bioIDE™ - The bioinformatics IDE for the AI era
An AI that runs BLAST, GATK, and bioinformatics pipelines - right alongside instant viewers for FASTA, BAM, VCF, PDB, and more. Ask questions about your data, execute tools, and track results. No installation, no upload required.
Every bioinformatics format, rendered instantly
Drop any genomics or structural biology file and the IDE detects the format automatically. No plugins, no conversion — just open and explore.
- •Sequence viewer — FASTA, FASTQ, GenBank, EMBL
- •Alignment viewer — SAM, BAM, CRAM with on-demand streaming
- •Variant viewer — VCF and BCF with interactive filtering
- •Structure viewer — PDB and mmCIF powered by Molstar
- •Data viewer — CSV and TSV with sortable, filterable tables
- •Code editor — Python, R, shell scripts with Monaco syntax highlighting
Ask anything about your data
The AI chat panel sits alongside your viewer. Ask questions in plain language, run bioinformatics pipelines, search databases, and get results without leaving the IDE.
- •"What variants in this VCF are pathogenic?"
- •"Run BLAST on this sequence and summarize hits"
- •"Align these reads and call variants with GATK"
- •Attach open files as context with a single click
Workspace file management built in
Upload, organize, and open files from your smarts.bio workspace directly inside the IDE. Drag a file onto the panel to upload — no separate file browser needed.
- •Upload by drag-and-drop or file picker
- •Click any file to open it instantly in the viewer
- •Rename, download, or delete with right-click
- •Files stored securely in your private workspace
Track every pipeline run in real time
Long-running bioinformatics jobs — sequence alignment, variant calling, structure prediction — run on smarts.bio cloud infrastructure. Monitor progress and open output files without leaving the IDE.
- •Live status updates: queued, running, completed, failed
- •Step-by-step progress for multi-stage pipelines
- •Click output files to open them directly in the viewer
- •Cancel running jobs at any time
Works where you work
The same IDE experience is available in your browser, inside VS Code, and embedded in JupyterLab — all powered by the same smarts.bio platform.
Browser
Open ide.smarts.bio in any browser — no installation, no signup required for local files.
VS Code
Install the smarts.bio VS Code extension and open any genomics file directly in the editor sidebar.
JupyterLab
pip install smartsbio-jupyterlab — file viewers and AI chat embedded right in your notebook environment.
Open your first file now
No installation. No account required. Just open the IDE and drop a file.
Frequently asked questions
Yes — the bioIDE™ is completely free. Open your browser, drop a file, and start exploring. No account required for local files. Sign in with your smarts.bio account to access workspace files stored in the cloud.
The IDE supports FASTA, FASTQ, GenBank (.gb/.gbk), SAM, BAM, CRAM, VCF, BCF, PDB, mmCIF, CSV, TSV, and many more. Files can be plain or gzip-compressed (.gz). Python scripts and other code files open in a full Monaco editor.
Never. Local files are opened entirely in your browser — nothing leaves your machine. Workspace files (from your smarts.bio account) are fetched securely over HTTPS directly to your browser for viewing.
Absolutely. The AI chat panel runs alongside the file viewer. You can ask questions about what you are seeing — "What variants are in this VCF?", "Summarize this sequence" — and the agent can run analyses on your workspace files.
Yes. The same IDE experience is embedded in the smarts.bio VS Code extension and JupyterLab extension. Open any bioinformatics file from the sidebar and it renders instantly inside your editor.
The IDE is optimized for large genomic files. BAM and CRAM files stream reads on demand so only the visible region is loaded. VCF and FASTA files are parsed efficiently in the browser with virtual scrolling for datasets with millions of entries.