Scolyer: A development environment for scientific papers.

Every journal has its own rules, spread across an author guide that is easy to misread and tedious to re-check, and a manuscript can come back unreviewed for a missing statement or a summary ten words over the limit. Pick the journal you are submitting to and Scolyer keeps a live checklist beside the manuscript, updated as you type.

• Word, figure, table and reference limits, counted per section and against the journal's numbers
• Required statements: data availability, ethics, funding, competing interests, author contributions/CRediT
• Section order, keywords, title length and citation style
• Reporting guidelines such as CONSORT, ARRIVE and PRISMA, plus statistics reporting, accession numbers and nomenclature
• Ensures abbreviations are managed

Each checklist item jumps to the passage it is about, so problems are identified before submission instead of after a note from the editorial office. Rules for 70 journals are read from their own author guides, and grant proposals and theses follow their sponsors' formats. The checklist only advises; nothing is rewritten for you.

When a paper is rejected and you move on to the next journal, choose the new target and Scolyer shows what has to change. The mechanical changes are prepared as edits you review and accept one by one: citation style, section names and order, and the statements the new journal requires. Anything that needs real rewriting, such as an abstract now over the limit, is pointed out and left to you.

Passing a draft around by email leaves a folder of files called final, final_v2 and final_revised, and no way to tell what changed, who changed it, or what the journal actually received. In Scolyer the manuscript has one history that every co-author works from.

Each co-author writes in their own copy. When they are ready, they send their changes for review, and the others see exactly which sentences changed, with a note explaining why.

• Accept a proposal whole, tick only the sentences you agree with, or send it back with comments anchored to the text
• Conflicting edits to the same sentence are laid side by side for you to choose
• Compare any two versions sentence by sentence, and restore a paragraph, a section or the whole paper
• Submissions and revisions are marked as milestones, so you can always see the manuscript exactly as the journal received it
• See who drafted and who revised each section, for the author-contributions statement

The manuscript is plain text in a Git repository, so nothing is locked into a format you can't open without the app.

One retracted paper, or a preprint cited long after its journal version appeared, undermines a manuscript, and checking sixty references by hand is a day nobody budgets for. Bring your existing library from any reference manager as BibTeX, RIS or XML, or add a paper by DOI, PubMed ID, arXiv ID or ISBN. Every entry is then checked against the published record. If one of your co-authors uses AI and falsely cites a paper that doesn't exist, this will help catch that.

• Titles, authors and years compared with the publisher's record
• Retracted papers and unresolvable DOIs flagged
• Cited preprints with a journal version found, and swapped in one click
• Citations formatted in the target journal's style, switchable at any time

An optional assistant, using your own API key, finds sentences that need a citation and proposes candidates with reasons. You decide which to cite.

A paper points to dozens of records held elsewhere: cited articles, deposited datasets, registered trials, antibodies, compounds and the authors' institutions. Each identifier is a chance for a typo or a placeholder left from drafting. Scolyer looks them up in the public databases where they live, so a broken link is caught while you write instead of by a reviewer.

• Add a reference by PubMed ID, PMC ID, DOI, arXiv ID or ISBN, and search OpenAlex, Europe PMC and Semantic Scholar for papers to cite
• Match each affiliation to its ROR identifier, and sign in with ORCID to put a verified iD in the author list
• Accession numbers checked against GEO, SRA, ENA, PDB, UniProt, PRIDE, ClinicalTrials.gov, PROSPERO, Addgene and more
• RRIDs resolved through SciCrunch, and resources that need one flagged
• Compound names looked up in PubChem for formula, weight and CAS number, with structures ready to insert as figures
• Zenodo deposits tracked, with the Data Availability statement kept in step

Every connection is read-only. Only the identifier or search term is sent, never the manuscript.

A figure made by hand can't be remade when a reviewer asks for one more sample or the journal wants it narrower; the clicks that produced it are gone. Choose a data file, a plot type and the target journal, and Scolyer writes a Python script that draws the figure at the journal's widths, font sizes and resolution. The script is saved with the manuscript, so the figure can be re-drawn from the data at any time. Python and the plotting libraries come with the app. Only column names and types are shared with the assistant, never your data points.

• Ask for changes in plain language, with every revision kept and reversible
• Edit the script by hand whenever you prefer
• Each script is audited: no network, no shell, no writes besides the image
• Preview the figure as readers with colour-vision deficiencies will see it

Submission day usually means an evening of renaming figure files, stripping names for a blinded copy and retyping the abstract into a web form. One export produces everything the submission system asks for, formatted in the journal's typography.

• The manuscript as .docx and PDF, a blinded copy and a separate title page
• Figures renamed and numbered the way the journal expects, and the supplement as its own file
• Every field of the online submission form prefilled, with a copy button for each
• When revisions come back: a point-by-point response letter and a copy with changes highlighted

Unpublished results are among a lab's most sensitive data, and most writing tools keep them on someone else's server. Scolyer runs no server and has no account. The paper lives in a folder on your computer and, if you choose to collaborate, in a private GitHub or GitLab repository your lab controls.

Everything that leaves the machine, listed