Summer 2021: Difference between revisions

Revision as of 03:03, 2 June 2021

Participants
Questions & Goals:
- Upgrade database, genome pipeline, and website
- Evolution of
Reading list

1. Learn, implement, and compare the existing tools
2. Fine-tuning for OspC, to be integrated with the centroid algorithm

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-==Project 1. HIV compartmentalized evolution==
+==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: [https://retrovirology.biomedcentral.com/articles/10.1186/s12977-014-0065-0 Evering et al (2014)]
-==Project 2. Natural Language models of proteins==
+==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
 * 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]
 ** [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]