Files and collections

Files is the saved file library for your active workspace. It contains uploaded files and outputs you explicitly save from jobs. A downloadable job output does not appear in the library until you save it.

A collection is a named set of saved files. The same file can belong to several collections without being copied, such as a structure used in both a target study and a benchmark dataset.

Upload files

You can upload individual files or the contents of a local folder:

1. Open Files and select Upload documents.
2. Choose one or more files. To upload a folder, open the upload menu and choose Upload folder instead.
3. Follow the upload progress and check that the files appear in the library.

Each file must be nonempty, use a supported format, and be no larger than 50 MB. Uploads also count toward your plan's storage allowance. If a file is rejected, use the error message to check its size, extension, and contents.

Where the upload form offers a project or collection selector, choose the destination before uploading.

Save job outputs

Open a job's result file list and choose Select files to show the checkboxes. Select the files you want to keep; the header checkbox selects all visible files.

Choose an action from the selection toolbar:

• Save to Files: Add the selected outputs to Files.
• Add to collection: Save the selected outputs if needed and add them to the collections you choose.
• Download: Download the files without saving them to the library.
• Send to tool: Use compatible files as input for another analysis.

Saving the same job output again reuses the existing library entry. In Add to collection, choose existing collections or enter a name under New collection and select Create collection. Select Add to finish adding the files to the selected collections.

Organize collections

To create a named set:

1. Open Collections and select Create new collection.
2. Enter a Collection name, such as Kinase reference structures, and an optional description.
3. Select Create collection.

Open the collection and use Upload documents or Upload folder to add new files directly. For an existing job output, use Add to collection from that job's result file list. Collection actions affect membership as follows:

• Add a file: Include it in one or more collections without duplicating it.
• Remove from collection: Remove only that membership. The file remains in Files and any other collections.
• Delete a collection: Remove the collection and its memberships. Its files remain in the workspace.

Projects group several kinds of research work, while collections group files. Collections belong to the workspace and can include files from different projects. Files can also remain outside any collection.

Find and inspect files

Search the library by filename or file ID. Use the available filters and sorting controls to narrow the list by properties such as file type, origin, project, size, or upload date. Switching workspaces changes the visible files and collections.

Open a file's actions menu for:

• Preview: Inspect a supported text, image, or molecular structure file. Archives and other unsupported preview formats must be downloaded.
• Download: Save the file to your computer.
• Open job: Return to the source analysis when the file is associated with a job.
• Send to tool: Choose a compatible destination tool.
• Delete: Remove the saved file, if your role allows it.

The file's origin indicates whether it was uploaded, saved from a job, or imported. It is independent of the file's project and collection membership.

Send files to a tool

Use Send to tool from a file's actions menu, or select several files and use the bulk action. Choose a destination from the compatible tools shown in the dialog.

Review the assignment before continuing. ProteinIQ matches file formats to the tool's input slots; files without a compatible available slot are skipped. Select Send to [tool name] to open the destination page, then check the inputs, settings, and credit cost before submitting the analysis.

Delete files

Use Delete from the file's actions menu and confirm. Deleting a file removes it from the library and every collection that contains it.

• Uploaded file: The saved file and its uploaded contents are permanently deleted.
• Saved job output: The library entry is deleted, but the original output remains available on its job.

The reverse is different: deleting the source job also deletes its output files and the library entries that reference them.