Read the week in plain language, refresh the foundations, follow each challenge step by step, and check what evidence to keep. Includes worked examples, answer keys and prompts for visual study resources.
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.
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.
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.
Checklist, learning assessment, gate status, shortfalls, next actions and carryover
Notes on artifact states
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.
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.
▦
600 MINUTES MAXIMUM
Seven-day plan
Monday90 min
Target. 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.
Target. 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.
Target. 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.
Target. 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.
Target. 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.
Target. 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.
Target. 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.
Block ritual: read your next action → start the 90-min timer → open one file. Close: write tomorrow's action and one log line.
Feels pointless? Does today's Done when need it? No → skip it and log it. Yes → let AI do the boring part, you review. Still stuck → the smallest version in 25 minutes. Pulled into a rabbit hole? Write it in Parked thoughts and save it for Saturday.
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.
Week 00 is setup. Tuesday/Thursday are orientation/setup blocks; no mandatory science coursework.
◎
WHAT TO WATCH, READ AND RUN
Materials for this week
Before a long expedition, good expedition leaders spend a whole day on something that looks boring: packing. Every item has a pocket, every pocket has a label, and the map is on top. They do this because on day 20, exhausted and cold, they will not have the willpower to search for the compass. Week 0 is packing day. You are not learning biology yet and you are not writing a simulator yet. You are building the cockpi…
In the plan's running order: each card says which block it belongs to and what has to come
before it. The seven-day plan lists the same cards under the day that owns them.
Any block this week — the plan names no day
9 · 280 min total
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
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
Sunday, before writing post 0
· after Barbara Oakley · "Learning how to learn"
· Only if you prefer voice to text — it replaces R1, it does not add to it. Play at 1.25× while packing the cockpit
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.
02
READ FIRST
Deeper walkthrough (v6)
Read v6 · 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, NotebookLM protocol, chapter anatomy. 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.
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."
03
OPEN WHEN NEEDED
Required inputs and dependency check
No earlier execution week. Read the supplied v5/v4 documents and establish the actual starting baseline.
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; explicitly record inaccessible resources.
04
READ FIRST
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: 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.
05
OPEN WHEN NEEDED
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. 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 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.
06
OPEN WHEN NEEDED
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.
07
READ FIRST
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.
08
READ FIRST
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: 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.
09
OPEN WHEN NEEDED
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.
10
OPEN WHEN NEEDED
Ready-to-copy model prompt
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.
11
OPEN WHEN NEEDED
Preserved original v5 weekly brief
v6 reproduces this brief unchanged inside v6 · 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.
State: UNCONFIRMED. Owner: Peter Ciancaglini. Specification
Start date: not set. End date: not set. Available hours: confirm (planned ceiling 10).
Primary outcome: cockpit and positioning.
Minimum that keeps the next gate alive: the cockpit repo with TODAY.md filled for Monday.
Deliverables to commit
☐ profile-baseline.md: Five next actions and an evidence-backed skills baseline exist.
☐ environment-checklist.md: A future model has exact setup steps, success checks, and a CPU fallback.
☐ positioning.md: Every experience claim is supported or marked for Peter to confirm.
☐ Bounded learning exercise and personal teach-back.
☐ Evidence-backed branding and opportunity pack.
☐ Sunday review and next physical action.
Proposed calendar
Day
Minutes
Physical action / outcome
Actual slot
Done
Mon
90
Create the five cockpit files and record a truthful baseline of Python, statistics, biology, portfolio links, and available time.
Not set
☐
Tue
90
A five-line account of the operating rules and the next physical action.
Not set
☐
Wed
90
Specify repository skeletons, environment smoke checks, offline fake mode, secrets handling, and local hardware inventory. Last ten minutes: optional note.
Not set
☐
Thu
90
A five-line account of the operating rules and the next physical action. Include relevant founder-paper work within this block.
Not set
☐
Fri
90
Draft LinkedIn headline/About, GitHub bio, ORCID setup checklist, and two target-role narratives: applied scientist and scientific AI lead.
Not set
☐
Sat
90
Resolve critical spillover; long-form draft if due; sandbox only if done.
Not set
☐
Sun
60
Build log, evidence, gap review, next actions.
Not set
☐
Dependency and capacity check
Missing essential inputs: not yet inspected.
Human/external dependency, owner and expected date: not yet inspected.
Week-specific constraint: 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.
Existing session authorization for external actions or spending: not assessed; local planning only at scaffold creation.
Scope to cut first: optional polish/additional examples; preserve scientific validity.
If the forecast exceeds available time: record a concrete reduced scope or revised delivery proposal before committing.
Peter's commitment / adjustments: pending.
Reviewing model and date: pending.
Execution state: COMPLETED. Specification
This file is a blank register with planned artifact names; none of the rows prove completion.
Item
Path / URL / version
State
Verification / actual result
Verified by / date
profile-baseline.md
Not created
NOT_STARTED
Pending: Five next actions and an evidence-backed skills baseline exist.
—
environment-checklist.md
Not created
NOT_STARTED
Pending: A future model has exact setup steps, success checks, and a CPU fallback.
—
positioning.md
Not created
NOT_STARTED
Pending: Every experience claim is supported or marked for Peter to confirm.
—
Learning exercise / Peter's quiz
Not created
NOT_STARTED
Peter's actual answers required
—
Founder paper digest
Not created
NOT_STARTED
Source/content and access checked
—
Branding pack
Not created
NOT_STARTED
Claims audited; drafted/public status distinct
—
Opportunity actions
Not created
NOT_STARTED
Drafted/sent/replied/booked/held distinct
—
Reproduction and scientific measurements
Question / metric
Dataset, N and unit
Split / seed / config
Command or verification method
Output path and measured value
Uncertainty / limitation
External events, when authorized and actually performed
Date
Action / counterpart
Receipt or private reference
State
Next action / date
Actual learning and decisions
Peter's teach-back / quiz score: not assessed.
Scientific assumptions and deviations: none recorded yet.
Budget allocated / spent: not assessed / no spend recorded.
Missing evidence and responsible owner: pending inspection.
Do not put API keys, source full texts with restricted rights, client data or invoice personal details in a public version of this register. Keep private evidence references private.
☐ Five next actions and an evidence-backed skills baseline exist. Evidence: pending.
☐ A future model has exact setup steps, success checks, and a CPU fallback. Evidence: pending.
☐ Every experience claim is supported or marked for Peter to confirm. Evidence: pending.
☐ Learning assessed from Peter's actual answers. Evidence: pending.
☐ Branding/opportunity states recorded correctly. Evidence: pending.
Learning and outcome
What Peter can explain or reproduce now: not assessed.
Quiz / teach-back gaps: not assessed.
Measured result and limitations: pending.
Best evidence link for a scientist/recruiter/buyer: pending.
What failed or changed, and why: pending.
Gate and capacity
Gate requirement: No standalone gate; check this week's acceptance criteria and next gate dependencies.
Gate status: NOT_STARTED.
Original target week: See next gate in specs.
Actual completion date / forecast: not set.
Missing external evidence: pending inspection.
Blocks completed / 7: not recorded.
Days with commits / 7: not recorded.
Sunday build log / optional Wednesday note: not recorded.
Founder conversations cumulative: not recorded.
Earned evidence level and proof: not assessed.
Consecutive lost weeks: not assessed.
Week-specific risk to revisit: 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.
Decision and next-model handoff
Continue / recover / blocked: not decided.
Retain as the minimum: the cockpit repo with TODAY.md filled for Monday.
Skipped permanently with reason: none recorded.
Carryover with owner, dependency and target week: none recorded.
Canonical repository paths and versions: pending.
Data permissions, split definitions or assumptions to preserve: pending.
External action authorization that still applies: not assessed.
Next physical action, exact file/function/paragraph: pending.
Updates to root PROGRESS / LOG / TODAY completed: ☐