannon · Pull Request #11162 · galaxyproject/galaxy

Automatic formatting via black and import sorting with isort of the galaxy codebase. To run the full thing locally, make sure you have python dev dependencies installed and then just run make form...

github.com
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We have an open #DevOps position in the European #usegalaxy team. Do you enjoy challenges like distributed global compute, millions of jobs by thousands of users every month, and working with other Galaxy admins worldwide? Drop me a DM :) @UniFreiburg #jobs #hiring
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Want to help conda-forge but don't know where to start? Check our status page and look for the packages that errored out: conda-forge.org/status/#vers… Most of the time the fix it is just a simple PR away :-)
Webpage screenshot showing conda-forge's status page. Link is in the tweet.

ALT Webpage screenshot showing conda-forge's status page. Link is in the tweet.

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A short thread on scripting and automating computational workflows in @galaxyproject courtesy of this fantastic @gxytraining tutorial 🧵 1/6 training.galaxyproject.org/t…
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@condaforge will now use #mamba by default when building packages. Expect all your builds to be 3-4 minutes faster! Huge props to @wuoulf and @QuantStack for making this possible!
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We're delighted to share our new work on CRISPR-Cas. CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems academic.oup.com/nar/advance…

CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems

Abstract. CRISPR–Cas systems are adaptive immune systems in prokaryotes, providing resistance against invading viruses and plasmids. The identification of

academic.oup.com
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This was a really nice project from Erik, have a look at some of the code he wrote here: github.com/galaxyproject/bio…
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