Available Tools
Computational bioinformatics tools available in SmartsBio — AI protein design, sequence alignment, quality control, variant analysis, file processing, and more. Tools can be called directly via the API or invoked automatically by the agent.
Looking for database tools? Sequence search, protein databases, genomics, pathways, clinical data, literature, and patents are covered on the Available Databases page.
Sync
Results returned immediately via POST /v1/tools/:id/run. Best for fast, lightweight operations.
Pipeline
Async execution via POST /v1/pipelines. Get a pipeline ID immediately, then stream or poll. Used for compute-heavy tools.
Both
Supports either mode. A single long-running tool submitted to /v1/pipelines is valid — no multi-step chain required.
Tool Reference
32 tools across 8 categories. Tool IDs are stable across versions.
AI Protein Design6 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| protein_structure_prediction | Protein Structure Prediction | AI-powered 3D protein structure prediction using Boltz-2. Accepts sequence or FASTA, outputs PDB/mmCIF. | Pipeline |
| binding_affinity_prediction | Binding Affinity Prediction | Predict binding affinity between a protein binder and target using Boltz-2 thermodynamic scoring on GPU. | Pipeline |
| protein_binder_design | Protein Binder Design | Design protein binders with enhanced binding affinity for a given target structure. | Pipeline |
| peptide_binder_design | Peptide Binder Design | Design short peptide binders for target proteins, optimizing for binding specificity. | Pipeline |
| nanobody_design | Nanobody Design | Design nanobodies (VHH antibodies) with high specificity for a target epitope. | Pipeline |
| enzyme_design | Enzyme Design | Design enzymes for targeted catalytic functions using generative protein models. | Pipeline |
Sequence Alignment3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| bwa_toolkit | BWA | Burrows-Wheeler Aligner for short read alignment to reference genomes. Outputs SAM/BAM. | Pipeline |
| bowtie2_toolkit | Bowtie2 | Ultrafast and memory-efficient short read aligner for DNA and RNA-seq reads. | Pipeline |
| hisat2_toolkit | HISAT2 | Hierarchical, splice-aware aligner for RNA-seq reads. Supports spliced and alternative alignment. | Pipeline |
Quality Control3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| fastqc_toolkit | FastQC | Quality assessment of raw high-throughput sequencing data. Generates per-base quality plots. | Pipeline |
| trimmomatic_toolkit | Trimmomatic | Read trimming and adapter removal for paired-end and single-end Illumina data. | Pipeline |
| fmlrc_toolkit | FMLRC | FM-index based long-read error correction using short-read data as reference. | Pipeline |
Variant Analysis3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| gatk_toolkit | GATK | GATK4 variant discovery and genotyping on AWS infrastructure. Germline and somatic calling. | Pipeline |
| annovar_toolkit | ANNOVAR | Comprehensive variant annotation with multiple databases (refGene, COSMIC, ClinVar, gnomAD). Requires license. | Pipeline |
| vcftools_toolkit | VCFtools | VCF/BCF file filtering, statistics, format conversion, and population genetics analyses. | Both |
Genomic File Processing7 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| bedtools_toolkit | BEDTools | Genome interval manipulation: intersect, merge, complement, closest, coverage for BED/GFF/VCF. | Both |
| picard_toolkit | Picard | High-throughput sequencing data manipulation: mark duplicates, sort, index, and compute metrics. | Pipeline |
| tabix_query | Tabix | Fast indexed random-access queries on bgzipped genomic files (VCF, BED, GFF). | Sync |
| genomicranges_toolkit | GenomicRanges | Bioconductor GenomicRanges for interval operations, overlap analysis, and range arithmetic. | Sync |
| format_conversion_toolkit | Format Conversion | Convert between bioinformatics formats: FASTA/FASTQ, SAM/BAM, VCF/BCF, GFF/GTF, BED, and archives. | Both |
| sequence_editor_toolkit | Sequence Editor | DNA/RNA/protein sequence editing: trim, translate, reverse complement, GC content, motif search. | Sync |
| zip_toolkit | Archive / Zip | File compression and decompression: ZIP, GZIP, BZIP2, XZ, 7-Zip, and TAR archive formats. | Sync |
Analysis & Statistics2 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| data_statistics | Data Statistics | Descriptive statistics, t-test, ANOVA, correlation analysis, and outlier detection on tabular data. | Sync |
| visualization_generator | Visualization Generator | Create charts, heatmaps, volcano plots, Manhattan plots, and 3D structure visualizations. | Sync |
File Management3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| file_reader | File Reader | Read and parse workspace files: Word, Excel, CSV, PDF (with OCR via AWS Textract), FASTA, GenBank. | Sync |
| file_writer | File Writer | Save reports, tables, and documents to the workspace. | Sync |
| file_search | File Search | Find and discover files in the workspace by name, extension, or metadata. | Sync |
Pipeline Management5 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| start_pipeline | Start Pipeline | Launch a predefined multi-step bioinformatics pipeline by pipeline ID or custom steps. | Both |
| pipeline_status | Pipeline Status | Check progress of a running multi-step pipeline — current step, logs, and completion percentage. | Sync |
| list_pipelines | List Pipelines | Discover predefined bioinformatics pipelines with descriptions, steps, and estimated runtimes. | Sync |
| process_status | Process Status | Check status of a long-running background process by process ID. | Sync |
| process_results | Process Results | Retrieve output files and results from a completed background process. | Sync |
Looking for predefined pipelines? Multi-step bioinformatics workflows (WES alignment, RNA-seq, GATK variant calling, protein binder design, and more) are documented on the Predefined Pipelines page.
Fetch the Tool List at Runtime
Call GET /v1/tools to retrieve the live tool registry with each tool's ID, parameter schema, and description.
from smartsbio import SmartsBio
client = SmartsBio(api_key="sk_live_...")
tools = client.tools.list()
for tool in tools:
print(f"{tool.id:40s} [{tool.category}]")
# Filter by category
protein_design = [t for t in tools if t.category == "AI Protein Design"]
pipeline_tools = [t for t in tools if t.invocation in ("pipeline", "both")]
# Inspect a tool's parameter schema
blast = next(t for t in tools if t.id == "ncbi_blast")
for param in blast.parameters:
print(f" {param.name} ({'required' if param.required else 'optional'}): {param.description}")Run a Tool Directly
# Sync tool — results returned immediately
result = client.tools.run(
tool_id="ncbi_pubmed",
input={"query": "BRCA1 breast cancer 2024", "maxResults": 5},
)
for article in result["results"]:
print(f"{article['pmid']}: {article['title']}")
# Pipeline tool — submit and poll
pipeline = client.pipelines.create(
tool_id="protein_structure_prediction",
workspace_id=ws_id,
input={"sequence": "MKTIIALSYIFCLVFA...", "model": "boltz2"},
)
pipeline = client.pipelines.wait(pipeline["id"], workspace_id=ws_id,
on_progress=lambda p: print(p["progress_pct"], "%"))
client.files.download(pipeline["output_keys"][0], workspace_id=ws_id, dest="./structure.pdb")