Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs), and protein-protein interactions. Processes MaxQuant, Spectronaut, DIA-NN, and other MS platform outputs. Performs normalization, statistical analysis, pathway enrichment, and integration with transcriptomics. Use when analyzing proteomics data, comparing protein abundance between conditions, identifying PTM changes, studying protein complexes, integrating protein and RNA data, discovering protein biomarkers, or conducting quantitative proteomics experiments.

mims-harvard1.3k

Computación Científica

Tooluniverse Systems Biology

Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.

mims-harvard1.3k

Computación Científica

Tooluniverse Organic Chemistry

Teaches reasoning strategies for organic chemistry problems — reaction product prediction, spectroscopy interpretation, stereochemistry, and quantitative calculations. Use when users ask about reaction products, spectra, mechanisms, stereochemistry, or molecular formulas.

mims-harvard1.3k

Computación Científica

Computational Biophysics & Quantitative Biology Skill

Solve quantitative problems in biophysics, pharmacokinetics, epidemiology, toxicology, population genetics, and statistical mechanics. Provides reasoning strategies and Python templates for calculations alongside ToolUniverse data lookups. Use when users ask about drug dosing, half-life decay, radioactive tracers, R0, herd immunity, diffusion, Hardy-Weinberg, binding equilibria, or any computation-heavy biology/chemistry question.

mims-harvard1.3k

Computación Científica

Tooluniverse Gwas Finemapping

Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and suggests validation strategies. Use when asked to fine-map GWAS loci, prioritize causal variants, identify credible sets, or link GWAS signals to causal genes.

mims-harvard1.3k

Computación Científica

Inorganic & Physical Chemistry

Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, bonding theory (covalency, orbital mixing), symmetry/point groups, thermodynamics, kinetics, spectroscopy interpretation, noble gas compounds, lanthanide/actinide chemistry. Use for questions about crystal systems, unit cells, density calculations, metal complexes, solid-state chemistry, or physical chemistry calculations.

mims-harvard1.3k

Computación Científica

Metabolomics Research

Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.

mims-harvard1.3k

Computación Científica

Metabolomics Analysis

Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR data from targeted and untargeted experiments. Performs normalization, statistical analysis, pathway enrichment, metabolite-enzyme integration, and biomarker discovery. Use when analyzing metabolomics datasets, identifying differential metabolites, studying metabolic pathways, integrating with transcriptomics/proteomics, discovering metabolic biomarkers, performing flux balance analysis, or characterizing metabolic phenotypes in disease, drug response, or physiological conditions.

mims-harvard1.3k

Computación Científica

Neuroscience Research Skill

Neuroscience research and reasoning workflows using ToolUniverse tools. Covers computational neuroscience (rate models, integrate-and-fire neurons, synaptic plasticity, network dynamics), neuroanatomy (cortical regions, basal ganglia, cerebellum, brainstem, model organism connectomes), neurophysiology (ion channels, action potentials, synaptic transmission), neural circuits (E/I balance, oscillations, central pattern generators), synaptic dynamics (STDP, short-term plasticity, neuromodulation), neurodegenerative diseases (Alzheimer's, Parkinson's, ALS, Huntington's), and clinical neurology (cranial nerves, stroke localization, neuromuscular disorders). Use when researchers ask about brain regions, neural computation, firing rates, synaptic plasticity, connectomics, neurodegeneration, or clinical neurological questions.

mims-harvard1.3k

Computación Científica

Precision Medicine Patient Stratification

Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, genomic data (germline variants, somatic mutations, expression), and optional clinical parameters, performs multi-phase analysis covering disease disambiguation, genetic risk assessment, disease-specific molecular stratification, pharmacogenomic profiling, comorbidity/DDI risk, pathway analysis, clinical evidence and guideline mapping, clinical trial matching, and integrated outcome prediction. Generates a quantitative Precision Medicine Risk Score (0-100) with risk tier assignment, treatment algorithm, pharmacogenomic guidance, clinical trial matches, and monitoring plan.

mims-harvard1.3k

Computación Científica

Protein Post-Translational Modification Analysis

Analyze post-translational modifications (PTMs) of proteins — modification sites, types, proteoforms, functional effects at PTM sites, and PTM-dependent protein interactions. Integrates iPTMnet, ProtVar, UniProt, and STRING databases. Use when asked about protein phosphorylation, ubiquitination, acetylation, glycosylation, methylation, SUMOylation, or other PTMs; proteoform diversity; PTM-regulated interactions; or functional impact of PTM sites.

mims-harvard1.3k

Computación Científica

Tooluniverse Sequence Analysis

Retrieve and analyze biological sequences -- gene/protein sequences from NCBI, Ensembl, and UniProt. Search nucleotide databases, fetch by accession, find orthologs, get gene summaries. Use when users ask about DNA/RNA/protein sequences, gene lookups, ortholog searches, or sequence retrieval.

mims-harvard1.3k

Computación Científica

Running Placebo Analysis

Performs placebo-in-time sensitivity analysis with hierarchical null model and optional Bayesian assurance. Use when checking model robustness, verifying lack of pre-intervention effects, or estimating study power.

pymc-labs1.1k

Computación Científica

Protein Mutation Analysis

Analyze protein mutations by retrieving protein data, explaining mutation effects, predicting protein structure, and visualizing results. Use this skill when the user asks about protein mutations, wants to understand mutation effects, or needs to analyze genetic variants. Triggers on phrases like "analyze mutation", "explain mutation", "what does this mutation do", "protein variant analysis".

PharMolix1.0k

Computación Científica

Iupac Name Identification Biot5

Identify the IUPAC name of a molecule using BioT5 question answering model. Use this skill when: (1) User wants to find the IUPAC name of a molecule, (2) User asks "What is the IUPAC name?" or "What's the systematic name?", (3) User provides a SMILES string and wants the IUPAC nomenclature.

PharMolix1.0k

Computación Científica

Similar Protein Retrieval

Retrieve proteins with similar structures, sequences, or from the same family. Use this skill when: (1) Finding similar proteins or homologs, (2) Searching for proteins with similar 3D structure, (3) Performing sequence similarity search, (4) Discovering proteins in the same family.

PharMolix1.0k

Computación Científica

Molecule Biochemical Significance Query

Query a molecule's biochemical significance and roles in biology and chemistry using BioT5 multi-modal model. Use this skill when: (1) Understanding a molecule's biological roles and functions, (2) Describing a molecule's chemical significance and applications, (3) Getting natural language explanations of molecular properties, (4) Summarizing what a molecule is used for or its metabolic relevance.

PharMolix1.0k

Computación Científica

Protein Function Prediction

Predict protein function and properties from amino acid sequence using BioT5. Use this skill when: (1) You have a protein sequence and want to understand its biological function, (2) You need to identify enzyme activity, pathway involvement, or molecular interactions, (3) You want a concise description of protein properties from sequence alone.

PharMolix1.0k

Computación Científica

Single Cell Foundation Model Geneformer

Use this skill when a task involves Geneformer workflows, especially TranscriptomeTokenizer input preparation, tokenized `.dataset` generation, cell or gene classification with `Classifier`, embedding extraction with `EmbExtractor`, and in silico perturbation analysis with `InSilicoPerturber`.

PharMolix1.0k

Computación Científica

Uniprot Query

Query UniProt database for protein sequences, metadata, and search by criteria. Use this skill when: (1) Looking up protein information by UniProt accession ID, (2) Searching proteins by gene name, organism, function, or disease, (3) Retrieving comprehensive protein metadata including domains, PTMs, and annotations.

PharMolix1.0k

Computación Científica

Csv Processing

Use this skill when reading sensor data from CSV files, writing simulation results to CSV, processing time-series data with pandas, or handling missing values in datasets.

benchflow-ai990

Computación Científica

Pymatgen

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

benchflow-ai990

Computación Científica

Cobrapy

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

wu-yc965

Computación Científica

Etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

wu-yc965

Computación Científica

Proteomics Analysis

wu-yc965

Computación Científica

Flowio

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

wu-yc965

Computación Científica

Deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

wu-yc965

Computación Científica

Cosmic Database

Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

wu-yc965

Computación Científica

Tooluniverse Systems Biology

wu-yc965

Computación Científica

Exploratory Data Analysis

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

wu-yc965

Computación Científica Skills | Skills Pool