Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret) header
Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret) profile picture

Cyril Matthey-Doret @[email protected]

@cmdoret

Data Science Engineer @SDSCdatascience | Genomics, Reproducibility, Open data | Previously @institutpasteur and @UNIL

 Lausanne, Switzerland
github.com/cmdoret
Joined May 2011
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Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)Photo by Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)
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Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler. With @lh3lh3. myloasm-docs.github.io/
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Hello to all #bioinformatics #rustlang, I often copy code to generate data when writing tests. After 3 or 4 times, I got fed up and created biotest crates. biotest can generate fasta, fastq and vcf, I'm open to any suggestion, feedback or contribution. github.com/natir/biotest
Image from Pierre Marijon 🏳️‍🌈 (@pierre_marijon)
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RECRUITING two PhD candidates: on butterfly colour & behaviour, and on flower colour & scent; Please RT
Image from Casper van der Kooi (@CaspervdKooi)
Image from Casper van der Kooi (@CaspervdKooi)
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Cyril Matthey-Doret @[email protected] retweeted
Vim Club (@ClubVim) profile picture
Vim Club@ClubVim5 Aug 2023
RIP Bram Moolenaar en.wikipedia.org/wiki/Bram_M…
Bram Moolenaar - Wikipedia

Bram Moolenaar - Wikipedia

en.wikipedia.org
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Here's our pre-print describing our GPT-3 based knowledge extraction tool SPIRES: arxiv.org/abs/2304.02711. Great work from @harry_caufield et al! SPIRES allows you to specify a knowledge schema (in @linkml_data) and then populate instances of that schema from unstructured text
depiction of SPIRES approach: input is a schema and text, the OntoGPT engine will run SPIRES by recursively querying GPT-3 for prompt completions, the end result is grounded using public databases and ontologies

ALT depiction of SPIRES approach: input is a schema and text, the OntoGPT engine will run SPIRES by recursively querying GPT-3 for prompt completions, the end result is grounded using public databases and ontologies

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Cyril Matthey-Doret @[email protected] retweeted
Ben Franta (@BenFranta) profile picture
Ben Franta@BenFranta2 Apr 2023
Compiled by @VatanHuzeir, the latest cache of internal documents describing Big Oil's concealed knowledge of global warming is a gold mine. One bombshell is a confidential @Shell scenario report from 1989 which imagined two futures: SUSTAINABLE WORLD and GLOBAL MERCANTILISM 🧵
Image from Ben Franta (@BenFranta)
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Cyril Matthey-Doret @[email protected] retweeted
Yann LeCun (@ylecun) profile picture
Yann LeCun
@ylecun24 Feb 2023
LLaMA is a new *open-source*, high-performance large language model from Meta AI - FAIR. Meta is committed to open research and releases all the models the research community under a GPL v3 license. - Paper: research.facebook.com/public… - Github: github.com/facebookresearch/…

LLaMA: Open and Efficient Foundation Language Models - Meta Research

We introduce LLaMA, a collection of foundation language models ranging from 7B to 65B parameters. We train our models on trillions of tokens, and show that it is possible to...

research.facebook.com
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The collapse of insects reuters.com/graphics/GLOBAL-…
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Starting off SWAT4HCLS 2023 with a keynote from @CrameriKatrin about the Swiss Personalized Health Network @SPHN_ch @ISBSIB #personalizedhealth #SWAT4HCLS #SWAT4LS – at Basel, Switzerland
Image from Deepak Unni (@deepakunni3)
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I'm finally ready to introduce #anywidget - a new #Python library that makes creating and sharing custom @ProjectJupyter Widgets easy. No fiddling with messy build configs, packaging, or bundlers. Just start coding! anywidget.dev/blog/introduci…
Introducing anywidget

Introducing anywidget

reusable interactive widgets made easy

anywidget.dev
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Building a knowledge graph for biomedical tasks usually takes months or years. 😰 What if you could do it in weeks or days? 🏃 We created BioCypher (biocypher.org) to make it easier than ever, but still flexible and transparent. 🧵⬇️
Image from Saez-Rodriguez Group (@saezlab)
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It's time we adopted more recent algorithms for FASTQ compression bioinformaticszen.com/post/u…
We're wasting money by only supporting gzip for raw DNA files.

We're wasting money by only supporting gzip for raw DNA files.

Stylised graphics of money with DNA helix in the foreground.

bioinformaticszen.com
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Replying to @scrumtuous @microlinux_eu
I think people use Github mainly because it has more users. Both are good IMO, but on a related note sfconservancy.org/GiveUpGitH…
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Replying to @ThacienN @driscollis
Indeed, this is the definition of multiprocessing.cpu_count() 😁
Image from Cyril Matthey-Doret @cmdoret@fosstodon.org (@cmdoret)
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Published online @genomeresearch yesterday: Our two high quality reference genome sequences for Acanthamoeba castellanii Neff and C3, and an exploration of genome folding changes in response to Legionella infection genome.cshlp.org/content/ear…
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Cyril Matthey-Doret @[email protected] retweeted
RenkuIO (@RenkuIO) profile picture
RenkuIO@RenkuIO26 Jul 2022
Do you work with Renku datasets ? 🐸💾 Then you may want to use dataset "tags" to export and share stable versions of your data! Learn how to use dataset tags for data versioning on Renku 🏷️ renku.discourse.group/t/data…
Dataset versioning on Renku

Dataset versioning on Renku

Do you use Renku to share datasets ? Then you may be interested in dataset tags! Tags allow you to label a specific dataset version and make it accessible to yourself or others in the future. This...

renku.discourse.group
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Replying to @yokofakun @marianattestad
Softwarecarpentry has a nice Make tutorial :) swcarpentry.github.io/make-n…
Replying to @cabbagesofdoom
I've enjoyed duckdb so far duckdb.org/
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Plastic pollution endangers wild and human life more every day. Can we clean this up? What to do with the waste once collected? With the Ellington,@at_lynd, and Zhang labs, we’ve developed an enzyme that can break down PET plastic: FAST PETase. nature.com/articles/s41586-0… @EnergyUT
Machine learning-aided engineering of hydrolases for PET depolymerization

Machine learning-aided engineering of hydrolases for PET depolymerization

Nature - Untreated, postconsumer-PET from 51 different thermoformed products can all be almost completely degraded by FAST-PETase in 1 week and PET can be resynthesized from the recovered...

nature.com
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Cyril Matthey-Doret @[email protected] retweeted
RenkuIO (@RenkuIO) profile picture
RenkuIO@RenkuIO29 Apr 2022
Are you looking to enhance your digital classroom experience? Then we share your passion for technology and its role in teaching. Check out this post to learn how to automate your digital classroom with Renku and Gitlab bit.ly/3koTsKU
Classroom automation with Renku + Gitlab

Classroom automation with Renku + Gitlab

Are you looking to enhance your digital classroom experience? Then we share your passion for technology and its role in teaching. However, we know that managing digital classrooms requires extra...

renku.discourse.group
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