Concepts

This page defines the main resources in ProteinIQ and how they relate to each other. For a step-by-step example, follow the Start guide.

Tools, inputs, jobs, and results

These terms describe the parts of an analysis:

• Tool: Performs an analysis or conversion. Its page describes the accepted inputs, settings, and outputs.
• Input: The data you give a tool, such as a sequence, structure, or small molecule. Depending on the tool, you can paste text, upload a file, choose a saved file, or retrieve a database record. The input controls show the supported methods and formats.
• Job: Records a run of a hosted tool, including its input, settings, status, credit usage, and results. Running the tool again creates another job.
• Result: The output of an analysis, such as a table, structure, plot, text, files, or logs. The job page displays the outputs for that run.

Some calculators and converters run in your browser without creating a hosted job. Keep the page open while they run and download the output before leaving. Do not assume a browser calculation will appear in workspace job history.

Workspaces, projects, and collections

You need a workspace to submit a hosted job. Projects and collections are optional ways to organize its contents:

• Workspace: Holds jobs, files, workflows, and credits. Workspace membership controls access. Switch workspaces from the account menu in the sidebar; if an expected job or file is missing, check your active workspace.
• Project: Groups related work for a target, experiment, or paper. A resource belongs to one project at a time or remains in No project. Projects do not have separate members or permissions.
• Collection: Groups saved files for reuse. A file can belong to several collections without being duplicated. Collections can contain files from different projects within the same workspace.

Job outputs and saved files

A job output can be available on its job without appearing in the file library:

• Results: Holds the record of your analyses, including available job outputs.
• Files: Holds files you upload to the library or explicitly save from a job.

Use Select files in a supported result file list, select the outputs, and choose Save to Files to add them to the library. You can then include them in collections or send them to a compatible tool.

Saving a file organizes the artifact; it does not create another analysis.

Credits and access

Job submission depends on your workspace's credits, plan limits, and your role:

• Credits: Belong to the workspace. The cost depends on the tool's input, configuration, and billing model. Fixed-price jobs charge a set amount; time-based jobs authorize credits as they run and settle against billable runtime. Review the displayed cost before submitting.
• Plan limits: Set usage allowances for the workspace. A job must fit within those allowances as well as the available credit balance.
• Workspace role: Determines which actions you can take. A viewer cannot submit jobs, even when the workspace has credits.

Batches and workflows

Use batches to repeat an analysis and workflows to connect multiple analyses:

• Batch: Runs a supported tool across multiple inputs to repeat the same kind of analysis across a dataset.
• Workflow: Defines connected steps that pass compatible tool outputs to later analyses.
• Workflow run: Records one execution of a workflow, including its steps and associated jobs.