Creating a batch

A batch setup defines the tool, inputs and settings for a group of jobs. Start with the analysis you want each job to perform, then choose how to supply its inputs.

Prepare the batch

Open Batches and select New batch:

1. Choose a tool. Only supported batch tools appear in the selector.
2. Enter a batch name and choose a project if needed.
3. Select the tool's primary operation or input mode, then add your inputs. Use CSV import for a spreadsheet of complete experiments.
4. Configure the shared settings. CSV setting columns can override these for individual rows.
5. Choose the pairing or combination mode when available.

Keep alignments, complexes and other collections together when the tool expects them as one input. Follow the tool's input guidance rather than assuming every file or FASTA header becomes a separate job.

For Boltz-2, numbered molecule fields contribute members to each complex. Three lines in Protein 1 with one entry in DNA 1 create three protein-DNA predictions. Counts beside each field identify alternatives and shared entries; the submission summary names the members in each prediction.

Multirecord FASTA inputs show FASTA records. Keep Separate predictions to use records as alternatives, or choose Members of one complex to put each record in its own molecule field. Wrapped lines stay within their FASTA record. Conversion preserves molecular controls and refuses to discard records if the tool's field limit would be exceeded.

Review and submit

Select Preview to check job counts, members, sequences and copies. Expand long sequences to inspect their contents. CSV previews include every prepared row; regular-input previews show up to 25 jobs alongside the full count.

Check the credit estimate, resolve any reported issues, then select Submit. Scientific validation, tool limits, workspace access and credit checks still apply on submission. An import that parses successfully is not yet a scientifically validated experiment.

Revise the setup

Use Edit CSV to change imported text, Map columns to change its interpretation, or Clear to remove the import and use the regular form. Changing shared settings updates CSV rows that do not override those settings.

Keep a copy of your source spreadsheet and files. Batch setups are not saved drafts; changing the selected tool resets the setup. After submission, open the run to follow its jobs.