BioCompLab tools hub
The catalog is organized by area and subarea so the growing tool set stays searchable as the platform adds more wrappers, local services, and proprietary modeling pipelines.
BioCompLab-built tools
These tools are developed or orchestrated by BioCompLab. External wrappers remain available in the directory, but they are grouped separately because their execution, data, attribution, and rate limits belong to outside providers.
BioCompLab proprietary
BioCompLab Python/BioPython retrieval pipeline for curated organism whole-cell modeling data, including normalized JSON, SBML, SBOL, provenance, and coverage reporting.
Catalog filter
Genomics
NCBI Datasets
Retrieve NCBI Datasets assembly reports and prepare genome package download URLs for assembly accessions.
European Nucleotide Archive
Search ENA assemblies, reads, samples, studies, and sequence records using the ENA Portal API.
NCBI
Search NCBI Entrez databases such as nucleotide, protein, assembly, gene, genome, and PubMed.
Ensembl
Lookup gene symbols or Ensembl identifiers and retrieve genomic coordinates, transcripts, and feature metadata.
EMBL-EBI MGnify
Search microbiome and metagenomics studies, including biome metadata and ENA-linked accessions.
EMBL-EBI BioSamples
Search sample metadata linked to ENA, BioStudies, PRIDE, MetaboLights, and other omics archives.
NCBI
Submit a public BLAST job through the NCBI URL API and return the RID plus status and result links.
NCBI
Resolve organism names or taxonomy identifiers against the curated NCBI Taxonomy database.
Proteomics
EMBL-EBI InterPro
Retrieve protein family, domain, and functional site annotations from InterPro for a UniProt accession.
RCSB PDB
Retrieve metadata for experimental and computed macromolecular structures by PDB or CSM identifier.
STRING
Resolve protein names to STRING identifiers and open functional association networks.
EMBL-EBI QuickGO
Search Gene Ontology terms and definitions for biological process, molecular function, and cellular component annotation.
EMBL-EBI Proteins
Retrieve UniProt-derived protein records, sequence metadata, and feature annotations from the EBI Proteins API.
UniProt
Retrieve protein names, organism, sequence, function, Gene Ontology annotations, and database cross-references.
BioCompLab compute adapter
Submit a protein sequence to a configured local or institutional AlphaFold-compatible prediction service.
AlphaFold DB / EMBL-EBI
Find predicted protein structures, confidence metadata, and structure download links by UniProt accession.
PRIDE Archive
Search public mass-spectrometry proteomics projects and evidence metadata in PRIDE Archive.
Protein Data Bank in Europe
Retrieve PDBe entry summaries, deposition metadata, experimental methods, and structure links by PDB ID.
Metabolomics
ChEMBL
Search bioactive molecules, drug-like compounds, approvals, synonyms, and ChEMBL identifiers.
EMBL-EBI OLS / ChEBI
Search ChEBI chemical entities through the EMBL-EBI Ontology Lookup Service.
PubChem
Resolve compounds and retrieve identifiers, formulas, masses, SMILES, InChI, and source links.
EMBL-EBI MetaboLights
Search public MetaboLights metabolomics study accessions through EBI Search.
Systems modeling
EMBL-EBI BioModels
Search curated and non-curated mathematical models, including SBML pathway and systems-biology models.
WikiPathways
Search pathway references through EBI Search and retrieve official WikiPathways JSON, GPML, and SVG assets when a WPID is supplied.
BioCyc
Query a configured BioCyc web service endpoint when institutional access and BIOCYC credentials are available.
Reactome
Search curated pathways, reactions, and biological entities in Reactome.
KEGG
Search KEGG entries for pathways, genes, compounds, reactions, enzymes, and modules.
BioCompLab proprietary
BioCompLab Python/BioPython retrieval pipeline for curated organism whole-cell modeling data, including normalized JSON, SBML, SBOL, provenance, and coverage reporting.
Evidence and literature
Crossref
Search DOI metadata for articles, books, proceedings, and scholarly records connected to biological evidence trails.
Europe PMC
Search life-science literature across Europe PMC, including abstracts, preprints, books, patents, and open-access records.
NCBI PubMed
Search PubMed for literature connected to genes, organisms, pathways, proteins, and bioengineering topics.
Visualization
JBrowse
Launch an embedded JBrowse instance when JBROWSE_BASE_URL is configured, with assembly and genomic location parameters.
Synthetic biology
BioCompLab
A safe conceptual workspace for non-operational biological computing and synthetic biology design notes.
BioCompLab wrappers use official APIs, permitted linkouts, or local visualization components. The portal must not bypass provider authentication, usage policies, rate limits, CORS, or attribution requirements.
Users should not submit confidential, clinical, unpublished, controlled, or proprietary sequences to external public services. BioCompLab provides an integrated access layer, not ownership of external data.