Wiki Pages

Overview

A Wiki page is a markdown document stored as an ELN item. Wikis live alongside experiments inside a project and provide a place for goals, ideas, literature notes, analysis write-ups, and reference material that does not fit the experiment / action / specimen hierarchy.

Each wiki page is a Wiki-typed item with a single .md body file plus zero or more image or document attachments. The page renders as formatted HTML in the Content Viewer using the Markdown Viewer plugin, and can be edited in place with the Markdown Editor.

Property	Value
Item type	Wiki (level: Item)
Body file	One `.md` file per page
Attachments	Any file types (images, PDFs, datasets, etc.)
Storage	Same WebDAV layout as other items
Audit	Edits and uploads recorded in the audit log like any other item

Topic-Wiki Layout

To keep wiki pages organized, each project uses a fixed five-section layout under a top-level Wiki folder:

<Project>/
  Wiki/
    Goals/         — project goals, milestones, deliverables
    Ideas/         — brainstorms, hypotheses, design notes
    Literature/    — literature reviews, paper notes
    Analysis/      — cross-experiment analysis, summaries
    References/    — standards, calibrations, manuals, SOPs
      <page title>     — ELN Wiki item
        body.md          — rendered when the page is selected
        figure-1.png     — zero or more attachments

The five section names are fixed (Goals, Ideas, Literature, Analysis, References). Inside a section, you can add as many wiki pages as you need.

Creating a Wiki

Seed the Topic-Wiki Folders

To add the standard Wiki sub-folders to an existing project, right-click the project (or any folder inside it) in the Projects panel and choose New Topic-Wiki. The five section folders (Goals, Ideas, Literature, Analysis, References) are created inside a Wiki folder under the selected location. Existing folders with matching names are reused.

Add a Wiki Page

Open the target section folder (for example, Wiki / Ideas) in the Projects panel.
Click New in the Items toolbar (or press Ins).
Choose Wiki as the item type and give the page a title.
Save. An empty page is created, ready for content.

Viewing a Page

Select a wiki item in the Items panel. The Content Viewer activates the Markdown Viewer plugin, which:

Renders the body .md file as formatted HTML (headings, lists, tables, code blocks, links).
Resolves ![](image.png) references against files attached to the same item, so screenshots and diagrams display inline.
Resolves eln:// links to other items and specimens (see the ELN Links section below).
Provides an Edit button that opens the page in the Markdown Editor.

Editing a Page

Click the Edit button in the viewer toolbar to open the Markdown Editor. The editor opens with the current page body loaded.

Edit the markdown source directly in the text area.
Click Save to write the changes back to the page’s .md file. The viewer reloads to show the rendered result.
Click Cancel to discard changes.

Conflict Detection

When you save, the editor checks the file’s ETag (a server-side version marker) against the version that was loaded. If another user — or an AI assistant via MCP — has modified the page in the meantime, the save is rejected with a conflict warning so your edits are not silently overwritten.

Attachments & Images

Any file type can be attached to a wiki page (right-click the page and choose Add File, or drop the file onto the item). To display an image inline, reference it from markdown:

![Architecture overview](architecture.png)

See [the protocol](sop-2024.pdf) for details.

The Markdown Viewer enumerates the page’s attached files and rewrites the references to point at the on-disk filenames, so you can write the unprefixed name (architecture.png) regardless of the internal storage prefix the application adds.

ELN Links

Wiki pages can cross-reference any ELN record using the eln:// URL scheme. Clicking such a link in the rendered page navigates the application to the target item — switching projects if needed.

Link form	Target
`eln://item/42`	Item with `id = 42` in any project
`eln://specimen/SPEC-2024-007`	Specimen with the given specimen code

Use these in markdown the same way as any other link:

The samples used in this analysis are documented in
[experiment 42](eln://item/42) and specimen
[SPEC-2024-007](eln://specimen/SPEC-2024-007).

Authoring with AI (MCP)

The MCP server exposes three wiki-specific tools that let an AI assistant draft, read, and revise wiki pages directly:

Tool	Description
`wiki_create_page`	Create a new wiki page in a project under one of the five sections. Optionally upload attachments at creation time. Errors if a page with the same title already exists in that section.
`wiki_get_page`	Read an existing wiki page. Returns the body markdown plus metadata and the list of non-`.md` attachments.
`wiki_update_page`	Update an existing page identified by item ID. Overwrites the body `.md`, appends attachments, or both. Existing attachments are never removed.

See AI Integration > Wiki Tools for full parameter details and examples.