A single, portable LaTeX repository for computational-neuroscience manuscripts that carries a paper through the whole publication lifecycle: draft → submission → peer review → tracked revision → camera-ready.
It is opinionated about structure and compliance, not about content: standardized typography, canonical sections with per-journal overrides, machine-readable journal limits, editorial correspondence, a self-contained rebuttal format, and journal-standard change tracking.
make # build main.pdf (draft mode)
make submission # review-ready manuscript (line numbers, figures at end)
make check JOURNAL=elife # check word/figure/abstract limits for a journal
git tag submitted # tag the version you submit
make diff OLD=submitted # after revising: marked-up diff.pdf
make rebuttal # build the response-to-reviewers letter
make cover # build the cover letterFull manual: INSTRUCTIONS.md.
| Path | Purpose |
|---|---|
cnnclab.cls |
Document class — typography + draft/submission/review/final options. |
sections/ |
Canonical content (write here). |
variants/<journal>/ |
Override-only per-journal sections. |
journals/<journal>.md |
Machine-readable journal limits (drives make check). |
correspondence/cover-letter.tex |
Letter to the editor. |
review/response-to-reviewers.tex |
Rebuttal (\point/\reply, tcolorbox boxes). |
scripts/check-limits.py |
Word/figure/reference limit checker (reports only). |
templates/main-elife.tex |
Worked example wiring a variant + journal profile. |
ADAPTATION.md |
Guardrails for the optional formatting agent. |
The Makefile is a convenience, not a requirement — the template is Overleaf-native. Import the
repo (New Project → Import from GitHub), set the main document (main.tex, or
templates/main-elife.tex for the eLife variant), and compile with pdfLaTeX; Overleaf runs biber
automatically. Switch modes by editing \documentclass[submission]{cnnclab} directly. See
INSTRUCTIONS.md §1b. Every document compiles from the project root with a bare
latexmk — the same invocation Overleaf uses — and CI enforces it.
TeX Live 2023+ (full), Git, Python 3.11+. Everything used ships with a standard TeX Live install —
no extra CTAN fetches. Optional texcount for sharper word counts.
Derived from the Henriques Lab LaTeX template by Ricardo Henriques. Original and derivative are both MIT-licensed — see LICENSE. Adaptation (publication-lifecycle tooling: journal profiles, limit checker, rebuttal format, change-tracking targets) by the CNNC Lab.