Dashboard

The Dashboard is the landing page after login. It holds three things: a pair of shortcut cards (File Manager and Activity), the Available Workflows list, and — if your account has access — an Experimental section.

Shortcuts

Two cards sit above the workflow list. Both are also reachable from the top navigation bar on any page.

Card	What it opens
File Manager	Everything you have uploaded and everything your jobs have produced — download files, or reuse an existing input on a new job
Activity	Every job you have run, across all pipelines, in one list

Available Workflows

Workflows are grouped into collapsible sections — normally Data Workflows (getting raw instrument or repository data into AIRR format) and AI Workflows (analysis on top of processed AIRR data). Click a section header to expand or collapse it.

Both the grouping and the list itself come from your deployment’s configuration, so you only see the pipelines your account has been granted. If the page reports no workflows available, your account has no pipelines assigned yet — contact your administrator.

Data Workflows

Pipeline	Description
FASTQ Pipeline	Convert FASTQ files to AIRR-formatted TSV files with V(D)J gene calls
SRA Data Pipeline	Download data from SRA (Sequence Read Archive) and convert to AIRR format
Adaptive Biotech Pipeline	Convert data from Adaptive Biotechnologies’ immunoSEQ platform to AIRR format
TakaraBio to AIRR	Convert Takara Bio Cogent NGS Immune Profiler output into MyImmune-compatible AIRR files
TCR to Amino Acid Sequence	Convert TCR repertoire clonotype data (V/J gene calls plus CDR3 sequences) into germline amino acid sequences
Antibody Sequence Restoration	Restore missing N-terminal (FR1) and C-terminal (FR4) framework residues of antibody variable-domain sequences from germline V and J databases
Pseudo-Sequence Alignment	Align paratope amino acid sequences using the IMGT numbering scheme to produce pseudo-sequences for downstream analysis
Sequence Search	Bulk BCR/TCR sequence search across multiple databases with numerous comparison metrics

AI Workflows

Pipeline	Description
Clustering Pipeline	Cluster BCR / TCR paratope sequences
Stratification Pipeline	Run patient stratification models to classify responders from non-responders to a treatment
Paratope Tree	Render a cohort’s clustered paratope sequences as an interactive BLOSUM-distance tree over cluster representatives
Epitope Prediction	Bulk epitope prediction from BCR sequences (paired and unpaired)

Experimental

The Experimental section only appears for accounts entitled to it. These tools are under active development and their interfaces and outputs may change without notice. See Experimental Features for details.

Tool	Description
Single Sequence Search	Search a single amino acid sequence against reference databases with interactive scoring and visualization
Single Epitope Prediction	Predict epitope clusters for a single antibody by heavy and light chain sequences
AF3 Config Builder	Build an AlphaFold3 config from a UniProt accession for the antigen plus antibody heavy and light chains

Navigating to a pipeline

Click any workflow card to open that pipeline’s job list. From there you can create a new job, review past runs, and manage presets. Where a pipeline has documentation configured, its card and job page also link straight to it.

Recent jobs

Each pipeline’s job list shows the status of every run (created, queued, running, success, failed) and refreshes automatically while jobs are in flight. See Job Management.