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skill-python-research
Research Python/Z3 patterns and APIs for semantic theory development. Invoke for Python-language research tasks.
☆ 12View skill
Search results for “Python”
Skills matching the name, description or GitHub author.
Categories: blockchain computational chemistry
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gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
☆ 9View skill
GitHub
pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal pro...
☆ 9View skill
GitHub
julia-scientific
Julia package equivalents for 137 K-Dense-AI scientific skills. Maps Python bioinformatics, chemistry, ML, quantum, and data science packages to native Julia ecosystem.
☆ 5View skill
GitHub
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
☆ 3View skill
GitHub
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices...
☆ 3View skill
GitHub
simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service o...
☆ 3View skill
GitHub
gtars
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment...
☆ 3View skill
GitHub
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID map...
☆ 3View skill
GitHub
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conforme...
☆ 3View skill
GitHub
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
☆ 3View skill
GitHub
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch...
☆ 3View skill
GitHub
omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
☆ 3View skill
GitHub
uniprot-database
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use thi...
☆ 3View skill
GitHub
biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioin...
☆ 3View skill
GitHub
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, pro...
☆ 3View skill
GitHub
airalogy-protocol
Expert guide for creating Airalogy Protocols (AIMD), Assigners (Python logic), and Validation Models. Use this to design digital workflows and experiments.
☆ 1View skill
GitHub
reviewing-python-architecture
Review ADRs to check they follow testing principles. Use when reviewing ADRs or architecture decisions.
☆ 1View skill
GitHub
life-sciences-connector
Query PubMed and scientific databases for protocols, analyze biological data with Biopython, handle HIPAA-compliant data. Use for biology research, protocol searches, sequence analysis, or scientific data handl...
☆ 0View skill
GitHub
bio-blast
NCBI BLAST sequence similarity search using BioPython. Use when a user wants to run BLAST programmatically with blastn/blastp and retrieve results in JSON format.
☆ 0View skill
GitHub
spatialdata
SpatialData framework for handling spatial multi-modal and multi-scale data. Use this skill for questions about spatial omics data analysis, visualization, and the SpatialData Python ecosystem.
☆ 0View skill
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