Use Cases

All examples below use the current CLI form:

sciagent run --task "..."

Software Engineering

# Generate code from description
sciagent run --task "Create a REST API endpoint for user authentication"

# Fix bugs and refactor
sciagent run --task "Fix the memory leak in process_data.py"

# Write tests
sciagent run --task "Write pytest tests for the User class"

# Search and analyze
sciagent run --task "Find all TODO comments and summarize what needs work"

Research

# Literature search
sciagent run --task "Find recent papers on transformer architectures"

# API exploration
sciagent run --task "Show me how to use the pandas groupby function with examples"

# Comparative analysis
sciagent run --task "Compare React and Vue for building dashboards"

Scientific Computing

SciAgent runs simulations in isolated Docker containers. Ask naturally:

# Photonics & Electromagnetics
sciagent run --task "Simulate electromagnetic wave propagation through a metasurface using RCWA"
sciagent run --task "Design a photonic crystal waveguide with MEEP"
sciagent run --task "Trace rays through a lens system using pyoptools"

# Chemistry & Materials
sciagent run --task "Analyze molecular properties of this compound from SMILES"
sciagent run --task "Run a molecular dynamics simulation of a protein-ligand complex"
sciagent run --task "Build a crystal structure with ASE and compute its lattice properties"

# Math & Optimization
sciagent run --task "Solve this optimization problem using CVXPY"
sciagent run --task "Derive the symbolic integral of this expression with SymPy"
sciagent run --task "Tune hyperparameters for my ML model using Optuna"

# Circuit & IC Design
sciagent run --task "Simulate this RC circuit with ngspice"
sciagent run --task "Run RTL-to-GDS flow for this Verilog design using OpenROAD"

# Quantum Computing
sciagent run --task "Implement Grover's algorithm and simulate it with Qiskit"

# Bioinformatics
sciagent run --task "Analyze this DNA sequence and find ORFs using Biopython"
sciagent run --task "Run BLAST search against a local database"

# Network & Graph Analysis
sciagent run --task "Find communities in this social network using NetworkX"

# Chemical Process Engineering
sciagent run --task "Simulate a distillation column using DWSIM"

# Differential Equations (Julia)
sciagent run --task "Solve this system of ODEs using Julia's DifferentialEquations.jl"

Available Services

Domain	Services	Capabilities
Math & Optimization	scipy-base, sympy, cvxpy, optuna	Numerical computing, symbolic math, convex optimization, hyperparameter tuning
Chemistry & Materials	rdkit, ase, dwsim	Molecular analysis, atomistic simulations, chemical process simulation
Molecular Dynamics	gromacs	Biomolecular simulations, soft matter
Photonics & Optics	rcwa, meep, pyoptools	RCWA for gratings, FDTD electromagnetics, optical ray tracing
CFD & FEM	openfoam, gmsh, elmer	Fluid dynamics, mesh generation, multiphysics FEM
Post-processing & Visualisation	paraview	Multi-arch (with EGL) — pairs with the OpenFOAM services
Circuits & EDA	ngspice, openroad, iic-osic-tools	SPICE simulation, RTL-to-GDS flow, 80+ IC design tools
Quantum Computing	qiskit	Quantum circuits, gates, algorithms (Grover, VQE, QAOA)
Bioinformatics	biopython, blast	Sequence analysis, BLAST searching, phylogenetics
Network Analysis	networkx	Graph algorithms, centrality, community detection
Scientific ML	sciml-julia	Julia ODE/SDE solving, symbolic modeling, neural DEs

Multi-Step Workflows

Combine services for complex pipelines:

# Drug screening pipeline
sciagent run --task "Screen molecules from compounds.sdf for binding affinity to target protein"
# Uses: rdkit -> gromacs -> scipy-base

# Photonic optimization
sciagent run --task "Optimize a metasurface unit cell for maximum transmission at 1550nm"
# Uses: scipy-base (optimization) -> rcwa (simulation)

# Chip analysis
sciagent run --task "Analyze power/performance/area for this RTL design"
# Uses: openroad -> scipy-base

# Protein structure pipeline
sciagent run --task "Find similar proteins to this sequence and run MD simulation"
# Uses: blast -> biopython -> gromacs

# Optical system design
sciagent run --task "Design a lens system and optimize for minimum aberration"
# Uses: pyoptools (ray tracing) -> optuna (optimization) -> scipy-base (analysis)

# Crystal structure + analysis pipeline
sciagent run --task "Build a crystal structure and analyze its lattice properties"
# Uses: ase (structure) -> scipy-base (analysis)

# Network-based drug discovery
sciagent run --task "Build protein interaction network and identify key drug targets"
# Uses: biopython (sequences) -> networkx (graph analysis) -> scipy-base (statistics)

# Chemical process optimization
sciagent run --task "Optimize reactor conditions for maximum yield"
# Uses: dwsim (process sim) -> optuna (optimization)

# Quantum chemistry workflow
sciagent run --task "Calculate ground state energy using VQE algorithm"
# Uses: qiskit (quantum simulation) -> scipy-base (classical optimization)

Example Pipeline: Multi-Service Workflows

Workflow	Services	Output
Drug screening	rdkit → gromacs → scipy-base	Ranked molecules by binding affinity
Metasurface design	scipy-base → rcwa	Optimized nano-structure geometry
IC design flow	openroad → scipy-base	Power/performance/area report
Protein pipeline	blast → biopython → gromacs	MD trajectory from sequence
Optical design	pyoptools → optuna → scipy-base	Optimized lens parameters
Crystal structure analysis	ase → scipy-base	Lattice properties
Process engineering	dwsim → optuna	Optimal reactor conditions

See Case Studies for real-world examples of SciAgent in published research.