Barbara Oakley · "Learning how to learn"
Sunday, before writing post 0 · Sunday, before writing post 0
Produce: One line in notes/craft/W00.md: which ritual in Part 0.3 is your diffuse-mode slot
In: LABLOOP-W00 Notebook
455 CARDS · 41 WEEKS · EVERY SOURCE THE PLAN NAMES
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.
103 cards shown. Stashes: LABLOOP-W00 Notebook (15) LABLOOP-W01 Notebook (18) LABLOOP-W02 Notebook (15) LABLOOP-W03 Notebook (19) LABLOOP-W04 Notebook (17) LABLOOP-W05 Notebook (16) LABLOOP-W06 Notebook (12) LABLOOP-W07 Notebook (12) LABLOOP-W08 Notebook (15) LABLOOP-W09 Notebook (10) LABLOOP-W10 Notebook (11) LABLOOP-W11 Notebook (12) LABLOOP-W12 Notebook (12) LABLOOP-W13 Notebook (13) LABLOOP-W14 Notebook (12) LABLOOP-W15 Notebook (10) LABLOOP-W16 Notebook (14) LABLOOP-W17 Notebook (13) LABLOOP-W18 Notebook (10) LABLOOP-W19 Notebook (10) LABLOOP-W20 Notebook (10) LABLOOP-W21 Notebook (13) LABLOOP-W22 Notebook (10) LABLOOP-W23 Notebook (9) LABLOOP-W24 Notebook (9) LABLOOP-W25 Notebook (12) LABLOOP-W26 Notebook (11) LABLOOP-W27 Notebook (10) LABLOOP-W28 Notebook (6) LABLOOP-W29 Notebook (7) LABLOOP-W30 Notebook (10) LABLOOP-W31 Notebook (8) LABLOOP-W32 Notebook (5) LABLOOP-W33 Notebook (13) LABLOOP-W34 Notebook (12) LABLOOP-W35 Notebook (10) LABLOOP-W36 Notebook (8) LABLOOP-W37 Notebook (7) LABLOOP-W38 Notebook (6) LABLOOP-W39 Notebook (6) LABLOOP-W40 Notebook (6)
Sunday, before writing post 0 · Sunday, before writing post 0
Produce: One line in notes/craft/W00.md: which ritual in Part 0.3 is your diffuse-mode slot
In: LABLOOP-W00 Notebook
Sunday, before writing post 0 · after Barbara Oakley · "Learning how to learn" · Only if you prefer voice to text — it replaces R1, it does not add to it. Play at 1.25× while packing the cockpit
Produce: Same output as R1
In: LABLOOP-W00 Notebook
Any block this week · Optional substitute for V1 if you want the full treatment
Produce: Nothing. Do not enrol in the whole course
In: LABLOOP-W00 Notebook
Monday build block · Monday, before coding
Produce: A hand-sketched growth curve taped next to the screen
In: LABLOOP-W01 Notebook
Thursday · M1 · Thursday, first
Produce: notes/ml/M1.md: what a matrix does to a vector; one example redone in NumPy
In: LABLOOP-W01 Notebook
Saturday sandbox · after OpenStax Biology 2e, ch. 3 "Biological Macromolecules"
Khan Academy, Energy and enzymes → Activation energy (article) — One article + the practice set. Moved out of core on 2026-09-29
In: LABLOOP-W01 Notebook
Saturday sandbox · after Khan Academy, Energy and enzymes → Activation energy
Crash Course Biology #3 · "Biological Molecules — You Are What You Eat" — youtube.com/watch?v=H8WJ2KENlK0. Moved out of core on 2026-09-29
In: LABLOOP-W01 Notebook
Saturday sandbox · after Crash Course Biology #3 · "Biological Molecules — You Are What You Eat"
Khan Academy (MCAT) · "Enzymes and activation energy" — khanacademy.org/…/v/enzymes-and-activation-energy. Moved out of core on 2026-09-29
In: LABLOOP-W01 Notebook
Saturday sandbox · after Khan Academy (MCAT) · "Enzymes and activation energy"
LearnChemE · "Washout Derivation in CSTR Bioreactor (Bio)" — watch?v=L_bzv0bbU4M. The engineer's version of what happens when the feed stops — which is exactly Friday's injected fault
In: LABLOOP-W01 Notebook
Saturday sandbox · after LearnChemE · "Washout Derivation in CSTR Bioreactor (Bio)"
MIT OCW 18.06 Linear Algebra (Gilbert Strang), lectures 1-3 — ocw.mit.edu/courses/18-06-linear-algebra-spring-2010. Only if 3Blue1Brown leaves you wanting proofs
In: LABLOOP-W01 Notebook
Saturday sandbox · after MIT OCW 18.06 Linear Algebra
NPTEL Bioreactors (Suraishkumar, IIT Madras), lecture 1 — nptel.ac.in/courses/102106053. A preview of week 09. (verify) course numbering
In: LABLOOP-W01 Notebook
Tuesday · B2 · Tuesday, first
Produce: Three lines in notes/bio/B2.md: why DO falls when biomass grows
In: LABLOOP-W02 Notebook
Thursday · M2 · Thursday
Produce: notes/ml/M2.md: what a derivative is, in your own words
In: LABLOOP-W02 Notebook
Thursday · M2 · after 3Blue1Brown · Essence of Calculus · Before Friday's PCA code
Produce: The 3-line explanation of scores vs loadings you will paste into Sunday's post
In: LABLOOP-W02 Notebook
Saturday sandbox · after OpenStax Biology 2e, ch. 7 "Cellular Respiration"
3Blue1Brown · Neural Networks, ch. 1-2 — Topic page: 3blue1brown.com/topics/neural-networks. Moved out of core on 2026-09-29
In: LABLOOP-W02 Notebook
Saturday sandbox · after 3Blue1Brown · Neural Networks
Steve Brunton (@Eigensteve) · SVD series, first 3 videos — playlist PLMrJAkhIeNNSVjnsviglFoY2nXildDCcv, overview video watch?v=gXbThCXjZFM. PCA's engine explained by an engineer; you will want this again in weeks 12-17
In: LABLOOP-W02 Notebook
Saturday sandbox · after Deisenroth, Faisal & Ong, Mathematics for Machine Learning, ch. 10 "Dimensionality Reduction wit…
Ninja Nerd · glycolysis and Krebs cycle lectures (long, whiteboard) — channel search by title, only if respiration is still abstract. (verify) no fixed video ID recorded
In: LABLOOP-W02 Notebook
Thursday · M3 · Thursday, first
Produce: One sentence in notes/ml/M3.md: what last Friday's principal components actually are
Thursday · M3 · after 3Blue1Brown · "Eigenvectors and eigenvalues" · Thursday, after V4
Produce: The bias-variance sentence in notes/ml/M3.md
In: LABLOOP-W03 Notebook
Thursday · M3 · after StatQuest · "Machine Learning Fundamentals: Bias and Variance" · Thursday, after V2
Produce: One regression fitted on two IndPenSim variables and read aloud: slope, intercept, what it means
In: LABLOOP-W03 Notebook
Saturday sandbox
ISLP ch. 2 and 3.1-3.3 — statlearning.com (free PDF) + the matching Stanford Statistical Learning with Python videos. Moved out of core on 2026-09-29
In: LABLOOP-W03 Notebook
Saturday sandbox · after Kourti & MacGregor (1995), "Process analysis, monitoring and diagnosis, using multivariate proje…
Crash Course Statistics (YouTube), episodes on the normal distribution and control charts' ancestor, the z-score
In: LABLOOP-W03 Notebook
Saturday sandbox · after James, Witten, Hastie, Tibshirani & Taylor, An Introduction to Statistical Learning with Applica…
Stanford Online · Statistical Learning with Python (Hastie, Tibshirani et al.) — Playlist: youtube.com/playlist?list=PLoROMvodv4rPP6braWoRt5UCXYZ71GZIQ · course page: online.stanford.edu/courses/sohs-ystatslearningp-statistical-learning-python. Moved out of core on 2026-09-29
In: LABLOOP-W03 Notebook
Tuesday · B4 · Tuesday, first
Produce: One paragraph in notes/bio/B4.md: "what is a fermentation, really"
In: LABLOOP-W04 Notebook
Thursday · M4 · Thursday, first
Produce: The sentence "why random k-fold is wrong for batch data" in notes/ml/M4.md
In: LABLOOP-W04 Notebook
Saturday sandbox · after Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", PLOS Comp. Biol. 9…
StatQuest · "Bootstrapping Main Ideas!!!" — Channel: youtube.com/@statquest — search the exact title. (verify): no stable video ID confirmed on 2026-09-15. Moved out of core on 2026-09-29
In: LABLOOP-W04 Notebook
Tuesday · after OpenStax Biology 2e
Crash Course Biology #11 "DNA, Hot Pockets, & The Longest Word Ever" (YouTube, 13 min)
In: LABLOOP-W05 Notebook
StatQuest "Regularization Part 1: Ridge (L2) Regression" and "Gradient Boost Part 1: Regression Main Ideas" (YouTube, 25 min)
In: LABLOOP-W05 Notebook
Statistical Rethinking 2024, lectures 1-2 (YouTube, from github.com/rmcelreath/stat_rethinking_2024) or Murphy, Probabilistic Machine Learning: An Introduction, ch. 2 — probml.github.io/pml-book/book1.html (75 min). Pick Rethinking if you want stories; Murphy if you want equations
In: LABLOOP-W06 Notebook
Saturday sandbox · after McHugh (2012), "Interrater reliability: the kappa statistic"
3Blue1Brown "Bayes theorem, the geometry of changing beliefs" (YouTube, 15 min)
In: LABLOOP-W06 Notebook
MIT OCW 7.016 lectures on protein structure and enzymes (ocw.mit.edu/courses/7-016-introductory-biology-fall-2018), ~50 min
In: LABLOOP-W07 Notebook
Tuesday · after MIT OCW 7.016 lectures on protein structure and enzymes
Khan Academy "Steady states and the Michaelis Menten equation" (MCAT section) (15 min)
In: LABLOOP-W07 Notebook
Statistical Rethinking 2024 lectures 3-4 (YouTube, 75 min)
In: LABLOOP-W07 Notebook
Saturday sandbox · after DSPy (Stanford NLP) documentation "Optimizers"
Karpathy, "Deep Dive into LLMs like ChatGPT" (YouTube, 3.5 h; watch the first hour on hallucination and tool use)
In: LABLOOP-W07 Notebook
Saturday sandbox · after Karpathy, "Deep Dive into LLMs like ChatGPT"
Ninja Nerd "Enzyme kinetics" lecture (YouTube) for Michaelis-Menten in depth
In: LABLOOP-W07 Notebook
Karpathy, "The spelled-out intro to neural networks and backpropagation: building micrograd" (YouTube, 2 h 25 min; watch the first 75 min Thursday, the rest Saturday while rewriting from memory)
In: LABLOOP-W08 Notebook
Saturday sandbox · after Kadlec, Gabrys & Strandt (2009), "Data-driven soft sensors in the process industry"
3Blue1Brown Neural Networks ch. 3-4 ("Backpropagation, intuitively" and "Backpropagation calculus")
In: LABLOOP-W08 Notebook
Saturday sandbox · after Stanford CS231n notes "Backpropagation, intuitions"
Simon Peyton Jones, "How to write a great research paper" (YouTube) — watch now, not in week 18, because the report is a mini-paper
In: LABLOOP-W08 Notebook
NPTEL Bioreactors (Suraishkumar, IIT Madras), lectures 1-3 — nptel.ac.in/courses/102106053 (also on YouTube; ~75 min at 1.25x). Notebook: batch, fed-batch and continuous balances
In: LABLOOP-W09 Notebook
Karpathy, "The spelled-out intro to language modeling: building makemore" (YouTube, ~2 h; first 75 min Thursday)
In: LABLOOP-W09 Notebook
Saturday sandbox
MIT OCW 10.37 Chemical and Biological Reaction Engineering (Spring 2007), lecture notes on bioreactors — ocw.mit.edu/courses/10-37-chemical-and-biological-reaction-engineering-spring-2007
In: LABLOOP-W09 Notebook
Saturday sandbox · after Coursera Industrial Biotechnology
LearnChemE "mass balance" screencasts (YouTube)
In: LABLOOP-W09 Notebook
Saturday sandbox · after LearnChemE "mass balance" screencasts
Karpathy "Intro to Large Language Models" (YouTube, 1 h) for a bird's-eye view
In: LABLOOP-W09 Notebook
NPTEL Bioreactors lectures 4-6 (Monod, yields, maintenance) (75 min)
In: LABLOOP-W10 Notebook
Saturday sandbox
ritvikmath "Gaussian Processes" (YouTube, whiteboard intuition)
In: LABLOOP-W10 Notebook
Saturday sandbox · after ritvikmath "Gaussian Processes"
In: LABLOOP-W10 Notebook
NPTEL Bioreactors lectures on oxygen transfer (kLa), mixing and scale-up (75 min)
In: LABLOOP-W11 Notebook
Saturday sandbox · after NCBI Taxonomy and E-utilities documentation
Brunton "Bayesian optimization" lecture (search in his channel; verify)
In: LABLOOP-W11 Notebook
Brunton & Kutz, Data-Driven Science and Engineering (2nd ed.), ch. 7 on SINDy — databookuw.com (free PDF) (40 min) + Steve Brunton "Sparse Identification of Nonlinear Dynamics (SINDy)" (YouTube, 30 min)
In: LABLOOP-W12 Notebook
Saturday sandbox · after arXiv endorsement page
Steve Brunton "Physics Informed Machine Learning" series (YouTube), first 2 videos
In: LABLOOP-W12 Notebook
Saturday sandbox
Steve Brunton "Neural ODEs" (YouTube)
In: LABLOOP-W13 Notebook
Saturday sandbox · after Karniadakis et al. (2021), "Physics-informed machine learning"
Stanford CS197 (cs197.stanford.edu), lecture on "vertical paper structure" (verify lecture title)
In: LABLOOP-W13 Notebook
Tuesday · after Modern Statistics for Modern Biology ch. 6 "Testing"
StatQuest "False Discovery Rates, FDR, clearly explained" and "p-hacking: What it is and how to avoid it!" (YouTube, 20 min)
In: LABLOOP-W14 Notebook
Stanford CS336 lecture on evaluation (cs336.stanford.edu, videos on Stanford Online YouTube) (60 min); your week 7 notes on Zheng et al. 2023 judge biases (15 min)
In: LABLOOP-W14 Notebook
S. Keshav (2007), "How to Read a Paper", ACM SIGCOMM Computer Communication Review 37(3):83-84 (2 pages, 15 min); then three FermLit papers with P11 and IMRaD noted (60 min)
In: LABLOOP-W15 Notebook
Saturday sandbox · after ASAPbio preprint FAQ
StatQuest "Statistical Power, Clearly Explained" — reviewers may ask whether 50 gold papers is enough
In: LABLOOP-W15 Notebook
Tuesday · after Lin et al. (2023), "Evolutionary-scale prediction of atomic-level protein structure with a langu…
MIT 6.874 Deep Learning in the Life Sciences (Manolis Kellis, 2021, YouTube playlist), protein lecture (first 40 min)
In: LABLOOP-W16 Notebook
Saturday sandbox · after Rives et al. (2021), "Biological structure and function emerge from scaling unsupervised learnin…
DeepMind, "AlphaFold: The making of a scientific breakthrough" (YouTube, 8 min) — the emotional context of protein AI
In: LABLOOP-W16 Notebook
Saturday sandbox · after DeepMind, "AlphaFold: The making of a scientific breakthrough"
Nobel Prize in Chemistry 2024 lectures (Baker, Hassabis, Jumper) — nobelprize.org
In: LABLOOP-W16 Notebook
Saturday sandbox · after Nobel Prize in Chemistry 2024 lectures
Anastasios Angelopoulos' conformal prediction tutorial videos (YouTube; verify)
In: LABLOOP-W16 Notebook
Saturday sandbox · after Anastasios Angelopoulos' conformal prediction tutorial videos
Valence Labs (YouTube), search "ESM" or "protein language models" in the M2D2 reading group
In: LABLOOP-W16 Notebook
Hugging Face model card facebook/esm2_t33_650M_UR50D (10 min) + MIT 6.874 protein lecture second half (40 min); code block with ridge head
In: LABLOOP-W17 Notebook
Saturday sandbox
Yang, Wu & Arnold (2019), "Machine-learning-guided directed evolution for protein engineering", Nature Methods 16:687-694. The classic review; read it before week 21
In: LABLOOP-W17 Notebook
Saturday sandbox · after Yang, Wu & Arnold (2019), "Machine-learning-guided directed evolution for protein engineering"
Frances Arnold, Nobel Lecture 2018 "Innovation by Evolution: Bringing New Chemistry to Life" (nobelprize.org)
In: LABLOOP-W17 Notebook
StatQuest "Ridge vs Lasso Regression, Visualized!!!" (YouTube) for the head you fit
In: LABLOOP-W17 Notebook
Two founder or scientific-lead papers from extremophile-focused GridX companies (Puna Bio, Antarka, APEXzymes authors), found via Europe PMC / Google Scholar, digested with P11 (75 min). Background first: Crash Course Biology "Old & Odd: Archaea, Bacteria & Protists" (#35, YouTube, 12 min)
In: LABLOOP-W18 Notebook
Simon Peyton Jones, "How to write a great research paper" (YouTube, Microsoft Research, ~1 h) + NeurIPS Paper Checklist (neurips.cc, current year's author guidelines) (30 min)
In: LABLOOP-W18 Notebook
Saturday sandbox · after Rothschild & Mancinelli (2001), "Life in extreme environments"
Stanford CS197, lecture on "writing the paper" (verify title)
In: LABLOOP-W18 Notebook
Saturday sandbox · after Single-cell best practices
MIT 6.874 single-cell lecture (Kellis, YouTube)
In: LABLOOP-W19 Notebook
StatQuest "PCA main ideas", "t-SNE, Clearly Explained" and "UMAP Dimension Reduction, Main Ideas!!!" (YouTube, 30 min) — the three plots every single-cell talk shows
In: LABLOOP-W19 Notebook
Saturday sandbox · after Richard Hamming, You and Your Research
Stanford CS197 lecture on research talks and posters (verify title)
In: LABLOOP-W20 Notebook
Patrick Winston, "How to Speak" (MIT OCW / YouTube, ~1 h) — watch Saturday; it prepares both the mock sessions and the talk proposal
In: LABLOOP-W20 Notebook
Saturday sandbox · after Yang, Wu & Arnold
Valence Labs (YouTube) reading-group talks on protein language models
In: LABLOOP-W21 Notebook
Saturday sandbox · after Valence Labs
Frances Arnold on iBiology (directed evolution talks; verify)
In: LABLOOP-W21 Notebook
iBiology, "Uri Alon: How to Choose a Good Scientific Problem" (verify; talk version)
In: LABLOOP-W21 Notebook
Brady Neal, Introduction to Causal Inference, lecture 1 (YouTube) and book ch. 1 (free PDF on the course site) (75 min)
In: LABLOOP-W22 Notebook
Saturday sandbox
Cunningham, Causal Inference: The Mixtape — mixtape.scunning.com, ch. 3 (directed acyclic graphs)
In: LABLOOP-W22 Notebook
Saturday sandbox · after Huntington-Klein, The Effect
Coursera A Crash Course in Causality (Penn), week 1
In: LABLOOP-W22 Notebook
StatQuest "Spearman's Rank Correlation" if needed (search; verify) and "Bootstrapping Main Ideas" (carry over)
In: LABLOOP-W22 Notebook
Saturday sandbox
UniProt REST API documentation (rest.uniprot.org) and the BRENDA enzyme database (brenda-enzymes.org) for reported temperature optima
In: LABLOOP-W23 Notebook
Saturday sandbox · after UniProt REST API documentation
iBiology talks on extremophiles and enzymes (search; verify)
In: LABLOOP-W23 Notebook
Saturday sandbox · after iBiology talks on extremophiles and enzymes
Crash Course Biology #35 "Old & Odd" (carry over)
In: LABLOOP-W23 Notebook
Khan Academy / Crash Course refresh on protein folding and denaturation ("why heat unfolds proteins") (15 min)
In: LABLOOP-W23 Notebook
Saturday sandbox · after Bambi documentation
StatQuest on ANOVA and "Design matrices" (search in channel)
In: LABLOOP-W25 Notebook
Saturday sandbox · after Sprouffske & Wagner
Midani, Collins & Britton (2021), "AMiGA: software for automated analysis of microbial growth assays", mSystems 6:e00508-21 — an open-source Python tool that fits growth curves without assuming their shape (pip install amiga)
In: LABLOOP-W26 Notebook
Saturday sandbox · after NCATS Assay Guidance Manual
In: LABLOOP-W26 Notebook
Saturday sandbox
David Maister, Charles Green & Robert Galford, The Trusted Advisor (book, paid) — the trust equation
In: LABLOOP-W27 Notebook
Saturday sandbox · after Alan Weiss, Value-Based Fees
Stanford eCorner (ecorner.stanford.edu) — search talks on "customer discovery" and "B2B sales for technical founders"
In: LABLOOP-W27 Notebook
Y Combinator Startup School, "How to Talk to Users" (Eric Migicovsky, YouTube, ~20 min)
In: LABLOOP-W27 Notebook
Saturday sandbox
Getting to Yes (Fisher, Ury & Patton; book, paid) — principled negotiation, if price is contested
In: LABLOOP-W28 Notebook
Saturday sandbox · after Getting to Yes
Stanford eCorner talks on first customers (search)
In: LABLOOP-W28 Notebook
Coursera Process Mining: Data Science in Action (Eindhoven), week 1 lecture on event logs (30 min) — cycle time from timestamps is process mining in miniature
In: LABLOOP-W29 Notebook
Tuesday · after Cumming (2014) "The new statistics"
StatQuest "Statistical Power" (carry over)
In: LABLOOP-W30 Notebook
Saturday sandbox · after Target journal author guidelines chosen with the partner
Stanford CS197 lecture on co-authoring and feedback (verify)
In: LABLOOP-W31 Notebook
Lewis et al. (2020), "Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks", NeurIPS, abstract + figure 1 (15 min)
In: LABLOOP-W34 Notebook
Tuesday · after Lewis et al. (2020), "Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks"
Es et al. (2023), "RAGAS: Automated Evaluation of Retrieval Augmented Generation", arXiv:2309.15217 (30 min)
In: LABLOOP-W34 Notebook
Tuesday · after Es et al. (2023), "RAGAS: Automated Evaluation of Retrieval Augmented Generation"
Stanford CS224N lecture on retrieval/RAG (web.stanford.edu/class/cs224n; verify current lecture list) (30 min)
In: LABLOOP-W34 Notebook
Saturday sandbox · after Chip Huyen, Designing Machine Learning Systems
The Trusted Advisor (carry over) for running a pilot relationship
In: LABLOOP-W37 Notebook
Saturday sandbox
Nancy Duarte, "The secret structure of great talks" (TEDx, YouTube)
In: LABLOOP-W38 Notebook
Patrick Winston, "How to Speak" (MIT OCW / YouTube, ~1 h; re-watch the first 30 min)
In: LABLOOP-W38 Notebook
Simon Peyton Jones, "How to give a great research talk" (Microsoft Research, YouTube)
In: LABLOOP-W38 Notebook
Saturday sandbox
Uri Alon's talk and essay on "the cloud" in research (iBiology; verify)
In: LABLOOP-W40 Notebook
Bill Burnett & Dave Evans, Designing Your Life (book, paid) — chapters on "odyssey plans" and "choosing well"; or Bill Burnett's TEDx talk "Designing Your Life" (YouTube, free) (30 min)
In: LABLOOP-W40 Notebook