# Sources and resource verification

## Local source register

| ID | Source | Use |
|---|---|---|
| S1 | [LABLOOP-Master-Plan-v5.md](../LABLOOP-Master-Plan-v5.md), dated 2026-09-11 | Governing strategy, full weeks 0–20, outline 21–40, curriculum, gates and prompts |
| S2 | [AI-Upskilling-Plan-Biotech-v4.md](../AI-Upskilling-Plan-Biotech-v4.md), dated 2026-09-11 | Retained offers, company map, culture filter, instrument methods and content templates |
| S3 | [GridX Startups.csv](../GridX%20Startups.csv) | Private prospect-research seed; asserted company gaps are unverified hypotheses |
| S4 | [aiupskilling2026.json](../aiupskilling2026.json), document v3 | Historical Vara plan; not a scheduling authority |
| S5 | [labloop-plan.html](../labloop-plan.html) | v4 run-sheet presentation, identified by title/version |
| S6 | [LABLOOP-Master-Plan-v5.html](../LABLOOP-Master-Plan-v5.html) | Alternate presentation of v5; Markdown is the execution reference |
| S7 | [5.SINTESIS-Combinaciones-v1.html](../5.SINTESIS-Combinaciones-v1.html) | Earlier strategy context; not a new parallel project |

S1 was read in full for this expansion. Relevant S2 strategy, curriculum, offers and instrument sections were inspected. Historical artifacts were identified for precedence; this is not a line-by-line audit of every historical version or CSV company claim.

## Checks performed on 2026-09-12

- The [official ISLP site](https://www.statlearning.com/) provides the Python edition and free PDF/course routes. Select relevant sections within the weekly budget.
- The [official Karpathy course index](https://karpathy.ai/zero-to-hero.html) lists micrograd and makemore lessons longer than a single one-hour AI study segment. Prepare excerpts and a bounded exercise, not a requirement to finish the full videos that week.
- [Europe PMC API documentation](https://europepmc.org/RestfulWebService) documents article search and full-text retrieval. [Europe PMC help](https://europepmc.org/Help) explains that reuse remains subject to copyright/license terms; inspect each source's terms before release.
- [arXiv endorsement documentation](https://info.arxiv.org/help/endorsement.html) is the official route reference. Endorsement is distinct from scientific peer review and does not promise acceptance.
- [JOSS submission guidance](https://joss.readthedocs.io/en/latest/submitting.html) and its [maintained source](https://github.com/openjournals/joss/blob/main/docs/submitting.md) should be checked at week 36. Eligibility includes substantive research software, demonstrated use, open development and sustained public history; keep evidence from early releases. Submission is not acceptance.
- The [OpenStax Biology 2e landing page](https://openstax.org/details/books/biology-2e) was reachable but returned no extractable body in this check. Chapter availability/content must be verified during lesson preparation.
- The historical [IndPenSim site](https://www.industrialpenicillinsimulation.com/) could not be retrieved in this check. The [author paper in UCL's repository](https://discovery.ucl.ac.uk/id/eprint/10082538/7/Goldrick_Modern%20day%20monitoring%20and%20control%20challenges%20outlined%20on%20an%20industrial-scale%20benchmark%20fermentation%20process_VoR.pdf) is an author/institutional route to verify during week 2; dataset access, license, checksums and actual counts are still pending.
- The inherited [bioRxiv submission page](https://www.biorxiv.org/submit-a-manuscript) could not be retrieved in this check. Verify current submission portal, scope and policies before promising a venue; no blanket fallback eligibility is assumed.

These checks do not validate every lecture number, dataset link, company or hardware claim in the inherited plan.

## Weeks 00–04 reading and viewing lists (added 2026-09-15)

Act I now carries an explicit, per-week materials file with exact locators, section-level scope, minute budgets and the artifact each source must produce. These replace the bare titles inherited from v5 and expand the v6 "Learn it" blocks:

| Week | Materials file |
|---|---|
| 00 | [weeks/week-00-cockpit-and-positioning/materials.md](./weeks/week-00-cockpit-and-positioning/materials.md) |
| 01 | [weeks/week-01-fermentation-simulator/materials.md](./weeks/week-01-fermentation-simulator/materials.md) |
| 02 | [weeks/week-02-indpensim-data-and-baseline/materials.md](./weeks/week-02-indpensim-data-and-baseline/materials.md) |
| 03 | [weeks/week-03-statistical-batch-monitoring/materials.md](./weeks/week-03-statistical-batch-monitoring/materials.md) |
| 04 | [weeks/week-04-batchlens-first-release/materials.md](./weeks/week-04-batchlens-first-release/materials.md) |

Each file separates **Read**, **Watch (YouTube)** and **Deeper (Saturday sandbox only)**, and every item is placed in a specific day block so the 600-minute weekly cap still holds. Weeks 05–40 keep the inherited locator catalog below until the same treatment is applied to them.

### Links confirmed through search on 2026-09-15

DOI/article: Alon 2009 `10.1016/j.molcel.2009.09.013`; Wilson 2017 `10.1371/journal.pcbi.1005510`; Sandve 2013 `10.1371/journal.pcbi.1003285`; Goldrick 2015 `10.1016/j.jbiotec.2014.10.029`; Goldrick 2019 `10.1016/j.compchemeng.2019.05.037` (open copy at UCL Discovery 10082538, data record Mendeley `pdnjz7zz5x`); Nomikos & MacGregor 1995 `10.1080/00401706.1995.10485888`; Kapoor & Narayanan 2023 `10.1016/j.patter.2023.100804`.

Course/handbook pages: OpenStax *Biology 2e* `3-introduction`, `3-1-synthesis-of-biological-macromolecules`, `6-5-enzymes`, `7-introduction`, `7-5-metabolism-without-oxygen`; OpenStax *Microbiology* `8-1-energy-matter-and-enzymes`, `9-introduction`; NIST/SEMATECH `pmc34.htm`, `pmc543.htm`, `pmc5436.htm`; GitHub Docs "Referencing and citing content" and "About CITATION files"; Khan Academy energy-and-enzymes, activation-energy and fermentation articles; Hamming 1986 transcript (gwern mirror and Edinburgh PDF).

YouTube (video IDs confirmed): Crash Course Biology #3 `H8WJ2KENlK0`; Crash Course Biology #7 `00jbG_cfGuQ`; 3Blue1Brown linear-algebra playlist `PLZHQObOWTQDPD3MizzM2xVFitgF8hE_ab` and chapter 1 `fNk_zzaMoSs`; 3Blue1Brown calculus chapter 1 `WUvTyaaNkzM`; StatQuest PCA `FgakZw6K1QQ`, linear regression `7ArmBVF2dCs`, bias/variance `EuBBz3bI-aA`, cross-validation `fSytzGwwBVw`; Steve Brunton SVD playlist `PLMrJAkhIeNNSVjnsviglFoY2nXildDCcv` and overview `gXbThCXjZFM`; Stanford *Statistical Learning with Python* playlist `PLoROMvodv4rPP6braWoRt5UCXYZ71GZIQ`; Hamming 1995 talk `a1zDuOPkMSw`; Oakley TEDxOaklandUniversity `O96fE1E-rf8`; LearnChemE Monod `39kf7YdwNOs` and CSTR washout `L_bzv0bbU4M`.

### Known unverified on 2026-09-15, carried with a (verify) mark

StatQuest "Bootstrapping Main Ideas!!!" (no stable ID resolved; find from the channel or rely on ISLP 5.2); Ninja Nerd glycolysis/Krebs lectures; NPTEL *Bioreactors* course number 102106053; industrialpenicillinsimulation.com (also unreachable in the 2026-09-12 check — use the UCL/Mendeley routes and record the licence); Kourti & MacGregor 1995; *Century of Biology* newsletter. Durations given in the materials files are approximate and were not timed.

## Curriculum locator catalog

Entries below are inherited source locators to verify when preparing the relevant week. Match the concept/title if lecture numbering has changed. Do not invent exact timestamps or claim to have read inaccessible content.

| Resource | Locator | Selected scope |
|---|---|---|
| Biology 2e | https://openstax.org/details/books/biology-2e | B1–B6 chapter selections named in weekly source rows |
| Microbiology | https://openstax.org/details/books/microbiology | Growth, metabolism and microbial genetics selections |
| 3Blue1Brown | https://www.3blue1brown.com/topics/linear-algebra ; https://www.3blue1brown.com/topics/calculus | Selected foundational visual lessons; fit time budget |
| ISLP | https://www.statlearning.com/ | Chapters 2, 3, 5, 6 and 8 selections; Python labs |
| Rosalind | https://rosalind.info/problems/list-view/ | Verify IDs behind v5's 'problems 1–8'; do not depend on mutable display order |
| MIT OCW 7.016 | https://ocw.mit.edu/courses/7-016-introductory-biology-fall-2018/ | Protein structure and enzymes |
| NPTEL / MIT OCW | https://nptel.ac.in/ ; https://ocw.mit.edu/ | Verify bioreactors course and exact balances/kinetics/oxygen-transfer lessons; MIT 10.37 notes as source-proposed backup |
| Probabilistic ML | https://probml.github.io/pml-book/book1.html | Probability/statistics selections |
| Statistical Rethinking | https://github.com/rmcelreath/stat_rethinking_2024 | Lectures 1–4 selections |
| Karpathy | https://karpathy.ai/zero-to-hero.html | Micrograd and first makemore only as scheduled |
| GPML | https://gaussianprocess.org/gpml/ | Chapters 1–2 selections |
| Bayesian optimization | https://arxiv.org/abs/1807.02811 ; https://botorch.org/docs/tutorials/ | Frazier tutorial and one bounded simulator application |
| Data-driven dynamics | https://databookuw.com/ | SINDy topic; verify edition/chapter numbering |
| Modern Statistics for Modern Biology | https://www.huber.embl.de/msmb/ | Source chapter selections; verify actual testing/reporting topics |
| Conformal prediction | https://arxiv.org/abs/2107.07511 | Sections 1–2 and assumption checks |
| ESM-2 | https://github.com/facebookresearch/esm ; https://huggingface.co/facebook/esm2_t33_650M_UR50D | Embedding inference/model card, actual resource smoke test |
| FLIP | https://github.com/J-SN/FLIP | Task, label, split and baseline definitions |
| Meltome | Search Jarzab et al. 2020, 'Meltome atlas' on publisher/author repository | Verify assay target and download/version/license; no invented DOI |
| Causal inference | https://www.bradyneal.com/causal-inference-course | Lecture 1 confounding for Paper 3 |
| UniProt | https://www.uniprot.org/help | Accessions, evidence and sequence annotations |
| NIST statistics handbook | https://www.itl.nist.gov/div898/handbook/ | Chapters 5 and 6 on design and process monitoring |
| statsmodels | https://www.statsmodels.org/stable/mixed_linear.html | Mixed-model specification, diagnostics and examples |
| agridat | https://cran.r-project.org/package=agridat | Dataset provenance and design metadata |
| Assay QC | Search Zhang et al. 1999 Z-prime assay-quality paper on publisher/author source | Verify exact reference and relevant endpoint before use |
| BioModels | https://www.ebi.ac.uk/biomodels/ | Curated mechanistic comparator; exact relevant model required |
| Stanford evaluation | https://cs336.stanford.edu/ ; https://web.stanford.edu/class/cs224n/ | Evaluation/judge-bias topics; verify year and lecture number |
| Speech and Language Processing | https://web.stanford.edu/~jurafsky/slp3/ | Information extraction topic in current draft |
| scanpy | https://scanpy.readthedocs.io/ | PBMC 3k literacy tutorial; bounded exercise |
| HF datasets | https://huggingface.co/docs/datasets | Dataset card and distribution documentation |
| Zenodo | https://help.zenodo.org/ | Release deposit, versioning and GitHub integration |
| FDA PAT | https://www.fda.gov/regulatory-information/search-fda-guidance-documents/pat-framework-innovative-pharmaceutical-development-manufacturing-and-quality-assurance | Named PAT framework, selected definitions |
| ICH quality guidance | https://www.ich.org/page/quality-guidelines | Q8(R2) selected sections and Q10 overview, verify current document |
| 21 CFR Part 11 | https://www.ecfr.gov/current/title-21/chapter-I/subchapter-A/part-11 | Current official text, relevant records requirements only |
| MHRA data integrity | https://www.gov.uk/government/publications/guidance-on-gxp-data-integrity | Relevant ALCOA/data-integrity concepts and limits |
| eLabFTW | https://doc.elabftw.net/ | Deployment, API, security and record workflows |
| Research writing | Search Simon Peyton Jones 'How to write a great research paper' on author's page; current NeurIPS checklist | Selected writing/checklist material, no full new course |
| Journals | Official author pages for the selected Scientific Data/bioprocess journal and Paper 2 journal | Scope, costs, author approvals and submission format at week 36 |

For each selected resource in a prepared week, record exact title, author/provider, edition/date, URL, access date, chosen pages/sections or timestamps, and why it is needed for that week's deliverable. If inaccessible, choose a free authoritative substitute for the same objective and log the substitution.