Guide: Publishing & Formatting

You have a manuscript. Now comes the part nobody warned you about in grad school: choosing where to send it, wrestling it into that publisher’s document class, and making sure every DOI still resolves. These five skills handle the endgame, and they never invent a journal, a deadline, or a citation to fill a gap.

journal-finder

Recommends best-fit journals with a ranked shortlist and, crucially, a fit rationale for each one. Fit is argued from evidence rather than prestige: the recommendation names which venue published your manuscript’s actual predecessors or benchmark. For the running self-supervised-ECG example, IEEE JBHI ranks first because the PTB-XL benchmark itself was published there (Strodthoff et al., 2021, https://doi.org/10.1109/jbhi.2020.3022989), with Computers in Biology and Medicine close behind as the home of the closest methodological predecessor (Mehari & Strodthoff, 2022, https://doi.org/10.1016/j.compbiomed.2021.105114). Volatile numbers like impact factor and APC are never fabricated; each is tagged for you to confirm at a named source with an access date.

Trigger it: “/researcher:find-journal”, “Recommend target journals for my paper”.

conference-finder

Finds peer-reviewed venues and reports each one’s format and typical timing. Because submission deadlines shift every cycle, exact dates are never invented: each venue gets its stable characteristics plus a flag to confirm the current CFP at the homepage. Fit is again grounded in real prior work, so Computing in Cardiology, CHIL, and ML4H surface for the ECG example because that community actually publishes ECG self-supervised learning there.

Trigger it: “/researcher:find-conference”, “Find conferences for this work with deadlines”.

journal-formatting

Auto-applies a publisher’s submission requirements to your manuscript: the right document class, citation style, required sections, and structure. The local journal database ships 16 profiles covering Elsevier (elsarticle), Springer (svjour3), IEEE (IEEEtran), ACM (acmart), Nature, Science, PLOS, and MDPI; anything outside it is looked up from the publisher’s own author guidelines. That means the correct scaffold, plus the fiddly bits publishers reject over: Elsevier Highlights and a Data Availability Statement, IEEE Index Terms, Nature’s Methods-after-references ordering, CRediT contributions.

Trigger it: “Format this for Elsevier”, “Apply IEEE submission requirements”.

word-output

Produces a Microsoft Word DOCX for the co-authors and journals that live in Word. What ships today is templates/word/build-docx.js (Node, built on the docx library): it generates a formatted DOCX with a title page, numbered headings, paragraphs, and lists from your sections/*.md files. Tracked changes, comments, and table emission are specified in templates/word/article-imrad.md but are not implemented yet; treat them as planned work, not a delivery option.

Trigger it: “Export to Word”, “Build a DOCX from my section files”.

citation-management

Maintains your library.bib across its whole lifecycle: import, validate, convert, audit. It validates DOIs against the source, detects retractions and corrections before you cite something embarrassing, converts between citation formats, syncs with Zotero, and imports Mendeley exports (BibTeX or RIS; Mendeley has no live sync). The one rule it will not bend: every entry originates from a real source, and an unresolvable DOI gets flagged rather than guessed into existence.

Trigger it: “Validate my bibliography”, “Sync my Zotero library”.

See it in action

The find-a-home recipe runs journal-finder and conference-finder end to end on the ECG example, and the examples/publishing/ folder has the full worked reports.