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OpenStax Biology 2e

OpenStax Biology 2e ch. 14 (DNA structure and function) + ch. 15 (genes and proteins), sections 14.1-14.3, 15.1-15.5 (60 min)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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