Docs · Writing and submission
The manuscript editor
A collaborative editor built for papers: templates, tracked changes, object citations, figures, tables, equations, comments, versions and durable authorship — with your own AI agent writing into it over MCP.
Creating a manuscript
- Manuscripts tab → New manuscript.
- Pick a template: original research (IMRaD), systematic review, meta-analysis, case report, protocol, letter, review, thesis chapter, grant section and more. Templates seed the sections and the reporting checklist.
- Or import a Word document: headings, lists, tables, figures and numbered citations are recovered and re-linked to works in the project where possible.
Front matter
Title, running title, authors with CRediT roles and affiliations, structured or free abstract, keywords, disclosures (funding, conflicts, ethics, data availability), target journal with word and figure limits, page setup and citation style live in the Front matter panel and are rendered by exports and checked by the reporting checks.
Writing together
- Real-time collaboration: everyone sees everyone's cursor; nothing is lost on conflicting edits.
- Tracked changes with author and time for every insertion and deletion; accept or reject one by one or per author. Turn tracking off for your own drafting.
- Comments anchored to text with replies, resolution and @mentions; suggested edits from reviewers.
- Slash menu (/) for headings, lists, tables, figures, equations, page breaks and captions (AI actions join it where an administrator has switched platform AI on).
- Find and replace with case, whole-word and regular expressions; deleted text never matches.
Citations, figures, tables and equations
Citations are objects pointing to works in the project; the reference list and inline labels are rendered from those records in the chosen style. Figures carry captions, widths and alignment; tables have borders, shading, alignment, sorting and text-to-table. Equations are LaTeX, inline or display, rendered live.
Side panels
| Panel | Use |
|---|---|
| Outline | Headings; drag to reorder sections |
| Front matter | Metadata described above |
| Statistics | Words, characters, readability, estimated pages against the journal limit |
| Assistant | What your connected AI agent is doing in this manuscript, and how to connect one; its text arrives as tracked changes |
| Changes | Every pending change with accept and reject |
| Comments | Threads with resolution |
| Authors | Who wrote what: colour the manuscript by author and see every contributor's share |
| Checks | Reporting and house-style checks |
| Versions | Named snapshots, compare and restore |
| Notes | Scratch notes for this manuscript |
Versions
Save a named version before big edits or a submission. Compare any two versions as a diff, or restore one (the current state is saved first, so nothing is lost).
Export
Word (with revision marks and comments), PDF, HTML, Markdown, LaTeX (with .bib and figures) and PowerPoint for talks. Exports are blocked while a citation points to an unknown or retracted work or a number points to deleted evidence, unless you override with a reason. An AI-use statement is appended: composed from the record where the platform's own AI was used, and otherwise a line for you to complete with the agent and model you used.
Page view and layout
The editor lays the manuscript out as real pages: paper size (A4, US Letter, US Legal, A5, B5), orientation, margins, a header band and a footer band with page numbers, exactly as the export will print them. The Layout tab holds paper size, orientation, margin presets (Normal, Narrow, Moderate, Wide) or custom margins, header and footer text (use {page}, {pages}, {title} and {date}), the page-number position, line numbers (continuous or restarting on each page) and the switch between Page view and Web layout (one continuous column, handy on small screens). The status bar shows the current page; click it to jump to a page.
A hard page break (Insert → Page break) ends the page at that point in both the editor and the export.
The ribbon
On large screens the editor shows a ribbon. Home holds the clipboard, styles, fonts, formatting, paragraph controls, find and comments. Insert holds tables (a size picker or a custom size), figures from a file or an address, equations, quotes from PDFs, footnotes, links, captions, page breaks, dividers and code. Table appears while the caret is inside a table. Layout holds paper size, orientation, margins, headers and footers and line numbers. References holds citations, the bibliography and the citation style. Review holds the tracking mode, accept and reject (at the cursor or for the whole document), show-markup filters for insertions, deletions and formatting, comments, statistics, checks and versions. View holds the panels, focus mode, zoom, fit width, typewriter scrolling, page setup and the shortcut list. Phones and tablets keep the compact toolbar.
There is one more ribbon tab, Assistant, holding the AI writing actions — and it appears only where an administrator has switched the platform's own AI on. In the default mode you ask your connected agent for the same edits and they arrive as tracked changes.
Right-click anywhere in the text: the menu offers exactly what applies to the selection, the paragraph, the table, the figure or the tracked change under the pointer, including Accept and Reject. Its Assistant section — rephrase and the evidence checks — is there only where platform AI is switched on.
Figures and pictures
- Insert from a file, by drag-and-drop or paste, or from a web address; every figure gets a numbered caption and alt text for accessibility and exports.
- Select a figure for the picture tools: align left, centre or right; wrap text on either side (the picture floats and the text flows beside it); size presets (a third, half, three quarters, full width) or drag the side handles; rotate in 90° steps; crop by dragging the edge handles, with Reset crop; replace the image while keeping caption and settings; delete.
- Figures are numbered automatically in reading order, and cross-references in captions follow when you move them.
Inline pictures and the Images panel
- Insert → Inline places a small picture in the line of text (a symbol, a logo, a tiny chart) from a file or a web address; select it for size presets, drag-resize, alt text, aspect lock, or Convert to figure when it deserves a caption.
- The Images panel (Insert → Images, or the Images tab on the left) lists every figure and inline picture with a thumbnail, caption and alt text; jump to one, fix alt text in place, or remove it. Pictures without alt text are counted so accessibility and journal requirements are met before submission.
Tables
- Border presets (grid, horizontal rules, three-line journal style, none), banded rows, header row and header column, density (compact, normal, relaxed), width as a percentage of the text column and placement left, centre or right.
- Cell shading, horizontal and vertical alignment; per-column alignment and number formats (integer, one to three decimals, percent, scientific) from Table properties.
- Rows and columns, merge and split cells, split a table before a row, merge with the table below, convert selected text to a table and a table back to text, sort by a column, distribute columns evenly, add a totals row.
- Captions with automatic numbering and a description read by screen readers and carried into exports.
Table of contents and abbreviations
- References → Contents inserts a table of contents that follows the headings as you write: levels 1–3 by default, each entry a link to its heading, page numbers in page view. It exports as a plain list.
- References → Abbreviations opens the abbreviations panel: every abbreviation with its expansion, number of uses and issues — used before it is defined, never defined, defined twice, two different expansions, defined but never used. Jump to the definition or the first use, Define at first use to move the expansion where it belongs, Ignore tokens that are not abbreviations, Copy list or Insert list as a table. Definitions are recognised as “Full term (ABBR)” or “ABBR (full term)” when the letters fit; the reference list is skipped.
Table painter and ruler
- Table → Painter copies the current cell's shading and alignment; every cell you click afterwards receives them, until Esc or a second click on Painter.
- Table → Ruler shows a ruler above the table with each column's width in millimetres and its share of the table; drag a marker to resize the two columns around it. Widths are stored with the table and respected by exports.
Related
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