Europe PMC REST API docs
Monday build block · Read it inside Monday's build block
Build-block reading · Europe PMC REST API docs — europepmc.org/RestfulWebService (search syntax, OPEN_ACCESS:y, fullTextXML)
In: LABLOOP-W05 Notebook
455 CARDS · 41 WEEKS · EVERY SOURCE THE PLAN NAMES
Everything you could
study, filtered.
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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OpenStax Biology 2e
OpenStax Biology 2e ch. 14 (DNA structure and function) + ch. 15 (genes and proteins), sections 14.1-14.3, 15.1-15.5 (60 min)
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In: LABLOOP-W05 Notebook
Crash Course Biology #11 "DNA, Hot Pockets, & The Longest Word Ever"
Tuesday · after OpenStax Biology 2e
Crash Course Biology #11 "DNA, Hot Pockets, & The Longest Word Ever" (YouTube, 13 min)
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In: LABLOOP-W05 Notebook
Rosalind problems 1-4
Tuesday · after Crash Course Biology #11 "DNA, Hot Pockets, & The Longest Word Ever"
Rosalind problems 1-4 (rosalind.info)
In: LABLOOP-W05 Notebook
Dagdelen et al. (2024), "Structured information extraction from scientific text with large langu…
Saturday sandbox
Dagdelen et al. (2024), "Structured information extraction from scientific text with large language models", Nature Communications 15:1418. The closest methodological cousin of FermLit (materials science). Read it this week; you will cite it
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In: LABLOOP-W05 Notebook
Polak & Morgan
Saturday sandbox · after Dagdelen et al. (2024), "Structured information extraction from scientific text with large langu…
Polak & Morgan (2024), "Extracting accurate materials data from research papers with conversational language models and prompt engineering", Nature Communications 15:1569
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In: LABLOOP-W05 Notebook
Uri Alon (2009), "How to choose a good scientific problem"
Saturday sandbox · after Polak & Morgan
Uri Alon (2009), "How to choose a good scientific problem" (re-read from week 0, now with FermLit in mind)
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In: LABLOOP-W05 Notebook
Coursera Biology Meets Programming: Bioinformatics for Beginners
Saturday sandbox · after Uri Alon (2009), "How to choose a good scientific problem"
Coursera Biology Meets Programming: Bioinformatics for Beginners (UCSD), week 1, if Rosalind hooks you
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In: LABLOOP-W05 Notebook
MIT 7.00x
Saturday sandbox · after Coursera Biology Meets Programming: Bioinformatics for Beginners
MIT 7.00x (edX), molecular biology unit, for Lander's storytelling of the central dogma
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In: LABLOOP-W05 Notebook
StatQuest "Regularization Part 1: Ridge (L2) Regression"
StatQuest "Regularization Part 1: Ridge (L2) Regression" and "Gradient Boost Part 1: Regression Main Ideas" (YouTube, 25 min)
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In: LABLOOP-W05 Notebook
J535D165/pyalex
Query OpenAlex for works on "fed-batch fermentation titer" per year; plot counts. Tells you the size of the ocean before you fish
In: LABLOOP-W05 Notebook
danielnsilva/semanticscholar
Search Semantic Scholar for "literature-derived fermentation dataset"; save the top 20 to RELATED.md with citation counts
In: LABLOOP-W05 Notebook
titipata/pubmed_parser
Parse one PMC OA XML into title, abstract, methods paragraphs; this becomes corpus/parse.py
In: LABLOOP-W05 Notebook
google/langextract
Read the README and run the quickstart example: extraction with source grounding (every value mapped to its exact span). This is the provenance idea FermLit needs, already implemented
In: LABLOOP-W05 Notebook
intro-stat-learning/ISLP_labs
Colab: Ch08-baggboost-lab.ipynb (trees and boosting)
In: LABLOOP-W05 Notebook