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.
96 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)
Saturday sandbox · after Good enough practices in scientific computing, Wilson et al., PLoS Computational Biology 2017. T…
Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", PLOS Comp. Biol. 9(10):e1003285, 2013 — DOI 10.1371/journal.pcbi.1003285. This is week 04's reading; reading it early is allowed, re-reading it in week 04 is still required
In: LABLOOP-W00 Notebook
Saturday sandbox · after Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", PLOS Comp. Biol. 9…
Elliot Hershberg, Century of Biology newsletter — one essay, for where biotech is heading. (verify) search the title; no fixed URL recorded
In: LABLOOP-W00 Notebook
Saturday sandbox
SciPy documentation for scipy.integrate.solve_ivp (the solver you will use); read the "Examples" section
In: LABLOOP-W01 Notebook
Saturday sandbox · after SciPy documentation for scipy.integrate.solve_ivp (the solver you will use); read the "Examples"
Pioreactor project docs (pioreactor.com) — see a real, open-source mini bioreactor with optical density and temperature sensors; it makes "online variables" tangible
In: LABLOOP-W01 Notebook
Saturday sandbox · after Pioreactor project docs (pioreactor.com) — see a real, open-source mini bioreactor with optical…
OpenStax Biology 2e, ch. 3 "Biological Macromolecules" — 3-introduction, start at 3.1 Synthesis of Biological Macromolecules — 3.1 and the protein section; skim carbohydrates and lipids; finish on Chapter Summary. Moved out of core on 2026-09-29
In: LABLOOP-W01 Notebook
Saturday sandbox
OpenStax Biology 2e, ch. 7 "Cellular Respiration" — 7-introduction — Glycolysis → citric acid cycle → oxidative phosphorylation, then 7.5 Metabolism without Oxygen. Moved out of core on 2026-09-29
In: LABLOOP-W02 Notebook
Saturday sandbox · after Ninja Nerd · glycolysis and Krebs cycle lectures
industrialpenicillinsimulation.com — the original IndPenSim site. (verify): it was unreachable in the 2026-09-12 check; prefer the UCL/Mendeley routes in R4 and record whichever one actually served the data, with its licence
In: LABLOOP-W02 Notebook
Saturday sandbox · after ISLP
Nomikos & MacGregor (1995), "Multivariate SPC charts for monitoring batch processes", Technometrics 37(1):41-59 — the founding paper of batch MSPC. Read abstract + figures
In: LABLOOP-W03 Notebook
Saturday sandbox · after Nomikos & MacGregor (1995), "Multivariate SPC charts for monitoring batch processes"
Kourti & MacGregor (1995), "Process analysis, monitoring and diagnosis, using multivariate projection methods", Chemometrics and Intelligent Laboratory Systems 28:3-21 (verify)
In: LABLOOP-W03 Notebook
Saturday sandbox · after Crash Course Statistics
James, Witten, Hastie, Tibshirani & Taylor, An Introduction to Statistical Learning with Applications in Python — free PDF at statlearning.com — Ch. 2 (whole) and 3.1-3.3 only. Moved out of core on 2026-09-29
In: LABLOOP-W03 Notebook
Saturday sandbox · after Nomikos P. & MacGregor J.F., "Multivariate SPC Charts for Monitoring Batch Processes", Technomet…
Kourti T. & MacGregor J.F., "Process analysis, monitoring and diagnosis, using multivariate projection methods", Chemometrics and Intelligent Laboratory Systems 28:3-21, 1995. (verify)
In: LABLOOP-W03 Notebook
Saturday sandbox · after salvadorgarciamunoz/pyphi
Coursera Introduction to Statistics (Stanford, Walther), regression module — coursera.org/learn/stanford-statistics, free audit. Only if ISLP ch. 3 feels steep
In: LABLOOP-W03 Notebook
Saturday sandbox
In: LABLOOP-W04 Notebook
Saturday sandbox · after The Turing Way, chapter on "Version control" and "Research compendia"
OpenStax Microbiology, ch. 8 "Microbial Metabolism", sections 8.1-8.4 — start at 8.1 Energy, Matter, and Enzymes, chapter entry 8-introduction, recap 8-summary — 8.1 through 8.4; pay attention to aerobic vs anaerobic. Moved out of core on 2026-09-29
In: LABLOOP-W04 Notebook
Saturday sandbox · after OpenStax Microbiology, ch. 8 "Microbial Metabolism"
ISLP ch. 5 "Resampling Methods" — free PDF at statlearning.com — 5.1 cross-validation and 5.2 bootstrap; then the ch. 5 lab. Moved out of core on 2026-09-29
In: LABLOOP-W04 Notebook
Saturday sandbox · after ISLP ch. 5 "Resampling Methods"
Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", PLOS Comp. Biol. 9(10):e1003285, 2013. DOI 10.1371/journal.pcbi.1003285 — All ten rules, they are one page each. Moved out of core on 2026-09-29
In: LABLOOP-W04 Notebook
Saturday sandbox · after StatQuest · "Bootstrapping Main Ideas!!!"
The Turing Way — book.the-turing-way.org, chapters on "Version control" and "Research compendia". The grown-up version of what you shipped this week
In: LABLOOP-W04 Notebook
Saturday sandbox · after Zenodo help
JOSS submission guidance — you submit in week 36, not now. Read it once so that today's release history is already the kind reviewers want
In: LABLOOP-W04 Notebook
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
In: LABLOOP-W05 Notebook
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
In: LABLOOP-W05 Notebook
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)
In: LABLOOP-W05 Notebook
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
In: LABLOOP-W05 Notebook
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
In: LABLOOP-W05 Notebook
Saturday sandbox
Artstein & Poesio (2008), "Inter-coder agreement for computational linguistics", Computational Linguistics 34(4):555-596, sections 1-2. The bible of annotation agreement
In: LABLOOP-W06 Notebook
Saturday sandbox · after Artstein & Poesio (2008), "Inter-coder agreement for computational linguistics"
McHugh (2012), "Interrater reliability: the kappa statistic", Biochemia Medica 22(3):276-282. Short, open, written for biomedical readers
In: LABLOOP-W06 Notebook
Saturday sandbox · after Anthropic Claude Cookbooks (github.com/anthropics/claude-cookbooks) — "extracting structured JSON"
DSPy (Stanford NLP) documentation "Optimizers" — how to tune prompts against a metric instead of by feel
In: LABLOOP-W07 Notebook
Saturday sandbox
Kadlec, Gabrys & Strandt (2009), "Data-driven soft sensors in the process industry", Computers & Chemical Engineering 33(4):795-814
In: LABLOOP-W08 Notebook
Saturday sandbox · after Simon Peyton Jones, "How to write a great research paper"
Quarto guide for scientific manuscripts (quarto.org/docs/manuscripts)
In: LABLOOP-W08 Notebook
Saturday sandbox · after MIT OCW 10.37 Chemical and Biological Reaction Engineering
Coursera Industrial Biotechnology (University of Manchester), module on fermentation processes
In: LABLOOP-W09 Notebook
Saturday sandbox · after StatQuest "Confidence Intervals, Clearly Explained" and "The Standard Error"
Krippendorff's alpha (Wikipedia page is good) for when you have more than two annotators or missing ratings
In: LABLOOP-W10 Notebook
Saturday sandbox · after Krippendorff's alpha
Modern Statistics for Modern Biology (Holmes & Huber) ch. 3 "High quality graphics in R" — read for the design principles, ignore the R
In: LABLOOP-W10 Notebook
Saturday sandbox
Shields et al. (2021), "Bayesian reaction optimization as a tool for chemical synthesis", Nature 590:89-96 — BO beating expert chemists, the self-driving-lab argument
In: LABLOOP-W11 Notebook
Saturday sandbox · after Shields et al. (2021), "Bayesian reaction optimization as a tool for chemical synthesis"
Coursera Research Data Management and Sharing (UNC/Edinburgh), module on metadata
In: LABLOOP-W11 Notebook
Saturday sandbox · after Coursera Research Data Management and Sharing
NCBI Taxonomy and E-utilities documentation (ncbi.nlm.nih.gov/books/NBK25501) for the name-to-ID mapping
In: LABLOOP-W11 Notebook
Saturday sandbox
Narayanan et al. (2020), "Bioprocessing in the digital age: the role of process models", Biotechnology Journal 15(1):e1900172
In: LABLOOP-W12 Notebook
Saturday sandbox · after Narayanan et al. (2020), "Bioprocessing in the digital age: the role of process models"
Sansana et al. (2021), "Recent trends on hybrid modeling for Industry 4.0", Computers & Chemical Engineering 151:107365
In: LABLOOP-W12 Notebook
Saturday sandbox · after Sansana et al. (2021), "Recent trends on hybrid modeling for Industry 4.0"
arXiv endorsement page — info.arxiv.org/help/endorsement.html (read once, carefully)
In: LABLOOP-W12 Notebook
Saturday sandbox · after Steve Brunton "Neural ODEs"
Coursera Writing in the Sciences (Stanford, Kristin Sainani), module 1 "Principles of effective writing" — preview for week 14
In: LABLOOP-W13 Notebook
Saturday sandbox · after Coursera Writing in the Sciences (Stanford, Kristin Sainani), module 1 "Principles of effective…
Karniadakis et al. (2021), "Physics-informed machine learning", Nature Reviews Physics 3:422-440 (figures 1-2)
In: LABLOOP-W13 Notebook
Saturday sandbox
Gopen & Swan (1990), "The Science of Scientific Writing", American Scientist 78:550-558. The best 9 pages ever written on why readers get lost
In: LABLOOP-W14 Notebook
Saturday sandbox · after Gopen & Swan (1990), "The Science of Scientific Writing"
Whitesides (2004), "Whitesides' Group: Writing a Paper", Advanced Materials 16(15):1375-1377. Outline-first writing from a legendary chemist
In: LABLOOP-W14 Notebook
Saturday sandbox · after Whitesides (2004), "Whitesides' Group: Writing a Paper"
Benjamini & Hochberg (1995), "Controlling the false discovery rate", JRSS B 57(1):289-300 (abstract + procedure)
In: LABLOOP-W14 Notebook
Saturday sandbox · after Benjamini & Hochberg (1995), "Controlling the false discovery rate"
Scientific Data "Data Descriptor" article guidelines (nature.com/sdata) — preview of the week 36 venue
In: LABLOOP-W14 Notebook
Saturday sandbox
Coursera Writing in the Sciences, module on "The format of a scientific manuscript" and "Peer review"
In: LABLOOP-W15 Notebook
Saturday sandbox · after Coursera Writing in the Sciences, module on "The format of a scientific manuscript" and "Peer re…
Bourne (2005), "Ten simple rules for getting published", PLoS Computational Biology 1(5):e57
In: LABLOOP-W15 Notebook
Saturday sandbox · after Bourne (2005), "Ten simple rules for getting published"
ASAPbio preprint FAQ (asapbio.org) — what preprints mean for credit and journals
In: LABLOOP-W15 Notebook
Saturday sandbox
Rives et al. (2021), "Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences", PNAS 118(15) — the ESM-1b paper, for the "why it works" story
In: LABLOOP-W16 Notebook
Saturday sandbox · after Frances Arnold, Nobel Lecture 2018 "Innovation by Evolution: Bringing New Chemistry to Life"
Notin et al. (2023), "ProteinGym: large-scale benchmarks for protein fitness prediction and design", NeurIPS Datasets and Benchmarks
In: LABLOOP-W17 Notebook
Saturday sandbox
In: LABLOOP-W18 Notebook
Saturday sandbox · after Coursera Writing in the Sciences (Stanford), module "Writing the results and discussion"
Kapoor & Narayanan (2023) leakage paper (carry over) — use its checklist on Paper 2's Methods
In: LABLOOP-W18 Notebook
Saturday sandbox · after Kapoor & Narayanan
Rothschild & Mancinelli (2001), "Life in extreme environments", Nature 409:1092-1101 — the classic review of extremophiles
In: LABLOOP-W18 Notebook
Saturday sandbox
Single-cell best practices (Heumos et al., theislab) — sc-best-practices.org, introduction and quality-control chapters
In: LABLOOP-W19 Notebook
Saturday sandbox · after MIT 6.874 single-cell lecture
Cumming (2014), "The new statistics: why and how", Psychological Science 25(1):7-29 — the case for estimation and intervals over p-values
In: LABLOOP-W19 Notebook
Saturday sandbox · after Cumming (2014), "The new statistics: why and how"
Chip Huyen, ML Interviews Book — huyenchip.com/ml-interviews-book (free) — chapters on the interview process, for the applications you send this week
In: LABLOOP-W19 Notebook
Saturday sandbox
Richard Hamming, You and Your Research (re-read from week 0; you will hear it differently now)
In: LABLOOP-W20 Notebook
Saturday sandbox · after Stanford CS197 lecture on research talks and posters
Coursera Introduction to Public Speaking (Univ. of Washington), week 1
In: LABLOOP-W20 Notebook
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
In: LABLOOP-W21 Notebook
Saturday sandbox · after Pudžiuvelytė et al.
Yang, Wu & Arnold (2019) review (carry over)
In: LABLOOP-W21 Notebook
Saturday sandbox · after Cunningham, Causal Inference: The Mixtape
Huntington-Klein, The Effect — theeffectbook.net, ch. 6-7 (causal diagrams), friendlier tone
In: LABLOOP-W22 Notebook
Saturday sandbox · after Coursera A Crash Course in Causality
Steinegger & Söding (2017), "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets", Nature Biotechnology 35:1026-1028
In: LABLOOP-W22 Notebook
Saturday sandbox
McNutt et al. (2018), "Transparency in authors' contributions and responsibilities to promote integrity in scientific publication", PNAS 115(11):2557-2560 (CRediT roles)
In: LABLOOP-W24 Notebook
Saturday sandbox · after McNutt et al.
CRediT taxonomy (credit.niso.org) — the standard list of contributor roles; use it in the authorship paragraph
In: LABLOOP-W24 Notebook
Saturday sandbox · after CRediT taxonomy
Center for Open Science / OSF preregistration templates (osf.io)
In: LABLOOP-W24 Notebook
Saturday sandbox · after Center for Open Science / OSF preregistration templates
In: LABLOOP-W24 Notebook
Saturday sandbox · after StatQuest on ANOVA and "Design matrices"
Coursera Practical Time Series Analysis — only if a client's trials are longitudinal
In: LABLOOP-W25 Notebook
Saturday sandbox
Sprouffske & Wagner (2016), "Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves", BMC Bioinformatics 17:172
In: LABLOOP-W26 Notebook
Saturday sandbox · after Midani, Collins & Britton (2021), "AMiGA: software for automated analysis of microbial growth as…
NCATS Assay Guidance Manual (ncbi.nlm.nih.gov/books/NBK53196), chapters on assay validation and HTS statistics — the industry reference, free
In: LABLOOP-W26 Notebook
Saturday sandbox · after David Maister, Charles Green & Robert Galford, The Trusted Advisor
Alan Weiss, Value-Based Fees (book, paid) — why fixed price beats hourly; matches v4's rule
In: LABLOOP-W27 Notebook
Saturday sandbox · after Stanford eCorner (ecorner.stanford.edu) — search talks on "customer discovery"
Bruce Booth's Life Sci VC blog (lifescivc.com) — how biotech investors think about runway and milestones; vocabulary for the "months of runway" pitch
In: LABLOOP-W27 Notebook
Saturday sandbox
Wil van der Aalst, Process Mining: Data Science in Action (book, paid)
In: LABLOOP-W29 Notebook
Saturday sandbox · after Wil van der Aalst, Process Mining: Data Science in Action
NIST e-Handbook ch. 6.1 (process monitoring intro) as a vocabulary refresher
In: LABLOOP-W29 Notebook
Saturday sandbox · after Vaux, Fidler & Cumming (2012), "Replicates and repeats—what is the difference and is it signific…
Coursera Introduction to Statistics (Stanford), module on small-sample inference
In: LABLOOP-W30 Notebook
Saturday sandbox
Target journal author guidelines chosen with the partner (e.g., a protein engineering or applied microbiology journal; verify fit and open-access policy)
In: LABLOOP-W31 Notebook
Saturday sandbox · after Stanford CS197 lecture on co-authoring and feedback
Whitesides 2004 (carry over)
In: LABLOOP-W31 Notebook
Saturday sandbox
Andrew Ng, How to Build Your Career in AI (free eBook from DeepLearning.AI; verify availability) — chapters on job search and portfolio
In: LABLOOP-W32 Notebook
Saturday sandbox · after Andrew Ng, How to Build Your Career in AI
Life Sci VC (Bruce Booth) posts on how biotech boards evaluate consultants and fractional executives (search)
In: LABLOOP-W32 Notebook
Saturday sandbox
FDA, "Data Integrity and Compliance With Drug CGMP: Questions and Answers" (guidance, December 2018)
In: LABLOOP-W33 Notebook
Saturday sandbox · after FDA, "Data Integrity and Compliance With Drug CGMP: Questions and Answers"
FDA "Computer Software Assurance for Production and Quality System Software" guidance (verify final status and date)
In: LABLOOP-W33 Notebook
Saturday sandbox · after FDA "Computer Software Assurance for Production and Quality System Software" guidance
ICH E6(R3) Good Clinical Practice, data governance sections (only if a clinical client appears)
In: LABLOOP-W33 Notebook
Saturday sandbox · after ICH E6(R3) Good Clinical Practice, data governance sections
eLabFTW documentation — doc.elabftw.net (installation and API)
In: LABLOOP-W33 Notebook
Saturday sandbox · after eLabFTW documentation
Coursera Research Data Management and Sharing (UNC/Edinburgh), modules on data storage and preservation
In: LABLOOP-W33 Notebook
Saturday sandbox
Anthropic, "Introducing Contextual Retrieval" (engineering blog, 2024)
In: LABLOOP-W34 Notebook
Saturday sandbox · after Anthropic, "Introducing Contextual Retrieval"
Thakur et al. (2021), "BEIR: A Heterogeneous Benchmark for Zero-shot Evaluation of Information Retrieval Models", NeurIPS Datasets and Benchmarks
In: LABLOOP-W34 Notebook
Saturday sandbox · after Thakur et al. (2021), "BEIR: A Heterogeneous Benchmark for Zero-shot Evaluation of Information R…
Faysse et al. (2024), "ColPali: Efficient Document Retrieval with Vision Language Models", arXiv:2407.01449 — retrieval directly on page images
In: LABLOOP-W34 Notebook
Saturday sandbox · after Faysse et al. (2024), "ColPali: Efficient Document Retrieval with Vision Language Models"
Zheng et al. 2023 LLM-as-a-judge (carry over)
In: LABLOOP-W34 Notebook
Saturday sandbox
NIST Privacy Framework overview (nist.gov)
In: LABLOOP-W35 Notebook
Saturday sandbox · after Stanford HAI AI Index report, chapter on responsible AI
v4 Part 5.4 (phase-2 backlog) — re-read to decide nothing yet
In: LABLOOP-W35 Notebook
Saturday sandbox
In: LABLOOP-W36 Notebook
Saturday sandbox · after Coursera Writing in the Sciences module on "The publication process" and cover letters
Smith et al. (2018), "Journal of Open Source Software (JOSS): design and first-year review", PeerJ Computer Science 4:e147
In: LABLOOP-W36 Notebook
Saturday sandbox · after Smith et al. (2018), "Journal of Open Source Software (JOSS): design and first-year review"
COPE (Committee on Publication Ethics) guidance on preprints and duplicate publication (publicationethics.org)
In: LABLOOP-W36 Notebook
Saturday sandbox
Chip Huyen, Designing Machine Learning Systems (book, paid) — chapters on data and deployment for the system-design interview
In: LABLOOP-W37 Notebook
Saturday sandbox · after The Trusted Advisor
Company engineering/science blogs of the targets (DataHow, TetraScience, Benchling, Novasign; verify)
In: LABLOOP-W37 Notebook
Saturday sandbox · after Nancy Duarte, "The secret structure of great talks"
Coursera Introduction to Public Speaking (University of Washington), weeks 2-3
In: LABLOOP-W38 Notebook
Saturday sandbox
a16z Bio + Health podcast (search an episode on biotech operations or AI in R&D)
In: LABLOOP-W39 Notebook
Saturday sandbox · after a16z Bio + Health podcast
In: LABLOOP-W39 Notebook
Saturday sandbox · after Uri Alon's talk and essay on "the cloud" in research
Stanford Designing Your Life resources (designingyour.life) — odyssey plan worksheets
In: LABLOOP-W40 Notebook