Jarzab et al. 2020
Jarzab et al. 2020 (Meltome), methods and results
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455 CARDS · 41 WEEKS · EVERY SOURCE THE PLAN NAMES
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Every video, chapter, paper and repository in the programme, as one card each, with the time it costs and why it is there. Filter by how long you have.
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Dallago et al. 2021
Tuesday · after Jarzab et al. 2020
Dallago et al. 2021 (FLIP), thermostability task section (75 min)
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Pudžiuvelytė et al.
Saturday sandbox
Pudžiuvelytė et al. (2024), "TemStaPro: protein thermostability prediction using sequence representations from protein language models", Bioinformatics 40(4):btae157 — the closest published tool to what you are building
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Yang, Wu & Arnold
Saturday sandbox · after Pudžiuvelytė et al.
Yang, Wu & Arnold (2019) review (carry over)
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Valence Labs
Saturday sandbox · after Yang, Wu & Arnold
Valence Labs (YouTube) reading-group talks on protein language models
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Frances Arnold on iBiology
Saturday sandbox · after Valence Labs
Frances Arnold on iBiology (directed evolution talks; verify)
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Uri Alon (2009), "How to choose a good scientific problem"
Uri Alon (2009), "How to choose a good scientific problem" (third reading; this time fill his feasibility/interest chart for Paper 3) (15 min)
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iBiology, "Uri Alon: How to Choose a Good Scientific Problem"
iBiology, "Uri Alon: How to Choose a Good Scientific Problem" (verify; talk version)
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ievapudz/TemStaPro
Run it on 50 Meltome sequences; compare its predictions with your ridge head. This is your most relevant external baseline
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J-SNACKKB/FLIP
Use their exact splits so your numbers are comparable with the paper
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huggingface/transformers
EsmModel with torch_dtype=torch.float16; batch by sequence length to fit 6 GB
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agemagician/ProtTrans
Read the README; note ProtT5 as an alternative embedding for the ablation you might run in week 22
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biopython/biopython
Bio.SeqIO to read and length-filter FASTA; drop sequences > 1,022 residues or chunk them
In: LABLOOP-W21 Notebook