smartsbio-jupyterlab 0.1.4

smarts.bio bioinformatics AI agent — JupyterLab extension

AI Bioinformatics for JupyterLab (smarts.bio)

The bioinformatics AI agent that lives in your notebook. Design proteins, run GPU pipelines, search every major database, and visualize results — without leaving JupyterLab.

---

What you can do

Ask the agent anything in plain English and watch it work:

"Use Boltz to design a nanobody that binds the RBD of SARS-CoV-2 spike protein — give me 5 candidates ranked by predicted affinity."

"Run RFdiffusion to generate 10 novel enzyme scaffolds around this active site geometry, then score them with ProteinMPNN."

"My RNA-seq experiment has 6 samples (3 treated, 3 control) in my workspace. Run DESeq2 and tell me which pathways are enriched in the differentially expressed genes."

"Search PubMed, UniProt, and STRING DB for everything known about the interaction between BRCA1 and RAD51 — summarize the key structural contacts."

The agent chooses tools, runs them, and streams the answer back in real time. Long-running GPU jobs (RFdiffusion, Boltz, GATK, etc.) are dispatched to the cloud and tracked in the Processes panel — you keep working while they run.

Jupyter advantage: Insert any code block the agent writes directly as a new notebook cell with one click. Attach your active cell as context so the agent knows exactly what you're working on.

---

Features

AI agent chat

A persistent chat panel lives in the left sidebar. It understands biological context, remembers your conversation history, and can attach files from your workspace directly.

Example workflows:

• "BLAST this sequence against NCBI nt, then fetch the top 3 hits from GenBank and align them"
• "Explain the clinical significance of the variants in cohort.vcf — focus on BRCA1 and TP53"
• "Fetch the crystal structure of human HBB from PDB, run a stability analysis on the sickle-cell mutation E6V, and visualize the result"

Type / to browse all available tools and pipelines with autocomplete. Type @ to attach a file from your workspace directly into the message.

---

Notebook integration

smarts.bio is built for Jupyter workflows:

• Insert as cell — when the agent writes a code block, click Insert to create a new notebook cell below your current position
• Analyze active cell — right-click any cell or use the toolbar button to send it to the agent as context
• Attach kernel variables — share the current state of your kernel with the agent so it understands your data

---

3D structure viewer

Open any .pdb or .mmcif file directly in JupyterLab. A full interactive Molstar viewer renders the structure with a toolbar for instant control.

Controls:

• Representation — Cartoon, Ball & Stick, Surface, Spacefill, Backbone
• Color — By Chain, By Element, By Residue, Secondary Structure, Uniform
• Visibility — Toggle water molecules and hydrogens
• Background — Black, dark blue, white, teal

Click Analyze with smarts.bio on any structure in the Files panel to immediately send it to the chat for AI analysis.

---

Sequence & genomics viewers

Open .fasta, .fastq, .bam, .sam, .vcf, .bed, .csv, and .tsv files natively in JupyterLab. smarts.bio registers as the default viewer for all standard bioinformatics formats, with custom icons in the JupyterLab file browser for every recognized type.

• Sequence viewer — Colorized nucleotide / amino acid display for FASTA and FASTQ, with linear and circular views, reverse strand, and translation tracks
• Alignment viewer — BAM/SAM coverage histogram with per-base depth, mapped/unmapped read filtering, and region navigation
• Variant viewer — VCF/BED annotation with clinical context
• Table viewer — CSV/TSV with sortable columns — useful for reviewing DESeq2 output or BLAST hit tables

---

Processes panel — track long-running jobs

Submit GPU-heavy pipelines (RFdiffusion, Boltz, GATK, samtools, and more) and watch them run without blocking your notebook. The Processes panel shows live status, execution time, and error details.

• Real-time status updates (queued → running → completed / failed)
• Job duration and timestamps
• Cancel any running job directly from the panel

---

Files panel

A full file browser panel gives you access to your smarts.bio workspace — browse folders, upload, download, rename, move, and delete files without leaving JupyterLab.

Right-click any file to:

• Open in the built-in viewer
• Analyze with smarts.bio (sends the file as context to chat)
• Download, rename, move to a folder, or delete

Right-click any folder to:

• Upload files here
• Create a subfolder
• Rename or delete

---

Getting started

1. Install

pip install smartsbio-jupyterlab

Then start (or restart) JupyterLab:

jupyter lab

2. Sign in

Click the smarts.bio icon in the left sidebar → Sign In. A popup window opens, you authenticate, and JupyterLab resumes automatically.

No account? Get started at chat.smarts.bio — includes compute credits to try GPU pipelines.

3. Ask something

Use Boltz to design a nanobody targeting human PD-L1.
Use my workspace file antigen.pdb as the target.
Give me 3 candidates ranked by pLDDT score.

---

Requirements

• JupyterLab 4.x
• Python 3.8 or later
• A smarts.bio account (get started at chat.smarts.bio)
• Internet connection (GPU pipelines and AI run on smarts.bio cloud infrastructure)

---

Commands

All commands are available via the JupyterLab command palette (Ctrl+Shift+C / Cmd+Shift+C):

Command	Description
smarts-bio:open-chat	Open the AI chat panel
smarts-bio:new-chat	Start a new conversation
smarts-bio:analyze-cell	Send the active notebook cell to chat
smarts-bio:insert-cell-below	Insert agent output as a new code cell
smarts-bio:attach-kernel-context	Share kernel variables with the agent
smarts-bio:open-explorer	Open the Files panel
smarts-bio:open-processes	Open the Processes panel
smarts-bio:upload-file	Upload files to your workspace
smarts-bio:select-workspace	Switch active workspace
smarts-bio:sign-in	Sign in to smarts.bio
smarts-bio:sign-out	Sign out

---

Settings

Open Settings → Advanced Settings Editor → smarts.bio to configure:

Setting	Default	Description
sendOnEnter	true	Send message on Enter. Shift+Enter inserts a newline.
defaultWorkspaceId	""	Pin a workspace ID for this JupyterLab session.
enableKernelContext	true	Allow the agent to read kernel variable names for context.
apiBaseUrl	https://api.smarts.bio	API endpoint (advanced).

---

Privacy

Files and text you send to the agent are transmitted to smarts.bio servers for processing. The extension shows a one-time confirmation before uploading any file. Do not send files containing patient identifiers (PHI) unless your organization has a BAA with smarts.bio.

smarts.bio Privacy Policy

---

Feedback & support

• Issues & feature requests: github.com/smartsbio/smarts-bio-jupyterlab
• Documentation: smarts.bio/docs
• Website: smarts.bio