PyBEL

Python software for the Biological Expression Language, integrating biomedical knowledge, and systems biology

[PyBEL @pybelbio]

Home: https://t.co/15qiQnn3Xk
GitHub: https://t.co/yYUB05hETb
Docs: https://t.co/Q7VhXQQfHX
Paper: https://t.co/CaTJhKjWhx

[Gyori Lab for Computational Biomedicine @gyorilab]

We're happy to announce that Gilda has been published in @BioinfoAdv - read it at
https://t.co/rsi32xxaSg and try it at https://t.co/bwtqBouv1b

Next, we’ll use it for ontology alignment in @OBOFoundry and to make plugins in programs like Google Docs for dataset annotation 🚀

[Gyori Lab for Computational Biomedicine @gyorilab]

Our @benjamingyori is presenting today on automated hypothesis generation and human-machine collaboration at the 1st Workshop on Nobel Turing Challenge: https://t.co/B9TxemiOqa

[PyKEEN @keenuniverse]

🚨 We're happy to share one of our submissions to @GLB_Workshop outlining new, more comparable link prediction metrics than MR, MRR, and Hits@K including the zMR, zMRR, and zHits@K

Thanks to authors @cthoyt @BerrendorfMax @michael_galkin @vtresp @benjamingyori

[Yannik Schälte @yannik_schaelte]

Happy to release #pyABC 0.12! 👶 https://t.co/VYXugH6Blb
🧵Featuring a bunch of new features:

[Gyori Lab for Computational Biomedicine @gyorilab]

🚨 Our @Bioregistry project imports and standardizes prefixes/metadata for biomedical nomenclatures from 15 external registries (e.g. @OBOFoundry @IdentifiersOrg @bioportal) and allows for community 👪 extension using an open data model at https://t.co/rTk7RwtMo8.

[Kevin M Jablonka @kmjablonka]

Our speaker's list for our @cecamEvents workshop (/w @JoshuaSchrier @BenBlaiszik @petermurrayrust @helsoeste @cthoyt) is now finalized! Consider registering if you're interested in making chemical data machine-actionable! @EPFLOpenScience #chemtwitter

[PyKEEN @keenuniverse]

We’re so excited to see @BerrendorfMax pass his defense magna cum laude!

We already updated our team page 💪

[Gyori Lab for Computational Biomedicine @gyorilab]

Our @benjamingyori gave the first @cosi_sysmod webinar for @iscb Academy describing our team's work.

📽️ Full recording: https://t.co/Q0kaZNYica

🔗 More about what we do: https://t.co/9GaO8FtU1g

[PyKEEN @keenuniverse]

🚨 PyKEEN 1.7.0 is out! 🚨

New: 7 models, 3 encoders, 2 trackers, keras-style training callbacks, uncertainty estimation, and more

📖 Full Release Notes: https://t.co/oaYAAix2bL

💪 Huge S/O to external contributors @dobraczka @michael_galkin @SBonner0 @Ralph_Abb and others

[Int Soc Biocuration @biocurator]

ISB2022 Biocuration Conference first session 🎉
🗓️ 29 March 2022
➡️ Panel: Promotion and dissemination of biocuration efforts
➡️ Invited Speakers Talks
Submit your abstracts: https://t.co/i2IIFV2E6S
More info: https://t.co/hoTUy9ZUGW

[SysMod @cosi_sysmod]

📣The first SysMod Webinar is coming up. Dr. Gyori (@benjamingyori from @HavardUnivers) will talk about “Accelerating biomedical discovery with large-scale knowledge assembly and human-machine collaboration” – join us on January 18, 2022, at 11:00 AM EST: https://t.co/8JsRX4wFRZ

[PyBEL @pybelbio]

Welcome BioPAX to the Python scientific ecosystem :))

[Gyori Lab for Computational Biomedicine @gyorilab]

We've been developing PyBioPAX, a native Python object model for BioPAX Level 3 with parsing, serializing, and traversal of BioPAX models.

🚀 Install: pip install pybiopax

🖥️ Code: https://t.co/oDcUirobc9

📖 Docs: https://t.co/YAZ0jcZYl1

[Gyori Lab for Computational Biomedicine @gyorilab]

We’re still actively maintaining FamPlex, a resource for text mining and reasoning over human protein families/complexes. Here's some links to learn more and a thread on a few improvements we made recently:

🖥️Code/data: https://t.co/vTZHYr8NB1

📜Paper: https://t.co/3NaecZtIuL

[PyKEEN @keenuniverse]

PyKEEN 1.6.0 is out, now with batteries from PyTorch 1.9 built in!

🎁 It’s got new models, new datasets, new loss functions, bug fixes, and improvements.

🙏 Huge s/o to our many external contributors for this release

📖 Release notes: https://t.co/3LQ3DRZuO0

[Benjamin Gyori @benjamingyori]

Cool use of @indrasysbio to integrate text-mining systems and assemble models of cardiomyopathy mechanisms from literature. I'm proud that INDRA is increasingly picked up and applied (and in this case also carefully evaluated) by independent groups! @glavaski_mila @LazarVelicki

[PyBEL @pybelbio]

@egonwillighagen (Http)

[PyBEL @pybelbio]

@egonwillighagen Seems okay from DE

[PyKEEN @keenuniverse]

PyKEEN 1.3 is out, with new datasets, new trackers, faster and more elegant code, improved support for big datasets, and a better interface for running predictions on your trained models.

Full changelog at https://t.co/O6yD1QmItL

P.S. Happy Rosenmontag! Kölle alaaf 🤡

[PyBEL @pybelbio]

Useful for biologists making the transition to AI/ML - this is written for newcomers

[PyKEEN @keenuniverse]

Are you new to knowledge graph embedding models? Are you confused about loss functions?

We wrote a nice introduction for you: https://t.co/9sNqA4sdIu

[PyKEEN @keenuniverse]

Today, we added @earthling91’s Common Sense Knowledge Graph (CSKG) as a benchmark dataset.

Train your KGE model with:

>>> from pykeen.pipeline import pipeline
>>> results = pipeline(dataset=‘cskg’, model=‘RotatE’)

See how we did it: https://t.co/2uYLZkdMDd