Summer 2021: Difference between revisions
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* Participants | * Participants | ||
* Questions & Goals | * Questions & Goals | ||
# Learn, implement, and compare the existing tools | |||
# Fine-tuning for OspC, to be integrated with the centroid algorithm | |||
* Reading list | * Reading list | ||
** Strodthoff et al (2020). Bioinformatics. [https://academic.oup.com/bioinformatics/article/36/8/2401/5698270 UDSMProt: universal deep sequence models for protein classification]. [https://github.com/nstrodt/UDSMProt Source code on Github] | ** Strodthoff et al (2020). Bioinformatics. [https://academic.oup.com/bioinformatics/article/36/8/2401/5698270 UDSMProt: universal deep sequence models for protein classification]. [https://github.com/nstrodt/UDSMProt Source code on Github] | ||
** [https://www.pnas.org/content/118/15/e2016239118 Rives et al (2021). PNAS. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.] [https://github.com/facebookresearch/esm Github repository] | ** [https://www.pnas.org/content/118/15/e2016239118 Rives et al (2021). PNAS. Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.] [https://github.com/facebookresearch/esm Github repository] | ||
Revision as of 03:03, 2 June 2021
Project 1. Borrelia genomics
- Participants
- Questions & Goals:
- Upgrade database, genome pipeline, and website
- Evolution of
- Reading list
Project 2. HIV compartmentalized evolution
- Participants
- Reading list
- HIV compartmentalized evolution: Evering et al (2014)
Project 3. Natural Language models of proteins
- Participants
- Questions & Goals
- Learn, implement, and compare the existing tools
- Fine-tuning for OspC, to be integrated with the centroid algorithm