Journal and joss submissions

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: Select one suitable journal each for Papers 1 and 2; check current scope, fees, author instructions and prior-publication policy.
• Public/profile priority: Draft a submission-process note and update the CV with submitted status only.
• Career/relationship/commercial priority: Prepare evidence-oriented follow-ups to relevant hiring contacts and public software users; request concrete reuse feedback.

Read v6 · Week 36 · GATE 36: journal + JOSS before Monday. It expands this week's one-row v5 brief into daily build steps 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.

Act VIII · Threads: FL, BL, R · GATE 36

Where this week sits. - ← From: Papers 1-2 (weeks 16, 20), batchlens releases (weeks 4, 8, 17). - → Feeds: week 40 (L5 path), your academic credibility for years; JOSS acceptance can arrive within weeks. - ⟳ Returns in: revisions over the next months (plan 2 hours per revision round in Saturday blocks).

Goals. - 🎯 This week: two journal submissions (one each for Paper 1 and 2) and one JOSS submission, all logged. - 🏁 This gate (36): submissions logged. - 🌟 Final: L5 reviewed and invited.

The plan (from v5 Part 7, expanded; gate and output unchanged).

v5 row: 36 | GATE 36: journal + JOSS | Journal author guides | Paper 1 to Scientific Data or a bioprocess journal; Paper 2 to Computers & Chemical Engineering or Biotechnology and Bioengineering (pick one each); JOSS submission for batchlens | Submissions logged - Goal: three submissions in the system. - Tue (study): author guides for the chosen journals; JOSS review criteria. - Build: Mon: Paper 1 reformatted as a Scientific Data Data Descriptor (or a bioprocess journal's format); submitted. Wed: Paper 2 reformatted for Computers & Chemical Engineering or Biotechnology and Bioengineering; cover letter; submitted. Fri: JOSS paper.md (≤ 1,000 words), statement of need, tests, docs, community guidelines; submitted. Log all three in PUBLICATIONS.csv. - Sun: L-Sun "Three submissions: what changes between a preprint and a journal paper". - Gate 36 passes when: two journal submissions and one JOSS submission are logged. - Only one thing: the JOSS submission (fastest review, most useful for instruments).

Mentor check. "My work is in peer review at three venues, and I know what each reviewer will look for."

• Week 16: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 20: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 32: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Week 35: inspect its actual evidence and review; source/code artifacts must exist before the dependent task begins.
• Read commitment, evidence, review and the current root TODAY/PROGRESS/QUESTIONS files.
• Read this week's chapter, v6 · Week 36 · GATE 36: journal + JOSS, then the standing sections: Part 0 · how to use the document, Part 3 · the scientific thesis, Part 4 · curriculum, Part 8 · the prompt pack and Part 9 · branding and endorsement. The same sections exist in the v5 master, which remains the governing sequence; v6 reproduces them and adds depth. Retained commercial/instrument details come from v4.
• 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.

Biology/domain unit

Material: Read the selected journals' current author guides and JOSS scope/review requirements; list fees, article types and software readiness gaps.

Produce: One concise applied note, a worked decision/example and unresolved questions.

Understanding check: The note directly supports this week's experiment, collaboration, delivery or career action.

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: Perform manuscript/metadata checks and software reproduction; no new course. Read related work only to close a submission requirement.

Produce: One concise applied note, a worked decision/example and unresolved questions.

Understanding check: The note directly supports this week's experiment, collaboration, delivery or career action.

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

Select one verified founder/scientific-lead paper relevant to this week's domain. Use P11; save the question, method, numerical result with context, data workflow, three author questions and one connection sentence in founder-paper.md. Keep abstract-only access limitations explicit. On source weeks with no study, prioritize the commercial/submission task and log any skipped digest.

Branding: Draft a submission-process note and update the CV with submitted status only.

Opportunity action: Prepare evidence-oriented follow-ups to relevant hiring contacts and public software users; request concrete reuse feedback.

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.

JOSS eligibility is not automatic for a small tool. Week 36 seeks submissions, not acceptance; no L5 promotion from submission receipts alone.

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.

This is Gate 36: Journal and software submissions.

Required proof: Two journal submission receipts (one each for Papers 1 and 2) and one eligible JOSS submission receipt.

Reputation interpretation: L5 path; submission is not acceptance. Record target, forecast, actual date and evidence link. The original gate stays incomplete until the required external proof exists.

• Monday artifact satisfies: Prepare the two journal packages and JOSS readiness assessment; submit eligible packages when authorized and log any unmet gate item.
• Wednesday artifact satisfies: Actual receipts are tracked independently from drafts and acceptance.
• Friday artifact satisfies: Submit only if eligible; otherwise document the gaps without calling a DOI peer review.
• 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.

Expanded minimum derived from the source goal: Prepare the two journal packages and JOSS readiness assessment; submit eligible packages when authorized and log any unmet gate item.

Operational first step if stalled: open journal-fit-matrix.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.

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.

Prepare Week 36 of this LABLOOP execution plan.
Read execution-plan/specs.md, execution-plan/DECISIONS.md,
execution-plan/GATES.md and
execution-plan/weeks/week-36-journal-and-joss-submissions/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 36 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.

v6 expands this row into a full brief, with the gate and output unchanged, inside v6 · Week 36 · GATE 36: journal + JOSS. The following is source planning text, not a claim of completion. Apply the explicit evidence corrections in this specification and DECISIONS.md.