---
title: "Knowledge Atlas: upload, preview and edit lab files"
description: "Upload lab files to Biocompile's Knowledge Atlas, preview FASTA, FASTQ, VCF, CSV, Excel and PDF in the browser, and edit tables and workbooks online."
url: https://www.biocompile.com/docs/knowledge-atlas/
section: "Files and data"
last_updated: 2026-10-23
app_url: https://app.biocompile.com/knowledge-atlas
---

# Knowledge Atlas: upload, preview and edit lab files

> Upload lab files to Biocompile's Knowledge Atlas, preview FASTA, FASTQ, VCF, CSV, Excel and PDF in the browser, and edit tables and workbooks online.

Source: https://www.biocompile.com/docs/knowledge-atlas/. Index of all Biocompile documentation: https://www.biocompile.com/docs/index.md

The Knowledge Atlas is the file browser in Biocompile that shows your organization's files,
indexed folders and research records in one place and previews them in the browser. You
look at sequences, tables and papers without downloading anything, and the assistant reads
your files and records when you mention them in a question.

## Find your way around

The Knowledge Atlas has two panes. The tree on the left lists everything you can open,
grouped by where it comes from. The pane on the right shows whatever you select in the tree.
You can pin the tree open or collapse it to a rail with **Unpin the tree**, and you can resize it. Unpinning
clears the tree selection but keeps the open item in the preview.

Select a file, research record or connected item to preview it. Selecting a folder opens it
in the tree and leaves the last preview in place, so you can browse folders while a file
stays open. The address in your browser follows your selection, so you can send a link to
exactly what you are looking at. The breadcrumb above the preview links to each folder
above an open item.

Choose **Sources** at the bottom of the tree to return to the overview, titled
**What sources are there?**. Opening or closing a folder in the tree takes you back to the
tree. The overview shows:

- A search box labelled **Search knowledge** and chips for each type of research record,
  with a count. Choose a chip to filter by that type, and choose it again to clear the filter.
- The ring, a chart of everything your organization knows, with one segment per source.
- **File types**, a bar showing which formats your files use, and your organization's
  storage use.

### Read the ring

Each segment of the ring is sized by how many resources it holds. Click a segment to zoom
into it and filter what you see; click the center to zoom back out. A small source still
gets a segment wide enough to select.

At each level of the ring the largest resources keep their own segments. The remainder is
grouped in one segment labelled **and N more**. Click it to explore those resources.

The **Show items** switch controls whether individual items such as files are drawn. In a
large organization the ring starts with items collapsed, and your choice overrides that.

The legend beside the ring lists each source with a short description of what it holds,
such as your files and folders, research records, research outputs produced in compute
sandboxes, saved knowledge from assistant conversations, or documents from connected
services. Use it to hide a source from the ring or show it again, or to zoom into it.

### Search the Knowledge Atlas

Type in the search box above the tree to filter what is already loaded. Press `Enter` to
search every source: your files, workspace files and research records, and the names inside
every connected source. Results are grouped by where they come from. If one source cannot be
searched, the others still answer and a message names the one that failed.

## Upload and preview

Drag files into the tree, or choose **New** above it and then **Upload files** or
**Upload folder**. Choose **New folder** to create a folder. Biocompile detects each file's
type and shows a preview where it can, for example the first records of a FASTA or VCF file,
a table, a PDF or an image. Use the actions menu on a file or folder to **Rename…**,
**Move…** or **Delete…** it.

| Kind of data | Formats with a preview |
|---|---|
| Sequences and variants | FASTA, FASTQ, VCF |
| Tables | CSV, TSV, XLSX |
| Documents | PDF, Markdown, plain text |
| Images | Common raster formats |

Any other file type can be uploaded too. The assistant can work through it with code even
when there is no preview.

## Index a local folder

An organization admin can index a folder on a computer or a mounted network drive so that
it appears in the tree and the ring. Biocompile records only folder and file names, paths,
sizes and modification times, and shares them with everyone in the organization. File
contents stay on the device.

1. Choose **Add source**, then **Local file system**.
2. Optionally enter a **Connection name**. The selected folder's name is used if you leave
   it empty.
3. Choose **Choose folder and sync** and select the folder.

Folder selection needs desktop Chrome or Edge in a secure browser context. If you are not
an admin, **Add source** explains that an organization admin has to connect sources and
offers **Open Integrations**.

The index does not follow changes on its own. When files change, an admin selects an item
in the folder, chooses **Sync file system** and, when asked, selects the same folder again.
The computer must be awake and able to reach the folder. An incomplete scan does not
replace the published index.

Folders in an indexed source load a page at a time. Choose **Load more** to see further
items. The preview of an indexed file shows its details, not its contents. Upload the file
when you need to analyze it.

## Research records

Research records, skills, agent profiles, conversations and sandboxes appear in the tree
beside your files. Selecting one previews it. The preview offers a link that opens it on its
own page, such as **Open entity page**, **Open skill page**, **Open profile page**,
**Open conversation** or **Open sandbox**. The preview of a research record also has
**Ask about this**, which opens the assistant with a starter prompt that refers to the record.

## Edit tables and workbooks

Open a CSV, TSV or XLSX file to edit it in a spreadsheet grid. The first row is ordinary
data, so repeated or empty headers never merge columns. In an XLSX workbook you choose the
worksheet above the grid; hidden worksheets stay in the workbook and still take part in
calculations.

Select a cell to see its raw value or formula in the cell bar. Type in the grid, paste a
rectangular selection, or edit the cell bar and choose **Apply**.

- A leading `=` makes an entry a formula, including `=(...)`.
- Numbers and booleans are recognized automatically. Identifiers with leading zeros and
  long numeric identifiers stay text.
- Choose text entry, or start with an apostrophe, to keep a value as text.
- Text in an imported XLSX file that begins with `=` stays text until you change it.

Supported formulas recalculate in the browser as you edit. Common functions, absolute
references, references to other worksheets and simple named ranges work.

### Save your changes

Choose **Save**, or press `Ctrl+S` (`Cmd+S` on a Mac), to save immediately. The status
shows whether your changes are saved, stored locally, offline, or in conflict with another
change. XLSX edits are written back into the original workbook, keeping its formatting,
charts, validation and hidden worksheets. If saving fails, your local draft is kept and you
can try again.

## File scope

A file can belong to one project or be shared across your organization. Keep
experiment-specific data in the project, and put shared references, templates and standard
operating material where the whole organization can use them.

## Limitations

- CSV and TSV files store cell text only. A formula is saved as its text and does not
  recalculate when the file is reopened. Use XLSX when formulas and cell types must persist.
- The grid is not a full spreadsheet engine. External workbook references, structured table
  references and some advanced functions are not supported, and are shown as unsupported
  while staying in the file.
- Copying a formula does not adjust its cell references.
- Inserting rows or columns and changing formatting are not available.
- ODS, legacy XLS and encrypted workbooks cannot be edited. Download the file to open it in
  another application.
- Read-only files can be selected and copied but not edited.
- Searching a connected source matches item names, not file contents.
- An indexed folder holds file details only. The assistant reads a file's contents after
  you upload it.

## Common questions

### Which file formats can I upload and preview?

Any file type can be uploaded to the Knowledge Atlas. Biocompile previews FASTA, FASTQ and
VCF files, CSV, TSV and XLSX tables, PDF, Markdown and plain text documents, and common
image formats. The assistant can work through any other format with code.

### Can I edit a spreadsheet without downloading it?

Yes. The Knowledge Atlas opens CSV, TSV and XLSX files in a spreadsheet grid in the browser
and saves your changes back to the same file. XLSX edits keep the workbook's formatting,
charts, validation and hidden worksheets.

### Does indexing a local folder upload my files?

No. An indexed folder shares only folder and file names, paths, sizes and modification
times with your organization. File contents stay on the device until you upload a file.

### What happens to files when an organization is deleted?

Deleting an organization permanently removes its files, their stored copies and the records of
earlier and interrupted uploads. The confirmation in the organization settings says the action
cannot be undone, so download files you still need first.

## Related

- [AI research assistant: ask your files and the literature](https://www.biocompile.com/docs/ai-research-assistant.md)
- [Organization security: AI models, tools and EU processing](https://www.biocompile.com/docs/organization-security.md)

## Get access to Biocompile

Biocompile is used in the browser at https://app.biocompile.com. It is free to start and no payment method is required: sign up at https://app.biocompile.com/signup?mc_cta=docs-md&mc_path=/docs/knowledge-atlas.md. If your team already uses Biocompile, ask an organization admin to invite you. Research teams that want hands-on setup can apply for the founder-led pilot at https://www.biocompile.com/pilot/. Questions: https://www.biocompile.com/contact/.