scientific-computing
0
literature-search
Search PubMed for RNAi/dsRNA research on target genes or species (utility skill - use anytime)
katalyzeAI
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
scientific-computing
0
la-bench-parser
Parse LA-Bench format JSONL files to extract experimental protocol data by ID. This skill should be used when working with LA-Bench datasets to retrieve structured experimental instructions, materials, protocol steps, expected outcomes, and references for a specific experiment entry.
dakesan
research
scientific-computing
0
deep-researcher
Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources. Uses file-based research tracking, parallel investigation threads, and context-efficient patterns for deep investigations. ALL MEDICAL CITATIONS FROM PUBMED MCP ONLY.
drshailesh88
research
scientific-computing
0
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 handling. Cross-validates sources for high accuracy. Triggers on "PubMed", "biology", "scientific data", "sequences", "protocols", "life sciences", "HIPAA".
dredd-us
research
scientific-computing
0
lucy-ngcase
Full de novo structure elucidation - skip dereplication and solve the structure from NMR correlations. Use when dereplication returned no matches, the compound is known to be novel, or you want to solve the structure from first principles.
steinbeck
research
scientific-computing
0
cellcharter-local-optimized
CellCharter spatial transcriptomics analysis toolkit - complete documentation with precise file name-based categorization
Ketomihine
research
scientific-computing
0
matchms
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
MAF2414
research
scientific-computing
0
banksy-merged-v3
BANKSY spatial transcriptomics analysis tool - complete documentation with notebooks and source code
Ketomihine
research
scientific-computing
0
taxonomy-resolver
Resolves ambiguous organism names to precise NCBI taxonomy IDs and scientific names, then recommends appropriate IWC (Intergalactic Workflow Commission) Galaxy workflows for analysis. Use this skill when users provide common names (like "malaria parasite", "E. coli", "mouse"), abbreviated names, or when you need to convert any organism reference to an exact scientific name for API queries. This skill handles disambiguation through conversation, validates taxonomy IDs via NCBI Taxonomy API, provides ENA FASTQ search capabilities, and ALWAYS recommends existing IWC workflows rather than producing custom scripts or analysis steps.
dannon
research
scientific-computing
0
lucy-ng
Computer-Assisted Structure Elucidation (CASE) for organic natural products using NMR spectroscopy. Use when the user asks to identify an unknown compound from NMR data, perform structure elucidation, analyze HSQC/HMBC/DEPT/COSY spectra, run dereplication against natural product databases (COCONUT, NMRShiftDB), generate LSD solver input, rank candidate structures by 13C prediction, or determine molecular structure from Bruker NMR data. Requires molecular formula and Bruker-format NMR spectra.
steinbeck
research
scientific-computing
0
design-dsrna
Design dsRNA candidates using sliding window algorithm
katalyzeAI
research
scientific-computing
0
bio-igv
This skill should be used when the user needs to visualize BAM alignment files in IGV (Integrative Genomics Viewer). Triggers include requests to generate IGV screenshots, visualize genomic regions with multiple BAM tracks, or create batch visualizations for WGS analysis results.
dakesan
research
scientific-computing
0
envi-pkg-local-improved
ENVI spatial transcriptomics analysis toolkit - comprehensive documentation with tutorials and Python source code
Ketomihine
research
scientific-computing
0
ligandmpnn-reference
LigandMPNN sequence design reference. Use when working with LigandMPNN, ProteinMPNN, sequence design, amino acid biasing, fixed residues, temperature, side chain packing, or membrane protein design.
polaires
research
scientific-computing
0
alphafold-database
Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
Sologa
research
scientific-computing
0
lammps-simulation
Run LAMMPS molecular dynamics simulations. Use when asked to run MD simulations, energy minimization, equilibration, production runs, or calculate properties like diffusion, RDF, MSD. Supports both CPU and GPU execution.
fl-sean03
research
scientific-computing
0
bio-cosmic
This skill should be used when the user needs to query COSMIC Cancer Gene Census to check if genes are known cancer genes. Triggers include requests to annotate genes with cancer information, check if variants are in cancer genes, or retrieve cancer gene properties from COSMIC database.
dakesan
research
scientific-computing
0
tidy-itc-workflow
Master tidy modelling patterns for ITC analyses following TMwR principles. Covers workflow structure, consistent interfaces, reproducibility best practices, and data validation. Use when setting up ITC analysis projects or building pipelines.
choxos
research
scientific-computing
0
banksy-merged-v4
BANKSY spatial transcriptomics analysis tool - complete documentation with precise file name-based categorization
Ketomihine
research
scientific-computing
0
curate-genome-assembly
Process genome assembly datasets for VEuPathDB resources
VEuPathDB
research