Files and Collections

The Files area is the saved file library for the active workspace. Use it to upload documents, save important outputs from jobs, organize files into collections, preview supported formats, and send files into compatible tools.

Job results and file downloads can still exist on a job without being saved to the library. A file appears in /app/files only after you upload it there or save it from a job result.

Basic concepts

File

A file is a saved workspace asset. It has a required filename, format, MIME type, size, uploader, creation time, and storage reference.

Files enter the library in two main ways:

• Uploaded files: Files uploaded from /app/files with Upload documents or Upload folder
• Saved job outputs: Output files selected from a job result file list with Save to library or Add to collection

Not every job input or output becomes a file in the library. Tool pages can show downloadable result files that remain attached to the job until someone saves them.

Collection

A collection is a named set of saved files inside a workspace. Collections behave like libraries, not folders.

The same file can belong to more than one collection. For example, one structure file can appear in a target collection, a benchmark collection, and a paper figure collection without creating duplicate files.

Deleting a collection removes the collection and its file memberships. It does not delete the files themselves.

Origin

ProteinIQ records where a saved file came from.

• Upload: The file was uploaded directly to the library
• Job output: The file was saved from a completed job result
• Job input: The file represents a saved job input when that path is available
• Import: The file came from an import flow

Origin is different from collection membership. A job output can belong to multiple collections, and an uploaded file can exist without any collection.

Storage ownership

Files can point to different kinds of stored content.

• Library-owned storage: Uploaded files are stored as library files. Deleting the file removes the saved file record and its stored content.
• Job artifact storage: Files saved from job results point to the original job artifact. Deleting the saved file removes it from the library, but the job result remains available from the job.

This distinction keeps job history intact while still letting you curate a smaller file library.

Saving job outputs

Most tool result file lists include selectable rows. Use the checkbox on each row, or the header checkbox to select all visible files.

After selecting files, use the bulk action menu:

• Save to library: Saves the selected outputs as files in the workspace library
• Add to collection: Saves the selected outputs if needed, then adds them to one or more collections
• Send selected to tool: Sends compatible selected files into another tool
• Download selected: Downloads the selected files

Saving is idempotent. If the selected output was already saved, ProteinIQ reuses the existing file instead of creating a duplicate.

When you use Add to collection, you can choose existing collections or create a new collection from the dialog. The selected files are added to every collection you choose.

Uploading files

Open /app/files and use Upload documents to upload one or more files. Use the upload menu next to it for Upload folder when you want to upload the files from a local folder.

Uploaded files are saved directly to the workspace library. When an upload flow includes collection selection, the new files are added to those collections as part of the same save.

Uploads are validated before they are saved. ProteinIQ checks that a file is not empty, is within the upload size limit, uses a supported extension, and matches expected binary signatures for formats such as PNG, JPEG, PDF, ZIP, and GZIP.

Organizing with collections

Collections give files reusable context. They are useful when the same file matters to more than one analysis, target, screen, paper, or workflow.

Use collections for sets such as:

• Target libraries: Structures, ligands, alignments, or notes for one biological target
• Screening sets: Compound files, docking poses, and result tables for a screening campaign
• Figure assets: Structures, images, and tables that support a manuscript or presentation
• Workflow handoffs: Files that should be reused across several tools

A file can exist outside collections. This is useful for temporary files, one-off uploads, or assets you have not organized yet.

Removing a file from a collection only removes that membership. It does not delete the file from the workspace library.

Finding files

The Files library is scoped to the active workspace. Switching workspaces changes which files and collections are visible.

Use the file table to search and sort saved files:

• Search: Find files by filename or file ID
• File name: Sort alphabetically
• File type: See a file's general type, such as text, structure, image, spreadsheet, archive, or PDF
• File size: Sort by size
• Uploaded at: Sort by saved or uploaded date

Each row shows the filename, a shortened file ID, the file type, file size, upload date, and an actions menu.

Use Jobs when you need the full execution context for a run. Use the Files library when you need a reusable saved asset.

Previewing and downloading

Click Preview from a file row action when the format supports inline preview.

Common preview modes include:

• Text: FASTA, PDB, SDF, mmCIF, JSON, logs, and other text-like formats
• Images: PNG, JPG, and related image formats
• Structures: PDB, CIF, mmCIF, SDF, and MOL2 content in a structure viewer when supported
• Binary files: Download-only files such as archives

Use Download from the row menu or preview dialog to download a file. ProteinIQ serves downloads through authenticated file routes and preserves a safe download filename.

Sending files to tools

Files can be sent into compatible tools from the Files library or from job result file lists. Use Send to tool when a saved file should become input for another analysis.

Compatibility depends on file format and the destination tool's accepted input types. ProteinIQ assigns compatible files to matching tool inputs where possible and skips files that cannot be used by the selected tool.

Deleting files and collections

Deleting a file removes it from the workspace library and from every collection that contains it.

Deletion behavior depends on how the file is stored:

• Uploaded files: Deleting removes the library file and its stored upload
• Files saved from jobs: Deleting removes the saved library entry, but the original job result remains attached to the job

Deleting a collection removes only the collection. Files in that collection remain in the workspace library and in any other collections where they belong.