OPEN-SOURCE · SCIENTIFIC WRITING WORKFLOW

Build the argument
before polishing
the prose.

A modular workflow for Codex and Claude Code that connects scientific claims, evidence, figures, writing, citations and reviewer responses.

From first draft to submission. Built for life-science and computational-methods manuscripts—at the scale your task needs.

27specialized skills
19manuscript essentials
01connected workflow
EVIDENCE-AWARE REVISIONTEACHING EXAMPLE
Original claimUnsupported conclusion

These results demonstrate that the treatment improves both marker expression and survival.

Reference revision

The treatment therefore increased marker expression without a demonstrated survival benefit.

THE NUMBERS STAYn = 12
+18%Marker expression · Fig. 1a
95% CI 10–26%
+1 ppSurvival · Fig. 1b
95% CI −3 to 5 pp

Synthetic example · illustrative reference, not a live model run.

Your research. Your evidence. A clearer manuscript.

Start with paper-workflowNo need to memorize every skill.

01 /BEYOND SENTENCE POLISH

Scientific writing starts before the sentence.

A smoother sentence is not always a stronger paper. Connect the claim, the evidence and the job each section needs to do.

Claims before style

Build the argument before refining its wording. Do not make an unsupported conclusion sound more convincing.

Follow the logic →

Preserve what matters

Keep measured values, independent units, negative results and necessary conditions intact throughout the edit.

See the difference →

Each section has a job

Give the Abstract, Results and Discussion distinct roles, while keeping their scientific claims aligned.

Explore section contracts →
02 /ONE CONNECTED WORKFLOW

Start where your manuscript needs help.

Enter at any stage. A paragraph edit does not require a whole-paper pipeline.

Build the evidence chain before improving the sentences.

Your input

Main claims, result tables and the current manuscript.

Your outcome

A coherent argument and the gaps that need attention.

StatisticsCitation supportData availability
Checks throughout, not just at the end.
04 /SEE WHAT CHANGES

Same evidence. A more accurate claim.

Not stronger-sounding language. A conclusion the supplied results can actually support.

SYNTHETIC TEACHING EXAMPLE
01 / Original draftUnsupported claim

These results demonstrate that the treatment improves both marker expression and survival.

02 / Reference revisionEvidence-bounded

The treatment therefore increased marker expression without a demonstrated survival benefit.

What the supplied evidence actually says

  • The independent unit is a culture: 12 independent cultures, not 12 cells.
  • Marker expression: increase of 18%, 95% CI 10–26%; Fig. 1a.
  • Survival: change of 1 percentage point, 95% CI −3 to 5; Fig. 1b.
  • There is no demonstrated survival improvement. No P value or mechanism is supplied.

An illustrative reference revision, not a recorded live agent execution or a comparative benchmark. “No demonstrated survival benefit” does not mean “no effect.”

Follow the complete example Keep the measurement. Correct the interpretation.
THE SECTION CONTRACTS

Every section has a scientific job.

An Abstract is not a shortened Results section. A Discussion is not a list of limitations. Make each part do the work the paper needs.

Explore the section contracts ↗

Guidance informed by a sample of 28 method papers; not an official journal format. The journal’s current instructions take precedence.

The whole argument. Not every result.

Purpose
Put the reader in front of their problem by the second sentence, then connect the gap, approach, main finding and implication in terms a broad peer can follow.
Depends on
Settled Results, the central answer and the Introduction’s gap.
A common mistake
Adding a stronger headline claim than the Results support.
Evidence & figuresResultsDiscussionIntroductionAbstractTitle
06 /MAKE YOUR FIRST REVISION

Bring the workflow to your agent.

Use your existing research environment. Install a profile, choose the entry skill and start with a small, self-contained example.

01Choose an agent02Install a profile03Revise one paragraph
YOUR FIRST REQUESTpaper-workflow
› Use paper-workflow. Revise the Results paragraph using the supplied evidence.

Preserve measured values and figure references. Save a revised copy and explain the material changes.

Useful by design. Clear about its boundaries.

Skills provide instructions and helper scripts—not experimental evidence, a built-in editor or a guarantee of publication.

Your explicit scope and the target journal’s requirements come first. Unavailable tools and unchecked sources remain visible. Compatibility ↗