Everything you could
study, filtered.

Richard W. Hamming, You and Your Research, Bell Communications Research Colloquium, 7 March 1986…

Spare pocket 1

It is the argument for why a 40-week plan aimed at one thesis beats 40 weeks of interesting side quests — the exact failure mode your ADHD brain is best at

Read exactly: The passage on "important problems" (why most scientists never work on one) and the passage on open door vs closed door

Produce: 5 lines in notes/craft/W00.md: the one important problem you are choosing, and the two you are refusing

In: LABLOOP-W00 Notebook

Wilson G. et al., "Good enough practices in scientific computing", PLOS Computational Biology 13…

Spare pocket 3

Justifies, in one sitting, every folder you create today (data/raw read-only and never committed, reports/figures regenerated)

Read exactly: Sections "Data management" and "Project organization" only

Produce: Copy the two directory checklists into the README skeletons of batchlens and fermlit

In: LABLOOP-W00 Notebook

Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", PLOS Comp. Biol. 9…

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

Elliot Hershberg, Century of Biology newsletter

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

The Turing Way handbook

Your week-4 DOI release and week-36 JOSS submission are graded against exactly these habits

Read exactly: "Guide for Reproducible Research" → the overview chapter only; browse the table of contents

Produce: Two checklists saved to PARKING.md, not acted on yet

In: LABLOOP-W00 Notebook

OpenStax Biology 2e, 6.5 Enzymes

Tuesday · B1

Enzyme + substrate is literally the shape of the Monod term S/(Ks+S) you code on Monday

Read exactly: Whole section, plus the chapter-6 review questions reachable from Ch. 6 Introduction if time allows

Produce: 5 questions at the end of notes/bio/B1.md; answer them yourself next week

In: LABLOOP-W01 Notebook

eclipse-paho/paho.mqtt.python README

Wednesday build block

Wednesday's telemetry hop, nothing more

Read exactly: "Publish a single message" example

Produce: The publisher in the Wednesday artifact

In: LABLOOP-W01 Notebook

SciPy documentation for scipy.integrate.solve_ivp (the solver you will use); read the "Examples"

Saturday sandbox

SciPy documentation for scipy.integrate.solve_ivp (the solver you will use); read the "Examples" section

In: LABLOOP-W01 Notebook

Pioreactor project docs (pioreactor.com) — see a real, open-source mini bioreactor with optical…

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

OpenStax Biology 2e, ch. 3 "Biological Macromolecules"

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

Goldrick S. et al., "The development of an industrial-scale fed-batch fermentation simulation",…

Monday build block · Read it inside Monday's build block

This is the paper behind the dataset you are tidying. Paper 2 will cite it

Read exactly: Abstract, all figures, and section 2 (the model)

Produce: Five lines in notes/bio/B2.md: which state variables the simulator actually integrates

In: LABLOOP-W02 Notebook

Goldrick S. et al., "Modern day monitoring and control challenges outlined on an industrial-scal…

Wednesday build block

Your whole week-03 alarm evaluation depends on knowing which batches are the faulty ones — and on the licence for redistribution

Read exactly: Abstract + the dataset section: how many batches, which are faulty, how faults are labelled, what the Raman block is

Produce: A variable table (name, unit, online/offline) and the fault list, with quoted sentences and their page numbers

In: LABLOOP-W02 Notebook

OpenStax Biology 2e, ch. 7 "Cellular Respiration"

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

industrialpenicillinsimulation.com

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

NIST/SEMATECH e-Handbook of Statistical Methods

Monday build block

The public, citable reference for the limits you compute on Monday. Phase I vs Phase II is the distinction that stops you fooling yourself

Read exactly: 6.3.4 What are multivariate control charts? → 6.5.4.3 Hotelling's T² → 6.5.4.3.6 Constructing multivariate charts

Produce: The limit formula, with its source URL, in a comment above the code that implements it

In: LABLOOP-W03 Notebook

NIST/SEMATECH e-Handbook ch. 6.5 "Tutorials: multivariate control charts"

Monday build block · after NIST/SEMATECH e-Handbook of Statistical Methods · Read it inside Monday's build block

Build-block reading · NIST/SEMATECH e-Handbook ch. 6.5 "Tutorials: multivariate control charts" — https://www.itl.nist.gov/div898/handbook/pmc/section3/pmc34.htm (sections 6.3.4 and 6.5.4.3)

In: LABLOOP-W03 Notebook

OpenStax Microbiology, ch. 9 "Microbial Growth"

Tuesday · B3

You will discover your week-01 Monod model already explains the log phase — and what it does not explain

Read exactly: The growth-curve section only (lag, log, stationary, death). Oxygen, temperature and pH are parked

Produce: notes/bio/B3.md + a hand-drawn growth curve photographed into the notes

In: LABLOOP-W03 Notebook

erdogant/pca README

Wednesday build block

A second implementation to compare against. Compare numbers, never copy them without understanding

Read exactly: The Hotelling T² / SPE outlier section

Produce: One line in review.md: do your limits agree with theirs, and if not, why

In: LABLOOP-W03 Notebook

Nomikos & MacGregor (1995), "Multivariate SPC charts for monitoring batch processes"

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

Kourti & MacGregor (1995), "Process analysis, monitoring and diagnosis, using multivariate proje…

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

James, Witten, Hastie, Tibshirani & Taylor, An Introduction to Statistical Learning with Applica…

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

Kourti T. & MacGregor J.F., "Process analysis, monitoring and diagnosis, using multivariate proj…

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

Coursera Introduction to Statistics

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

GitHub Docs, "Referencing and citing content" and "About CITATION files"; format spec at citatio…

Wednesday build block

This is the literal procedure for Friday's DOI badge. Read it once, follow it exactly

Read exactly: The Zenodo-integration steps and the minimal CITATION.cff fields

Produce: CITATION.cff in the repo root and a rendering DOI badge in the README

In: LABLOOP-W04 Notebook

Kapoor S. & Narayanan A., "Leakage and the reproducibility crisis in machine-learning-based scie…

Thursday · M4 · after StatQuest · "Machine Learning Fundamentals: Cross Validation"

The single best paper on the exact mistake that would invalidate Paper 2. Cite it in week 08 and week 18

Read exactly: The taxonomy of eight leakage types; identify which one batch-wise CV prevents

Produce: One paragraph in the README's honest "Where it fails" section naming the leakage type you guarded against

In: LABLOOP-W04 Notebook

The Turing Way, chapter on "Version control" and "Research compendia"

Saturday sandbox

In: LABLOOP-W04 Notebook

OpenStax Microbiology, ch. 8 "Microbial Metabolism"

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

ISLP ch. 5 "Resampling Methods"

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

Sandve G. et al., "Ten Simple Rules for Reproducible Computational Research", PLOS Comp. Biol. 9…

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

The Turing Way — book.the-turing-way.org, chapters on "Version control"

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

JOSS submission guidance

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

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

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)

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

ISLP

ISLP ch. 6.1-6.2 (subset selection, ridge, lasso) and ch. 8 (trees, bagging, boosting) (75 min, skim the proofs)

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

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

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)

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

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

In: LABLOOP-W05 Notebook

Datasheets for Datasets: Gebru et al.

Monday build block · Read it inside Monday's build block

Build-block reading · Datasheets for Datasets: Gebru et al. (2021), Communications of the ACM 64(12):86-92. The questions your guidelines and dataset card must answer

In: LABLOOP-W06 Notebook

OpenStax Microbiology ch. 12.1-12.2 "Modern Applications of Microbial Genetics"

OpenStax Microbiology ch. 12.1-12.2 "Modern Applications of Microbial Genetics" (60 min)

In: LABLOOP-W06 Notebook

Rosalind problems 5-8

Tuesday · after OpenStax Microbiology ch. 12.1-12.2 "Modern Applications of Microbial Genetics"

In: LABLOOP-W06 Notebook

Artstein & Poesio (2008), "Inter-coder agreement for computational linguistics"

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

McHugh (2012), "Interrater reliability: the kappa statistic"

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

Zheng et al. (2023), "Judging LLM-as-a-judge with MT-Bench and Chatbot Arena"

Monday build block · Read it inside Monday's build block

Build-block reading · Zheng et al. (2023), "Judging LLM-as-a-judge with MT-Bench and Chatbot Arena", NeurIPS Datasets & Benchmarks, sections 1-3 (judge biases you must avoid in week 14)

In: LABLOOP-W07 Notebook

DSPy (Stanford NLP) documentation "Optimizers"

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

Review B1-B7 notes

In: LABLOOP-W08 Notebook

P3 quiz with the "PI in a lab meeting" persona

Tuesday · after Review B1-B7 notes

P3 quiz with the "PI in a lab meeting" persona (60 min)

In: LABLOOP-W08 Notebook

Kadlec, Gabrys & Strandt (2009), "Data-driven soft sensors in the process industry"

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

Quarto guide for scientific manuscripts

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

Coursera Industrial Biotechnology

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

McHugh

Monday build block · Read it inside Monday's build block

Build-block reading · McHugh (2012) kappa paper (carry over from week 6), results interpretation table

In: LABLOOP-W10 Notebook

Rasmussen & Williams, Gaussian Processes for Machine Learning, ch. 1-2 — gaussianprocess.org/gpm…

Rasmussen & Williams, Gaussian Processes for Machine Learning, ch. 1-2 — gaussianprocess.org/gpml (free) (45 min) after Görtler, Kehlbeck & Deussen (2019), "A Visual Exploration of Gaussian Processes", Distill — distill.pub/2019/visual-exploration-gaussian-processes (30 min, interactive; start here)

In: LABLOOP-W10 Notebook

Krippendorff's alpha

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

Modern Statistics for Modern Biology (Holmes & Huber) ch. 3 "High quality graphics in R"

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

Hugging Face "Dataset Cards" documentation

Monday build block · Read it inside Monday's build block

Build-block reading · Hugging Face "Dataset Cards" documentation (huggingface.co/docs/hub/datasets-cards)

In: LABLOOP-W11 Notebook

Wilkinson et al. (2016), "The FAIR Guiding Principles for scientific data management and steward…

Monday · after Hugging Face "Dataset Cards" documentation

Wilkinson et al. (2016), "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data 3:160018 (4 pages)

In: LABLOOP-W11 Notebook

Agnihotri & Batra (2020), "Exploring Bayesian Optimization"

Agnihotri & Batra (2020), "Exploring Bayesian Optimization", Distill — distill.pub/2020/bayesian-optimization (30 min, interactive; start here); then Frazier (2018), "A Tutorial on Bayesian Optimization", arXiv:1807.02811, sections 1-4 (45 min)

In: LABLOOP-W11 Notebook

Shields et al. (2021), "Bayesian reaction optimization as a tool for chemical synthesis"

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

Coursera Research Data Management and Sharing

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

NCBI Taxonomy and E-utilities documentation

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

Brunton, Proctor & Kutz

Monday build block · Read it inside Monday's build block

Build-block reading · Brunton, Proctor & Kutz (2016), "Discovering governing equations from data by sparse identification of nonlinear dynamical systems", PNAS 113(15):3932-3937 (abstract + figure 1)

In: LABLOOP-W12 Notebook

FDA

FDA (2004) PAT — A Framework for Innovative Pharmaceutical Development, Manufacturing, and Quality Assurance — fda.gov/media/71012/download (read sections I-IV, 45 min)

In: LABLOOP-W12 Notebook

ICH Q8(R2)

Tuesday · after FDA

ICH Q8(R2) sections 1-2 (ich.org) (15 min). Write the glossary

In: LABLOOP-W12 Notebook

Narayanan et al. (2020), "Bioprocessing in the digital age: the role of process models"

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

Sansana et al. (2021), "Recent trends on hybrid modeling for Industry 4.0"

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

arXiv endorsement page

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

Mensh & Kording (2017), "Ten simple rules for structuring papers"

Monday build block · Read it inside Monday's build block

Build-block reading · Mensh & Kording (2017), "Ten simple rules for structuring papers", PLoS Computational Biology 13(9):e1005619

In: LABLOOP-W13 Notebook

Holmes & Huber, Modern Statistics for Modern Biology, ch. 1 (generative models for discrete data…

Holmes & Huber, Modern Statistics for Modern Biology, ch. 1 (generative models for discrete data) and ch. 2 (statistical modeling) — search "Modern Statistics for Modern Biology Holmes Huber" (free online book

In: LABLOOP-W13 Notebook

EMBL link may move)

Tuesday · after Holmes & Huber, Modern Statistics for Modern Biology, ch. 1 (generative models for discrete data…

EMBL link may move) (75 min)

In: LABLOOP-W13 Notebook

von Stosch et al. (2014), "Hybrid semi-parametric modeling in process systems engineering: past,…

von Stosch et al. (2014), "Hybrid semi-parametric modeling in process systems engineering: past, present and future", Computers & Chemical Engineering 60:86-101 (sections 1-3)

In: LABLOOP-W13 Notebook

Chen et al. (2018), "Neural Ordinary Differential Equations"

Thursday · after von Stosch et al. (2014), "Hybrid semi-parametric modeling in process systems engineering: past,…

Chen et al. (2018), "Neural Ordinary Differential Equations", arXiv:1806.07366 (abstract + figure 1)

In: LABLOOP-W13 Notebook

Coursera Writing in the Sciences (Stanford, Kristin Sainani), module 1 "Principles of effective…

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

Karniadakis et al. (2021), "Physics-informed machine learning"

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

Modern Statistics for Modern Biology ch. 6 "Testing"

Modern Statistics for Modern Biology ch. 6 "Testing" (multiple testing, FDR) (60 min)

In: LABLOOP-W14 Notebook

Gopen & Swan (1990), "The Science of Scientific Writing"

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

Whitesides (2004), "Whitesides' Group: Writing a Paper"

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

Benjamini & Hochberg (1995), "Controlling the false discovery rate"

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

Scientific Data "Data Descriptor" article guidelines

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

Writing · Coursera Writing in the Sciences

Writing · Coursera Writing in the Sciences (Stanford), modules 1-2 (cutting clutter, active voice) — watch at 1.5x during Saturday buffer if needed

In: LABLOOP-W14 Notebook

Jurafsky & Martin, Speech and Language Processing

Jurafsky & Martin, Speech and Language Processing (3rd ed. draft, web.stanford.edu/~jurafsky/slp3), chapter on information extraction (relation extraction and evaluation sections) (60 min); write the kappa paragraph into Methods

In: LABLOOP-W15 Notebook

Coursera Writing in the Sciences, module on "The format of a scientific manuscript" and "Peer re…

Saturday sandbox

Coursera Writing in the Sciences, module on "The format of a scientific manuscript" and "Peer review"

In: LABLOOP-W15 Notebook

Bourne (2005), "Ten simple rules for getting published"

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

ASAPbio preprint FAQ

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

bioRxiv submission guide

Monday build block · Read it inside Monday's build block

Build-block reading · bioRxiv submission guide (biorxiv.org/submit-a-manuscript)

In: LABLOOP-W16 Notebook

Lin et al. (2023), "Evolutionary-scale prediction of atomic-level protein structure with a langu…

Lin et al. (2023), "Evolutionary-scale prediction of atomic-level protein structure with a language model", Science 379(6637):1123-1130 — abstract, introduction and figures (40 min)

In: LABLOOP-W16 Notebook

Angelopoulos & Bates

Angelopoulos & Bates (2021), "A Gentle Introduction to Conformal Prediction and Distribution-Free Uncertainty Quantification", arXiv:2107.07511, sections 1-2 (60 min)

In: LABLOOP-W16 Notebook

Rives et al. (2021), "Biological structure and function emerge from scaling unsupervised learnin…

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

Dallago et al. (2021), "FLIP: Benchmark tasks in fitness landscape inference for proteins"

Dallago et al. (2021), "FLIP: Benchmark tasks in fitness landscape inference for proteins", NeurIPS Datasets and Benchmarks (bioRxiv 2021.11.09.467890) — introduction, task table, thermostability split (40 min)

In: LABLOOP-W17 Notebook

Jarzab et al. (2020), "Meltome atlas — thermal proteome stability across the tree of life"

Tuesday · after Dallago et al. (2021), "FLIP: Benchmark tasks in fitness landscape inference for proteins"

Jarzab et al. (2020), "Meltome atlas — thermal proteome stability across the tree of life", Nature Methods 17:495-503 — abstract and figure 1 (20 min)

In: LABLOOP-W17 Notebook

Notin et al. (2023), "ProteinGym: large-scale benchmarks for protein fitness prediction and desi…

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

Coursera Writing in the Sciences (Stanford), module "Writing the results and discussion"

Saturday sandbox

In: LABLOOP-W18 Notebook

Kapoor & Narayanan

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

Rothschild & Mancinelli (2001), "Life in extreme environments"

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

scanpy "Preprocessing and clustering 3k PBMCs" tutorial

scanpy "Preprocessing and clustering 3k PBMCs" tutorial (scanpy.readthedocs.io, tutorials section) (75 min, run it)

In: LABLOOP-W19 Notebook

Single-cell best practices

Saturday sandbox

Single-cell best practices (Heumos et al., theislab) — sc-best-practices.org, introduction and quality-control chapters

In: LABLOOP-W19 Notebook

Cumming (2014), "The new statistics: why and how"

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

Chip Huyen, ML Interviews Book

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

Re-read all biology notes

In: LABLOOP-W20 Notebook

P3 with the "lab meeting PI" persona in LABLOOP-W20

Tuesday · after Re-read all biology notes

P3 with the "lab meeting PI" persona in LABLOOP-W20 (75 min)

In: LABLOOP-W20 Notebook

P3 with the "staff ML scientist at a bioprocess company" persona; record a 10-minute explanation…

P3 with the "staff ML scientist at a bioprocess company" persona; record a 10-minute explanation of Paper 2 (75 min)

In: LABLOOP-W20 Notebook

Richard Hamming, You and Your Research

Saturday sandbox

Richard Hamming, You and Your Research (re-read from week 0; you will hear it differently now)

In: LABLOOP-W20 Notebook

Coursera Introduction to Public Speaking

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

Jarzab et al. 2020

Jarzab et al. 2020 (Meltome), methods and results

In: LABLOOP-W21 Notebook

Dallago et al. 2021

Tuesday · after Jarzab et al. 2020

Dallago et al. 2021 (FLIP), thermostability task section (75 min)

In: LABLOOP-W21 Notebook

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

In: LABLOOP-W21 Notebook

Yang, Wu & Arnold

Saturday sandbox · after Pudžiuvelytė et al.

Yang, Wu & Arnold (2019) review (carry over)

In: LABLOOP-W21 Notebook

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)

In: LABLOOP-W21 Notebook

Huntington-Klein, The Effect

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

Steinegger & Söding (2017), "MMseqs2 enables sensitive protein sequence searching for the analys…

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

Partner-recommended reading (ask for it); if none yet, Rothschild & Mancinelli (2001) "Life in e…

Partner-recommended reading (ask for it); if none yet, Rothschild & Mancinelli (2001) "Life in extreme environments" (carry over) and the UniProt "Help" pages on EC numbers and taxonomy filters (75 min)

In: LABLOOP-W23 Notebook

The partner session (60 min) + Nosek et al. (2018), "The preregistration revolution"

The partner session (60 min) + Nosek et al. (2018), "The preregistration revolution", PNAS 115(11):2600-2606 (30 min)

In: LABLOOP-W24 Notebook

McNutt et al.

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

CRediT taxonomy

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

Center for Open Science / OSF preregistration templates

Saturday sandbox · after CRediT taxonomy

Center for Open Science / OSF preregistration templates (osf.io)

In: LABLOOP-W24 Notebook

Coursera Research Data Management and Sharing, module on data sharing agreements

Saturday sandbox · after Center for Open Science / OSF preregistration templates

In: LABLOOP-W24 Notebook

LabXchange simulations on protein expression/purification or enzyme assays

LabXchange simulations on protein expression/purification or enzyme assays (search the library; verify availability) so the partner's words land on a picture

In: LABLOOP-W24 Notebook

NIST e-Handbook

NIST e-Handbook ch. 5.1-5.3 — itl.nist.gov/div898/handbook (45 min)

In: LABLOOP-W25 Notebook

Penn State STAT 503 Design of Experiments online notes, lesson on randomised complete block desi…

Tuesday · after NIST e-Handbook

Penn State STAT 503 Design of Experiments online notes, lesson on randomised complete block designs — online.stat.psu.edu/stat503 (30 min)

In: LABLOOP-W25 Notebook

Coursera Practical Time Series Analysis

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

Piepho, Büchse & Emrich (2003), "A hitchhiker's guide to mixed models for randomized experiments"

Piepho, Büchse & Emrich (2003), "A hitchhiker's guide to mixed models for randomized experiments", Journal of Agronomy and Crop Science 189:310-322 (skim sections 1-3)

In: LABLOOP-W25 Notebook

Zhang, Chung & Oldenburg

Zhang, Chung & Oldenburg (1999), "A simple statistical parameter for use in evaluation and validation of high throughput screening assays", Journal of Biomolecular Screening 4(2):67-73 (20 min)

In: LABLOOP-W26 Notebook

Zwietering et al. (1990), "Modeling of the bacterial growth curve"

Tuesday · after Zhang, Chung & Oldenburg

Zwietering et al. (1990), "Modeling of the bacterial growth curve", Applied and Environmental Microbiology 56(6):1875-1881 (30 min)

In: LABLOOP-W26 Notebook

Ritz et al. (2015), "Dose-response analysis using R"

Tuesday · after Zwietering et al. (1990), "Modeling of the bacterial growth curve"

Ritz et al. (2015), "Dose-response analysis using R", PLoS ONE 10(12):e0146021, sections on the 4-parameter log-logistic model (25 min)

In: LABLOOP-W26 Notebook

Sprouffske & Wagner

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

NCATS Assay Guidance Manual

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

v4 Part 4 and Template F

v4 Part 4 and Template F (30 min)

In: LABLOOP-W27 Notebook

Rob Fitzpatrick, The Mom Test

Tuesday · after v4 Part 4 and Template F

Rob Fitzpatrick, The Mom Test (book, paid, ~130 pages; ch. 1-3 = 45 min)

In: LABLOOP-W27 Notebook

Alan Weiss, Value-Based Fees

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

Bruce Booth's Life Sci VC blog (lifescivc.com) — how biotech investors think about runway and mi…

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

Your own v4 Part 4 pricing hypotheses and Part 3.3 culture filter

In: LABLOOP-W28 Notebook

AFIP/ARCA guidance on issuing invoices as an independent professional in Argentina

AFIP/ARCA guidance on issuing invoices as an independent professional in Argentina (verify current rules with an accountant; this plan does not give tax advice)

In: LABLOOP-W28 Notebook

Wil van der Aalst, Process Mining: Data Science in Action

Saturday sandbox

Wil van der Aalst, Process Mining: Data Science in Action (book, paid)

In: LABLOOP-W29 Notebook

NIST e-Handbook

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

The client's papers/patents via P11

The client's papers/patents via P11 (60 min)

In: LABLOOP-W29 Notebook

Ho et al. (2019), "Moving beyond P values: data analysis with estimation graphics"

Ho et al. (2019), "Moving beyond P values: data analysis with estimation graphics", Nature Methods 16:565-566 (15 min)

In: LABLOOP-W30 Notebook

Cumming (2014) "The new statistics"

Tuesday · after Ho et al. (2019), "Moving beyond P values: data analysis with estimation graphics"

Cumming (2014) "The new statistics" (carry over), sections on small samples (30 min)

In: LABLOOP-W30 Notebook

Coursera Introduction to Statistics

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

Weissgerber et al. (2015), "Beyond bar and line graphs: time for a new data presentation paradigm"

Weissgerber et al. (2015), "Beyond bar and line graphs: time for a new data presentation paradigm", PLoS Biology 13(4):e1002128 (20 min)

In: LABLOOP-W30 Notebook

Gopen & Swan

Gopen & Swan (1990) re-read (30 min)

In: LABLOOP-W31 Notebook

Coursera Writing in the Sciences (Stanford), module on "Discussion"

Tuesday · after Gopen & Swan

Coursera Writing in the Sciences (Stanford), module on "Discussion" and "Abstract" (45 min)

In: LABLOOP-W31 Notebook

Target journal author guidelines chosen with the partner

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

Whitesides 2004

Saturday sandbox · after Stanford CS197 lecture on co-authoring and feedback

Whitesides 2004 (carry over)

In: LABLOOP-W31 Notebook

Andrew Ng, How to Build Your Career in AI

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

Life Sci VC

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

bioRxiv submission guide

bioRxiv submission guide (carry over); co-author's institution's preprint policy (ask)

In: LABLOOP-W32 Notebook

21 CFR Part 11, §11.10 and §11.50

21 CFR Part 11, §11.10 and §11.50 (ecfr.gov) (20 min)

In: LABLOOP-W33 Notebook

FDA Part 11 Scope and Application guidance

Tuesday · after 21 CFR Part 11, §11.10 and §11.50

FDA Part 11 Scope and Application guidance (2003), sections III-IV (25 min)

In: LABLOOP-W33 Notebook

MHRA GxP Data Integrity Guidance

Tuesday · after FDA Part 11 Scope and Application guidance

MHRA GxP Data Integrity Guidance (2018), definitions section (30 min)

In: LABLOOP-W33 Notebook

FDA, "Data Integrity and Compliance With Drug CGMP: Questions and Answers"

Saturday sandbox

FDA, "Data Integrity and Compliance With Drug CGMP: Questions and Answers" (guidance, December 2018)

In: LABLOOP-W33 Notebook

FDA "Computer Software Assurance for Production and Quality System Software" guidance

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

ICH E6(R3) Good Clinical Practice, data governance sections

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

eLabFTW documentation

Saturday sandbox · after ICH E6(R3) Good Clinical Practice, data governance sections

eLabFTW documentation — doc.elabftw.net (installation and API)

In: LABLOOP-W33 Notebook

Coursera Research Data Management and Sharing

Saturday sandbox · after eLabFTW documentation

Coursera Research Data Management and Sharing (UNC/Edinburgh), modules on data storage and preservation

In: LABLOOP-W33 Notebook

Anthropic, "Introducing Contextual Retrieval"

Saturday sandbox

Anthropic, "Introducing Contextual Retrieval" (engineering blog, 2024)

In: LABLOOP-W34 Notebook

Thakur et al. (2021), "BEIR: A Heterogeneous Benchmark for Zero-shot Evaluation of Information R…

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

Faysse et al. (2024), "ColPali: Efficient Document Retrieval with Vision Language Models"

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

Zheng et al. 2023 LLM-as-a-judge

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

GDPR Article 5

GDPR Article 5 (principles) and Article 25 (privacy by design) (20 min)

In: LABLOOP-W35 Notebook

Argentina's Ley 25.326 summary on argentina.gob.ar

Tuesday · after GDPR Article 5

Argentina's Ley 25.326 summary on argentina.gob.ar (verify page) (20 min)