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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

In: LABLOOP-W35 Notebook

HHS HIPAA "Summary of the Privacy Rule"

Tuesday · after Argentina's Ley 25.326 summary on argentina.gob.ar

HHS HIPAA "Summary of the Privacy Rule" (hhs.gov) (20 min)

In: LABLOOP-W35 Notebook

Scientific Data submission guidelines for Data Descriptors

Scientific Data submission guidelines for Data Descriptors (nature.com/sdata) (20 min)

In: LABLOOP-W36 Notebook

JOSS "Review criteria" and "Submitting a paper"

Tuesday · after Scientific Data submission guidelines for Data Descriptors

JOSS "Review criteria" and "Submitting a paper" (joss.theoj.org) (25 min); author guides of the chosen Paper 2 journal (20 min)

In: LABLOOP-W36 Notebook

For pilots: re-read your audit readout and the client's success metric definition

For pilots: re-read your audit readout and the client's success metric definition (20 min)

In: LABLOOP-W37 Notebook

v4 Part 4

v4 Part 4 (portfolio package) and Part 9.4 (funds)

In: LABLOOP-W39 Notebook

Bruce Booth, Life Sci VC

Bruce Booth, Life Sci VC (lifescivc.com) — one post on portfolio support or milestones (search)

In: LABLOOP-W39 Notebook

Richard Hamming, You and Your Research

Richard Hamming, You and Your Research (final re-read; compare your week 0 notes) (30 min)

In: LABLOOP-W40 Notebook