Finalize and export the protocol

Sample size

The Sample size section contains a Markdown editor to describe and justify the required number of subjects.

A built-in calculator (available in edit mode) lets you quickly estimate the sample size for three types of tests:

• Comparison of two proportions — you enter the expected proportions (p1 and p2)
• Comparison of two means — you enter the expected effect size
• Chi-squared test — you enter the expected effect size

For each test, you set the alpha risk (default 0.05) and power (default 0.80). The result shows the number of subjects per group and the total. A button lets you insert the result directly into the editor.

Missing data

The Missing data section is a Markdown editor to describe the missing data handling strategy: expected rate, imputation method, sensitivity analysis, etc.

Statistical analyses

The Statistical analyses section has two parts:

Structured analyses

You can add predefined analyses that reference the variables in your study. The main available types are:

• Regression — logistic, linear, Cox, propensity score matching (PSM), random forest, neural network, or XGBoost. For each model, you select the outcome variable and the covariates. Cox regression additionally requires a time variable.
• Table 1 — the classic descriptive table. You select the variables to display and the grouping variable.
• Comparison — Kaplan-Meier, t-test / Wilcoxon, ANOVA. You select the outcome variable and the grouping variable.
• Chi-squared / Fisher — cross-tabulation of two categorical variables.
• Other — for any analysis type not listed above. You provide a custom name and description.

Each analysis is summarized as a card with the referenced variables displayed as badges.

Software

A Markdown editor lets you specify the programming languages (R, Python…), software, and libraries used for the analysis, as well as important parameters.

Timeline

The Timeline section lets you define the main phases of the study.

The project start date and end date fields set the overall period. You then add phases (e.g., “Data collection”, “Statistical analysis”, “Writing”) with a name, start and end dates, description, and color for each.

Phases can be reordered by drag and drop. A Gantt chart is automatically generated to visualize the project schedule.

Regulatory

The Regulatory section is a Markdown editor to describe applicable regulatory procedures: data protection authority declaration, ethics committee approval, informed consent, applicable regulatory framework, etc.

References

The References section lets you manage the citations referenced in the protocol. Several methods are available:

• DOI lookup — enter a DOI to automatically retrieve the publication metadata
• BibTeX / RIS import — paste an export from your reference manager (Zotero, Mendeley, EndNote…)
• Manual entry — fill in the fields one by one (authors, title, journal, year, pages, DOI…)

Each reference is displayed as a collapsible card with all its fields. Available reference types include: journal article, book, chapter, conference, thesis, technical report, web page, software, and other.

You can choose the citation style (Vancouver or APA) in the section settings. Numbered references can be cited in the Markdown editors of other sections via built-in citation buttons.

References can be reordered by drag and drop.

Advanced sections

Three additional sections are accessible via the Advanced tab in the sidebar.

Custom sections

Lets you add as many free-form sections as needed. Each section has a title and content in Markdown. This is useful for protocol aspects not covered by the predefined sections (e.g., data management plan, monitoring, funding).

Model & schema

This section lets you describe the mapping between your source database and a standard data model. You define:

• The patient table — which table contains patients, with columns for ID, birth date, sex, and death date.
• The visit table — which table contains visits or admissions, with columns for visit ID, start and end dates, and care site.
• The event tables — one or more tables containing clinical events (labs, diagnoses, drugs, procedures…), with columns for code, value, date, and foreign keys to patients and visits.
• The gender values — which value represents “Male”, “Female”, and “Unknown” in your database.

Four presets are available — OMOP CDM v5.4, OMOP CDM v5.3, MIMIC-IV, MIMIC-III — to automatically pre-fill table and column names. You can also create, save, export, and import your own presets.

Scripts

For SQL scripts to be generated correctly, the data model and schema must be configured first.

Displays the automatically generated SQL scripts from your criteria, concept sets, and variables. The interface features a code editor (Monaco) with three files:

• 0_cohort.sql — the cohort construction query (inclusion and exclusion criteria)
• 1_filtered_views.sql — filtered views by concept sets
• 2_wide_format.sql — the variable extraction query in wide format

These scripts are read-only (they are generated, not manually edited). You can copy or download them individually, or download them all as a ZIP file.

Exporting the protocol

The Export section offers five formats to export your protocol.

JSON

Exports the complete project in a technical format (JSON) that can be re-imported into the Study Designer. This is the ideal format for backup and sharing between colleagues.

Word (.docx)

Generates a structured Word document with a title page, table of contents, and all protocol sections formatted. This is the appropriate format for submission to an ethics committee for example.

Excel (.xlsx)

Generates an Excel workbook with multiple sheets: project summary, author list, variables table, timeline, and custom sections. A Data collection sheet is also included: it contains the columns you configure in the setup panel (patient ID, admission dates, etc.) and one column per defined variable.

Before export, a panel lets you customize the data collection columns: add, remove, rename, and reorder columns by drag and drop.

Markdown

Exports the protocol as plain text in Markdown format. This format is useful for version control (Git) or integration into a wiki.

Export from a template

This option lets you use your own Word (.docx) template as the export base. You upload a Word file containing placeholders (tags) that the Study Designer will replace with the protocol data.

Placeholders use the format [[placeholder_name]]. You can place them anywhere in your Word document: in the body text, headers, footers, tables, etc.

Available placeholders

Here is the complete list of recognized placeholders:

Key takeaways