Knowledge Atlas: upload, preview and edit lab files

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.

Choose Add source, then Local file system.
Optionally enter a Connection name. The selected folder’s name is used if you leave it empty.
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.