From your first check to submission.

Quick start

1. Open the application on a computer and choose your research field.
2. Select a journal, article type and submission stage. Read the available instructions and source links.
3. Under Your submission files, add your main manuscript, or paste its text. Separate files are optional.
4. Check the extracted text and section assignments, then select Check my manuscript.
5. Review all five result tabs. Resolve warnings, inspect checks that could not be performed, and rerun after changes.
6. Save a working package before leaving. Export a report or prepare a submission folder, then submit through the journal’s official portal.

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Choose your field and target

The seven modules share an analysis engine but have their own catalogues and version numbers. Choose a specialty, then use Check manuscript, Respond to reviewers or Change journal. Congress submissions have a separate workspace.

Select the precise article type and stage: initial submissions and revisions may have different requirements. Review journal information, verification notes and official source links. A missing rule is not a pass. You can adjust counting limits where offered; these become custom limits. Use the restore control to return to official values.

On a phone, use the catalogue for information. A computer is recommended for files, detailed results and exports.

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Import and check your files

Add the main manuscript and optional figures, tables or supplements. You can add files in several batches from different folders; check each file’s assigned role. Adding an attachment does not mean it has become the main manuscript.

Word (.docx) and plain text are the most straightforward manuscript inputs. PDF extraction depends on a readable text layer and may lose tables, formatting and superscript citations. Always inspect the extracted text. An image-only scan needs text extraction outside this tool.

Check the text attributed to each section and correct it when necessary. Review the detected reference list; you can edit it or reset it to the detected list. File counts distinguish mentions in the manuscript, imported files and your declarations. These are different sources of evidence.

Image format, file size and pixel dimensions do not establish print resolution or scientific quality. The tool does not guarantee anonymisation: inspect images and file metadata yourself. It is not a clinical image viewer.

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Read the results

• Overview: start with the main findings, checks performed, checks not performed and analysis limits.
• Requirements: review journal and article-type limits, counting details and available sources. Confirm requirements that are not automatically checkable.
• Numbers: inspect numerical consistency findings in context. These are prompts to review written numbers, not a validation of statistics or scientific conclusions.
• References: inspect the reference list and citation-related findings. Online lookup is optional and separate.
• Files: review the inventory and discrepancies between mentions, declarations and files actually added.

If you change the text, target or relevant inputs, run the checks again. A previous report does not describe the changed manuscript. Comparing up to three journals helps compare documented limits; it does not predict journal fit or acceptance.

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References and optional online lookup

Local reference checks do not require uploading your manuscript. The optional Crossref and PubMed lookup requires separate confirmation and sends reference entries to those services. Leave it off if you do not want those entries sent.

A reference not found online is not necessarily incorrect: books, guidelines, recent articles and records outside a service’s coverage may be absent. Verify matches and discrepancies against the original source. A successful match does not validate the scientific claim citing it.

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Prepare a congress submission

Choose the congress, edition and call for submissions. Enter or import your abstract text, add the requested title, author or graphics information, and select Check my text.

Review What to change and the items to confirm yourself. Applicable checks depend on documented rules for that call. Confirm deadlines, timezone, eligibility and the current edition on the official website.

Dated public-source update notes may appear when available. These notes do not themselves replace the analysis engine’s rules. Where available, catalogue JSON import/export supports local updates. The workspace prepares your abstract; it does not submit it to the congress.

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Respond to reviewers

Open Respond to reviewers. In Epidemiology, the visible shortcut opens this workspace directly. Select cohort, case-control, cross-sectional or registry to display manual review prompts. This choice is saved in the local revision file; no response or manuscript content is generated. Fill in the manuscript and revision details, then import or paste editor and reviewer comments. Review extracted requests or add them manually. Extracting requests again can replace the current request list.

Use the response matrix to organise each request, response, evidence, status and responsibility. Counts describe progress, not response quality. Compare initial and revised text where useful, and inspect points requiring verification.

Prepare the response letter and review it before export. The final journal letter requires completed, validated responses; a draft export is available earlier. Internal notes are excluded from the journal letter and ordinary matrix export; the explicitly labelled internal-notes export includes them.

Save the revision file locally to resume later. Check whether manuscript text is included. Even a file without manuscript text may contain confidential reviewer comments.

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Change journal

Choose the current or revised text, or import/paste another manuscript. Select the target journal, article type and stage. Review the action list, detailed comparison and submission-file inventory.

The tool does not assume that the manuscript complied with the original journal, or that an editorial transfer includes every file. Review custom limits and official instructions. Use the explicit action to check against the new journal in the main workspace, confirming any replacement of existing input.

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Save, export and resume

Save working package creates a local package for continuing your work; Open working package restores one. Save before closing or refreshing the page. A local save is not a cloud backup.

Prepare submission folder helps organise a local submission package. Inspect the contents, names and required files before using the journal’s portal. It does not complete declarations, obtain signatures or submit on your behalf.

Reports can be copied as text, downloaded as .txt, or printed/saved as PDF. Revision and journal-transfer workspaces offer their own exports. Use the appropriate export for your purpose; a report is not the original manuscript.

Email to co-authors prepares a local .eml draft. First save your report as PDF, then attach it in the dialog, enter recipients and edit the message. Download the draft and open it in a compatible mail app to review and send. For webmail, copy the message and attach the PDF manually. Nothing is sent by the site.

Author tools (TEST) offers check-snapshot comparison, a user-declared submission checklist, local favourites, calendar files with confirmed deadlines, instruction feedback and a fictional example in a separate tab. Save a baseline before changing your manuscript, rerun the checks and compare with identical target rules. Baselines last only for this tab session. Checklist declarations are included in your working package. In congress cards, click the star beside the congress name to add or remove a local favourite. Use Add deadline next to the deadline or Add congress to export the event dates, location and official link. Dates not available in a supported explicit format must be entered manually. Check official information before confirming. Calendar files do not synchronise later changes.

Packages and exports may contain manuscript text, attached files or reviewer comments. Store and share them accordingly. To print this guide, use the button above and choose your browser’s Save as PDF option if needed.

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Journal AI policies and disclosure

Consult the selected journal’s available AI-use policy and its official source. Rules vary by journal and use case. Where offered, the disclosure draft is a local drafting aid: review it against your actual use and the current journal instructions before including it.

Public-source catalogue updates are separate from manuscript analysis. The application does not send your manuscript or abstract to an online AI service.

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Collaboration — in development

The collaboration workspace is a local prototype. You can prepare project or expertise cards and export/import them for manual sharing. Cards are not published to other visitors, and there is no operational shared researcher directory or automatic matching service.

Do not include patient information in cards. Keep a local export of any work you wish to retain.

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Privacy and limits

Manuscript and abstract checks run in your browser. Manuscript and abstract content is not uploaded to our server or sent to AI. Optional reference lookup sends reference entries only after your separate confirmation.

The hosted site uses aggregate page and action counters, without document content, filenames, results, cookies or visitor identifiers. Counts are retained for 90 days. Do Not Track or Global Privacy Control disables this counting. Standard hosting logs are separate.

Checks assist preparation. They do not certify scientific validity, ethics compliance, anonymisation, statistical analysis, journal suitability or acceptance. The official journal or congress instructions remain authoritative.

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Troubleshooting and feedback

• Text missing or garbled: inspect the extraction, try .docx or plain text, and correct section assignments.
• A requirement is unavailable: consult the official instructions. Do not interpret missing information as compliance.
• An attachment seems absent: check its role and the imported-file inventory; a mention in the text is not an imported file.
• Results look outdated: rerun the checks after changing inputs.
• Want to leave and return: save your working package first; a browser refresh is not a save.

For feedback, contact contact@manuscriptcompass.com. Include the application/module version and the steps to reproduce the issue. Prefer a fictional or anonymised example over a confidential manuscript.

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