Data Science Engineer @SDSCdatascience | Genomics, Reproducibility, Open data | Previously @institutpasteur and @UNIL
Lausanne, Switzerland
Joined May 2011
- Tweets191
- Following264
- Followers135
- Likes502
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler. With @lh3lh3.
myloasm-docs.github.io/
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
RECRUITING two PhD candidates: on butterfly colour & behaviour, and on flower colour & scent; Please RT
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
RIP Bram Moolenaar
en.wikipedia.org/wiki/Bram_M…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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
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
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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 🧵
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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/…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
The collapse of insects
reuters.com/graphics/GLOBAL-…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
Starting off SWAT4HCLS 2023 with a keynote from @CrameriKatrin about the Swiss Personalized Health Network @SPHN_ch @ISBSIB #personalizedhealth #SWAT4HCLS #SWAT4LS – at Basel, Switzerland
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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. 🧵⬇️
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
It's time we adopted more recent algorithms for FASTQ compression
bioinformaticszen.com/post/u…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
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
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
Ppl are on twitter for many reasons. I'm here to chew bubblegum & teach scientific inference. And I'm all out of gum. Engage yourself with 20+ hours of free lectures on causal inference and Bayesian data analysis. This isn't an ordinary statistics course. github.com/rmcelreath/stat_r…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
Rob Waterhouse @rmwaterhouse and @KarenMeusemann recommended the book “#Phylogenetics in the Genomic Era” edited by Céline Scornavacca, Frédéric Delsuc @freddelsuc and @GaltierNicolas. See their assessment at @PeerCommunityIn #genomics genomics.peercommunityin.org…
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
Analyses should be published as fully executable workflows with reproducible containers
Cyril Matthey-Doret @cmdoret@fosstodon.org retweeted
Using Jupyter notebooks for collaborative projects?
With Jupytext, turn your notebooks into plain text files and enjoy:
* 📖 Clear diffs in git commits
* 🪶 Lightweight notebooks
* 👥 Efficient collaboration
Find out more: bit.ly/3uVf0nc
