Quick Start

First Login

After logging into AI Scientist for the first time, you will enter a guided onboarding interface. This guide will help you complete the following initial setup:

• Create your first research project
• Get familiar with the AI Scientist interface layout, including the central conversation area, workspace, project & conversation panel, and entity display area

We recommend following the guide step by step to quickly master the basic workflow of AI Scientist.

Basic Usage Flow

Design Philosophy

AI Scientist is designed to let researchers complete the entire workflow — from sequence retrieval to analysis results — within a conversation.

Basic Workflow

The workflow consists of four main phases:

Phase 1: State Your Research Need

You can type your research question directly in the chat box, for example: “I want to overexpress the α-amylase gene from Bacillus subtilis in E. coli BL21 using the pET-28a vector with Gibson assembly.” AI Scientist will automatically understand your requirements and plan execution steps.

Phase 2: Automatic Task Execution

AI Scientist will automatically perform multi-step operations, including:

• Fetching gene sequences from NCBI
• Codon optimization for the expression host
• Loading standard vectors
• Designing Gibson assembly strategy
• Simulating the assembly process
• Adding feature annotations

You only need to confirm key decision points — the rest is handled automatically.

Phase 3: Get Results

Once the task is complete, AI Scientist will return:

• Downloadable GenBank files
• Primer ordering tables (CSV/TSV format)
• Interactive visualization results

You can directly download the files needed for your experiments.

Phase 4: Save & Manage

You can save sequences to the component memory library for quick retrieval later. AI Scientist also remembers your research context — including preferred host organisms, cloning methods, and lab constraints — to continuously optimize its service.

Quick Commands

AI Scientist provides a rich set of quick commands to help you quickly access the features you need. Type ”/” in the chat input box to see available commands:

Command	Description	Use Case
/deep-research	Multi-source deep research synthesis	Starting a new research topic or literature review
/research	Quick evidence retrieval	Finding specific facts, protocols, or data
/document	Create structured documents	Writing experimental protocols or technical routes
/sequence	Sequence design & analysis	DNA/RNA/protein sequence tasks
/plasmid	Plasmid design & annotation	Designing or analyzing plasmid constructs
/primers	Primer design	PCR, sequencing, mutagenesis, Gibson primers
/gibson	Gibson assembly design	Multi-fragment seamless cloning
/memory	Component library operations	Saving, retrieving, and searching biological components
/create-skill	Create personal skills	Packaging commonly used workflows
/save-skill	Save skill from session	Saving completed operations as reusable skills

Interactive Visualization

AI Scientist’s output goes beyond text, offering multiple interactive visualization components to help you understand analysis results more intuitively:

Visualization Type	Description
Sequence Map	Linear sequence visualization with feature annotations, restriction sites, GC distribution, ORF prediction
Plasmid Map	Circular plasmid map with functional elements (promoters, CDS, selection markers, etc.)
Protein 3D Structure	Interactive protein three-dimensional structure viewer
Sequence Alignment	Multiple sequence alignment visualization
Primer Result Table	Interactive primer design results with Tm, GC%, sequence, and one-click copy
Statistics Dashboard	Key metrics displayed in dashboard format
Gantt Chart	Project planning Gantt chart with dependencies and progress tracking