Explorar skills

Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.

Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision framework for picking methods by challenge type (stuck, improving, systematic exploration, contradiction). Use when generating research ideas or exploring interdisciplinary connections.

Consulte as bibliotecas de compostos virtuais ZINC15/ZINC22 (1.4B compostos, 750M compráveis) para pesquisar compostos tipo chumbo, fragmento ou medicamento por MW, logP, reatividade ou similaridade SMILES, e baixe conjuntos 3D para docking. Para bioatividade, use chembl-database-bioactivity; para medicamentos aprovados, use drugbank-database-access.

Query FDA drug labels (DailyMed) via REST API. Search structured product labels (SPLs) by name, NDC, set ID, or RxCUI; get indications, dosage, warnings, adverse reactions, packaging. No auth. For adverse events use fda-database; for DDIs use ddinter-database.

Annotated matrices for single-cell genomics. Stores X with obs/var metadata, layers, embeddings (obsm/varm), graphs (obsp/varp), uns. Use for .h5ad/.zarr I/O, concatenation, scverse integration. For analysis use scanpy; for probabilistic models use scvi-tools.

Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGG

Open-source bio-image data management. Use the omero-py client to connect to an OMERO server, retrieve images as numpy arrays, annotate with tags and key-value pairs, manage ROIs, and feed image data into Python analysis pipelines — programmatically, no GUI.

KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.

WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep, tile-based DL, slide QC. Use pathml for multiplexed imaging.

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinv

Python API v2 for Opentrons OT-2/Flex liquid handlers: protocols as Python files with metadata and run(); control pipettes, labware, and modules (thermocycler, heater-shaker, magnetic, temperature). Simulate via opentrons_simulate then upload. Use PyLabRobot for vendor-agnostic scripts (Hamilton, Tecan).

Scientific manuscript writing: IMRAD, citation styles (APA/AMA/Vancouver/IEEE), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA/ARRIVE), writing principles (clarity/conciseness/accuracy), venue-specific style. For LaTeX see companion assets.