# Week 00 — cockpit and positioning [**Full learning notebook: explanations, step-by-step challenges, stashes and evidence**](./learning-notebook.md) · [NotebookLM export](./notebooklm.txt) Status: NOT_STARTED. Calendar dates: not assigned. Owner: Peter Ciancaglini. Planning authority: v5 Part 6 with retained v4 details. Deeper walkthrough: [v6 · Week 0 · Cockpit and positioning](../../../LABLOOP-Master-Plan-v6.md#week-0--cockpit-and-positioning). Active project/repository: cockpit; labloop-notes; batchlens; fermlit. [Programme](../../README.md) · [Model instructions](../../specs.md) · [Decisions](../../DECISIONS.md) · [Resources](../../SOURCES.md) · [**v6 walkthrough**](../../../LABLOOP-Master-Plan-v6.md#week-0--cockpit-and-positioning) · [**Materials: read & watch**](./materials.md) · No previous week · [Next week](../week-01-fermentation-simulator/specs.md) ## Outcome and relevance This week delivers the three concrete artifacts below and the supporting learning/branding/opportunity pack. The scientific or commercial outcome follows the preserved source brief, while the acceptance checks make its evidence testable. The career objective is to turn this work into something a scientist, hiring manager or buyer can inspect. - Scientific/build priority: Create the five cockpit files and record a truthful baseline of Python, statistics, biology, portfolio links, and available time. - Public/profile priority: Evidence-first positioning, setup announcement, and a 30-second career introduction; distinguish current competence from learning objectives. - Career/relationship/commercial priority: Create the private target universe from v4 and GridX; record hypothesis status and separate employers, scientists, recruiters, and clients. ## Deeper walkthrough (v6) Read [v6 · Week 0 · Cockpit and positioning](../../../LABLOOP-Master-Plan-v6.md#week-0--cockpit-and-positioning) before Monday. It carries this week's v5 brief unchanged and adds the **Welcome** analogy, **Learn it** (▶ core and ＋ deeper sources), **Run it** (repos with a 20-40 minute exercise), the **NotebookLM kit** and the mentor check below. Standing v6 rules: [resource rules](../../../LABLOOP-Master-Plan-v6.md#prologue-3--the-resource-rules-so-you-never-waste-an-evening-on-a-bad-source), [NotebookLM protocol](../../../LABLOOP-Master-Plan-v6.md#prologue-4--the-notebooklm-protocol-one-notebook-per-week-zero-decisions), [chapter anatomy](../../../LABLOOP-Master-Plan-v6.md#prologue-5--how-to-read-a-chapter-the-anatomy-identical-for-all-41). v6 adds depth only; it does not change a goal, gate, output or the 600-minute cap, so this specification still governs execution. Verified links, exact scopes and durations for this week's reading and watching: [materials.md](./materials.md). **Act I · Threads: R (reputation), all repos · Next gate: 4** **Where this week sits.** - ← **From:** v4 and v5 thinking; your August 2026 synthesis ("I build instruments, never products"). - → **Feeds:** every week. Week 1 needs `batchlens` and `TODAY.md`; week 16 needs ORCID; week 20 needs the profile you start today. - ⟳ **Returns in:** every gate (4, 8, 13, 16, 20...) when you update the headline and the gauge. **Goals.** - 🎯 **This week:** the cockpit exists, Monday's `TODAY.md` line is written, post 0 is public. - 🏁 **Next milestone:** Gate 4, public and reproducible `batchlens v0.1`. - 🌟 **Final (week 40):** a public trail of 40 weeks that turns "applied AI engineer" into "AI scientist for biotech" in the eyes of people who never met you. **Mentor check.** *"I know exactly what I will open on Monday and why every file in my cockpit exists."* ## Required inputs and dependency check - No earlier execution week. Read the supplied v5/v4 documents and establish the actual starting baseline. - Read [commitment](./commitment.md), [evidence](./evidence.md), [review](./review.md) and the current root TODAY/PROGRESS/QUESTIONS files. - Read this week's chapter, [v6 · Week 0 · Cockpit and positioning](../../../LABLOOP-Master-Plan-v6.md#week-0--cockpit-and-positioning), then the standing sections: [Part 0 · how to use the document](../../../LABLOOP-Master-Plan-v6.md#part-0--how-to-use-this-document-read-this-every-monday-for-the-first-month), [Part 3 · the scientific thesis](../../../LABLOOP-Master-Plan-v6.md#part-3--the-scientific-thesis-explained-twice-like-a-kid-then-like-a-reviewer), [Part 4 · curriculum](../../../LABLOOP-Master-Plan-v6.md#part-4--curriculum-from-zero-four-tracks-all-free-exact-units), [Part 8 · the prompt pack](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets) and [Part 9 · branding and endorsement](../../../LABLOOP-Master-Plan-v6.md#part-9--branding-connection-ladder-endorsement). The same sections exist in the [v5 master](../../../LABLOOP-Master-Plan-v5.md), which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from [v4](../../../AI-Upskilling-Plan-Biotech-v4.md). - Inspect the actual canonical repository state, available data, existing figures and required human/external inputs. Never assume a previous week succeeded from its folder name. - Verify current resource links, versions, dataset rights and any live company/venue information before relying on them. Use [source catalog](../../SOURCES.md); explicitly record inaccessible resources. ## Seven-day plan: 600 minutes maximum The model must turn these into exact physical actions using the observed files and available inputs. Each 90-minute block includes start/stop rituals. All calls, posts, debugging, reading and exercises consume this same capacity. | Day | Budget | Work and stopping condition | |---|---:|---| | Monday | 90 min | Create the five cockpit files and record a truthful baseline of Python, statistics, biology, portfolio links, and available time. Stop when: Five next actions and an evidence-backed skills baseline exist. | | Tuesday | 90 min | Read v5 Part 0 twice and Part 14 once; no formal study units. Produce: A five-line account of the operating rules and the next physical action. | | Wednesday | 90 min | Specify repository skeletons, environment smoke checks, offline fake mode, secrets handling, and local hardware inventory. Stop when: A future model has exact setup steps, success checks, and a CPU fallback. Reserve the last 10 minutes for the optional Wednesday note. | | Thursday | 90 min | Read v5 Part 0 twice and Part 14 once; no formal study units. Select material/exercise that fits 60 minutes; use the last 30 for the founder paper. | | Friday | 90 min | Draft LinkedIn headline/About, GitHub bio, ORCID setup checklist, and two target-role narratives: applied scientist and scientific AI lead. Stop when: Every experience claim is supported or marked for Peter to confirm. | | Saturday | 90 min | Resolve the earliest critical spillover or dependency. Prepare any long-form publication draft from existing figures here if needed. Sandbox only after commitments are met. | | Sunday | 60 min | 20 min build-log draft/publication when authorized; 5 min evidence/checklist; 20 min source-grounded gap review; 15 min next week's six physical actions. | Week 00 is setup. Tuesday/Thursday are orientation/setup blocks; no mandatory science coursework. ## Learning specification ### Biology/domain unit Material: Read v5 Part 0 twice and Part 14 once; no formal study units. Produce: A five-line account of the operating rules and the next physical action. Understanding check: Peter can state the weekly rhythm, evidence rule and recovery minimum. During preparation, write one worked example connected to the week's actual task, one exercise with a separate answer key and five questions. Peter supplies answers; score explanation quality and flag misconceptions in QUESTIONS. Numeric/scientific conclusions require actual data or explicitly synthetic teaching values. ### AI/scientific-method unit Material: Read v5 Part 0 twice and Part 14 once; no formal study units. Produce: A five-line account of the operating rules and the next physical action. Understanding check: Peter can state the weekly rhythm, evidence rule and recovery minimum. Use the [prompt pack](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets): P1 explanation ladder, P2 concept-to-project bridge and P3 quiz. Coding practice belongs within the allocated study/build block. Where the source asks for a favorable scientific result, substitute an honest measured comparison as explained below. ### Founder/scientist paper Prepare the first candidate-paper shortlist; the weekly digest cadence begins in Week 01. ## Artifact contracts These filenames are outputs to prepare during this week's execution; this scaffold does not claim they already exist. Drafts and measured results have different states. Technical code/data stay in the canonical project repository and are referenced from these coordinating files. | Artifact | Required content / acceptance | Primary responsibility | |---|---|---| | `profile-baseline.md` | Create the five cockpit files and record a truthful baseline of Python, statistics, biology, portfolio links, and available time. Acceptance: Five next actions and an evidence-backed skills baseline exist. | Model assists; Peter checks and owns the outcome | | `environment-checklist.md` | Specify repository skeletons, environment smoke checks, offline fake mode, secrets handling, and local hardware inventory. Acceptance: A future model has exact setup steps, success checks, and a CPU fallback. | Model assists; Peter checks and owns the outcome | | `positioning.md` | Draft LinkedIn headline/About, GitHub bio, ORCID setup checklist, and two target-role narratives: applied scientist and scientific AI lead. Acceptance: Every experience claim is supported or marked for Peter to confirm. | Model assists; Peter checks and owns the outcome | | `study-notes.md` | Selected exact free resources; bounded lesson/exercise; separate solution; quiz and grading rubric; Peter's answers and gaps when executed | Model prepares; Peter learns | | `founder-paper.md` | Verified source and P11 digest; authentic question and connection sentence; access limitations | Model assists; Peter checks | | `branding-pack.md` | Wednesday note, Sunday build log, X adaptation, figure/caption/alt text and the week's special asset; each claim linked to real proof | Model drafts; Peter owns voice/public claims | | `opportunity-actions.md` | Qualified target/role, source/date, ladder stage, next action, message/interview/proposal draft and actual status | Model prepares; Peter owns external relationships | | `evidence.md` | Actual paths/URLs, versions, checks/metrics, preparation versus execution state and external receipts when applicable | Updated after each deliverable | | `review.md` | Checklist, learning assessment, gate status, shortfalls, next actions and carryover | Peter and reviewing model | During preparation, future measured tables get column definitions, input requirements and run instructions with PENDING status. During execution, replace pending values only with measured outputs. Do not create realistic-looking fake evidence. ## Branding and opportunity execution brief Branding: Evidence-first positioning, setup announcement, and a 30-second career introduction; distinguish current competence from learning objectives. Opportunity action: Create the private target universe from v4 and GridX; record hypothesis status and separate employers, scientists, recruiters, and clients. Use [career asset contracts](../../CAREER-ASSETS.md). Publish at most the agreed cadence; one figure and one supported number or admitted failure can support multiple drafts. In long-form weeks, prepare a 1,500–2,500-word article from existing evidence within the build/buffer allocation. In release/demo weeks, prepare a 60-second script: problem, input, command/action, result, limitation and proof link. Verify individuals, jobs and affiliations at execution time. The [GridX list](../../../GridX%20Startups.csv) and v4 company map are research seeds, not current facts. Do not reveal named company weaknesses or employer/client confidential information. Keep drafted/sent/replied/booked/held statuses separate. The planning request alone does not authorize external messages or publication; honor explicit authorization in the execution session. ## Quality risks and week-specific constraints Do not install an entire infrastructure stack to start learning. Verify Peter's preferred public name and experience claims; dates stay relative until a start Monday is chosen. Apply the root scientific evidence contract: provenance; meaningful independent splits; no future-data leakage; baseline comparison; actual denominators/uncertainty; failed cases; human review where required. State whether data are simulated, public experimental, synthetic or partner-provided. Keep source gates intact, and log scope/time conflicts in review. Missing people, money, access or results must not be replaced with invented evidence. Reduce optional polish first. A specific essential external dependency stays pending while independent preparation continues. ## Completion and gate review This is an enabling week. Its deliverables feed the next scheduled gate: 4. Complete the acceptance checklist below; do not promote reputation from a draft. - [ ] Monday artifact satisfies: Five next actions and an evidence-backed skills baseline exist. - [ ] Wednesday artifact satisfies: A future model has exact setup steps, success checks, and a CPU fallback. - [ ] Friday artifact satisfies: Every experience claim is supported or marked for Peter to confirm. - [ ] Study pack is prepared; Peter's actual learning/quiz result is recorded separately. - [ ] Branding and opportunity drafts use supported claims and the correct external-action state. - [ ] Reproduction or document checks are recorded with file/version references. - [ ] This week's special gate, if any, has real evidence or remains explicitly pending. - [ ] Review, root progress/log and the next physical action are updated. ## Minimum viable week and recovery Source-preserving minimum: the `cockpit` repo with `TODAY.md` filled for Monday. Operational first step if stalled: open `profile-baseline.md`, write the required inputs and produce the smallest checkable example in ten minutes. If a more urgent missing gate dependency controls the week, use the source minimum above. If the full week does not fit, use [P14](../../../LABLOOP-Master-Plan-v6.md#part-8--the-prompt-pack-copy-paste-fill-the-brackets): retain one gate-critical deliverable and one directly supporting study exercise; record what is skipped versus moved. Do not mark the original full gate passed merely because the minimum was completed. After a missed week, reforecast from actual evidence and avoid a second unexamined lost week. ## Handoff to the next model In review, state exactly what exists, what was verified, what Peter can now explain, which external events remain pending, where the canonical code/data live, and the next file/function or draft paragraph to touch. Link each fact to evidence. Carry scientific assumptions, split definitions and rights constraints forward explicitly. ## Ready-to-copy model prompt ```text Prepare Week 00 of this LABLOOP execution plan. Read execution-plan/specs.md, execution-plan/DECISIONS.md, execution-plan/GATES.md and execution-plan/weeks/week-00-cockpit-and-positioning/specs.md, commitment.md, evidence.md and review.md. Read prior prerequisite reviews and inspect actual repository/data state. Use v5 as the governing sequence, the v6 Week 00 chapter (LABLOOP-Master-Plan-v6.md) as the deeper walkthrough, and v4 only for retained details. Produce the full local preparation pack and the exact week-specific files named in the artifact table. Give me a bounded lesson with exercises/answer key, daily physical actions, technical runbook or draft, branding drafts and career/commercial actions. Keep the total to 600 minutes. Separate prepared artifacts from measured results and my learning completion. Verify sources and do not invent metrics, citations, papers, people or outcomes. Do not execute external communications, publication or spending unless the current session already authorizes the specific action. Finish by updating evidence/review and TODAY with the next physical action. ``` ## Preserved original v5 weekly brief v6 reproduces this brief unchanged inside [v6 · Week 0 · Cockpit and positioning](../../../LABLOOP-Master-Plan-v6.md#week-0--cockpit-and-positioning). The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md. ### Week 0 · Cockpit and positioning - **Goal:** everything exists and is empty, in the right place. - **Build:** [ ] `cockpit` repo with the five files; paste Part 6 and 7 into `PROGRESS.md`. [ ] `labloop-notes`, `batchlens`, `fermlit` repos with README skeletons. [ ] Local environment (5.3). [ ] LinkedIn headline and About (Part 9.1). [ ] NotebookLM notebooks created. - **Tue/Thu:** none. Read Part 0 twice. - **Sun:** L-Sun post 0: "40 weeks from applied-AI engineer to published AI scientist for biotech, in public, at 10 h/week. First: a fermentation in 80 lines." Write the six `TODAY.md` lines for week 1. - **Only one thing:** the `cockpit` repo with `TODAY.md` filled for Monday.