Data Upload & Management
Upload, browse, and manage multi-omics data files in your workspace.
Overview
Omics-OS Cloud provides a workspace-based file system for managing your multi-omics data. Upload data files directly through the browser, and the platform automatically detects the format, loads it as a modality, and makes it available to the AI agents for analysis. Supported formats include H5AD (AnnData), H5MU (MuData), CSV, TSV, VCF, 10X Genomics outputs, and common bioinformatics file types.
Each session has its own workspace directory. File paths are validated against that directory and every file route is scoped to the authenticated session, so files uploaded to one session are not reachable from another. Organization project files are an intentional exception: they are copied into a session's workspace when the session is created or when you import them.
Supported Formats
| Format | Extension | What It Contains |
|---|---|---|
| AnnData | .h5ad | Single-cell expression matrices with observations and variables |
| MuData | .h5mu | Multi-modal single-cell data (RNA + protein, ATAC, etc.) |
| CSV / TSV | .csv, .tsv | Tabular data (gene expression, metadata, sample sheets) |
| VCF | .vcf, .vcf.gz | Variant call format for genomics |
| 10X Genomics | .h5, matrix.mtx.gz | Cell Ranger outputs |
| Protein structures | .pdb, .cif, .mmcif | Molecular structure files for 3D viewing |
| Genome annotations | .gbk, .gb, .gff | GenBank and GFF annotation files |
How to Upload
Open the Files drawer
Click the Files icon in the left activity bar to open the files panel.
Drag and drop or browse
Drag files directly onto the drop zone, or click to browse your local filesystem. Multiple files can be uploaded at once.
Wait for processing
Upload progress appears in the panel. Once complete, H5AD and H5MU files are automatically loaded as modalities that appear in the data panel and become available to the AI agents.
Modalities and Lineage
When you run analysis steps (QC filtering, normalization, clustering), each transformation creates a new modality linked to its parent. This lineage chain is visible on the canvas as connected data table nodes. You can expand or collapse lineage groups to trace how your data was processed from raw upload through final results.
Modalities are the primary data abstraction in Omics-OS Cloud. Each modality represents a snapshot of an AnnData or MuData object at a specific processing stage.
Canvas Integration
Visualization-capable files can be dragged from the Files drawer directly onto the canvas:
- Structure files (
.pdb,.cif) open as interactive 3D Mol* viewers - Genome files (
.gbk) open as circular genome maps - Alignment files (
.bam) open in the IGV genome browser - Data files (
.h5ad) open as sortable, filterable data tables
Tips
Upload early, analyze later. Upload your data files at the start of a session, then ask Lobster to analyze them. The agents automatically discover loaded modalities without you needing to specify file paths.
Use the data table for exploration. Click a modality in the data panel to open it as a data table node on the canvas. Sort columns, filter rows, and select cells to ask the AI about specific subsets of your data.