@saibolla/ada 0.1.2

package/skills/scientific-workflows/SKILL.md

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+---
+name: scientific-workflows
+description: Catalog of 325 scientific workflow procedures across 22 disciplines. Read this skill when the user asks for a structured scientific task — data analysis, genomics pipelines, drug discovery, clinical analysis, financial modeling, visualization, grant writing, paper writing, or any domain-specific research workflow. Match the task to a workflow below and follow its procedure with the suggested skills.
+---
+
+# Scientific Workflow Catalog
+
+Match the user task to the most relevant workflow below. Activate the suggested skills, then follow the prompt as your procedure.
+
+If the task needs uploaded files, ask the user for the file path before starting.
+
+## Astronomy and Astrophysics
+
+### Stellar Classification
+**Skills:** astropy, scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Classify stars from the uploaded dataset. (1) Extract photometric features (magnitudes, colors, indices), (2) Place stars on the HR diagram (color-magnitude or temperature-luminosity), (3) Classify spectral types (O, B, A, F, G, K, M), (4) Identify luminosity class (dwarf, giant, supergiant), (5) Detect peculiar stars (WR, carbon, subdwarfs), (6) Generate an annotated HR diagram.
+
+### Exoplanet Detection
+**Skills:** astropy, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Search for exoplanets in the uploaded {method} data. (1) Preprocess the light curve or RV time series (detrending, outlier removal), (2) Search for periodic signals using BLS or Lomb-Scargle, (3) Fit a transit/RV model to candidate signals, (4) Estimate planet parameters (radius, mass, orbital period, semi-major axis), (5) Assess false positive probability, (6) Generate phase-folded plots and orbital diagrams.
+
+### Astronomical Spectral Analysis
+**Skills:** astropy, matplotlib, scientific-visualization **[needs files]**
+
+Analyze the uploaded astronomical spectrum ({object_type}). (1) Calibrate wavelength and flux, (2) Identify spectral lines (absorption/emission), (3) Measure line strengths (equivalent widths), (4) Determine radial velocity from Doppler shifts, (5) Estimate physical parameters ({params}), (6) Compare with template spectra and model atmospheres.
+
+### Galaxy Morphology Classification
+**Skills:** astropy, scikit-learn, scientific-visualization, pytorch-lightning **[needs files]**
+
+Classify galaxy morphology from the uploaded imaging data. (1) Detect and extract galaxy images, (2) Measure structural parameters (Sérsic index, effective radius, axis ratio, position angle), (3) Classify using the Hubble sequence (elliptical, spiral, irregular), (4) Identify features (bars, rings, tidal tails, mergers), (5) Compare with catalog classifications, (6) Generate a morphology summary with annotated images.
+
+### Orbital Mechanics Calculation
+**Skills:** astropy, sympy, matplotlib, scientific-visualization
+
+Calculate orbital mechanics for: {mission}. (1) Define the initial and target orbits (a, e, i, Ω, ω, ν), (2) Compute the transfer trajectory ({transfer_type}), (3) Calculate delta-v requirements, (4) Determine flight time and launch windows, (5) Analyze gravitational assists if applicable, (6) Visualize the trajectory in 3D. Report total delta-v budget.
+
+### Light Curve Analysis
+**Skills:** astropy, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded light curve of {object}. (1) Remove systematic trends (detrending), (2) Compute periodogram (Lomb-Scargle), (3) Determine the period and phase-fold the data, (4) Classify the variability type: {var_type}, (5) Fit a physical model (eclipsing binary, pulsation, rotation), (6) Extract physical parameters from the best-fit model.
+
+### Radio Astronomy Analysis
+**Skills:** astropy, matplotlib, scientific-visualization **[needs files]**
+
+Analyze the uploaded radio astronomy data ({observation_type}). (1) Calibrate and flag RFI, (2) Image the data (if interferometric: CLEAN deconvolution), (3) Measure source properties (flux density, position, size), (4) Construct the spectral energy distribution, (5) Identify spectral lines if present ({lines}), (6) Generate publication-quality radio maps and spectra.
+
+### Gravitational Lensing Analysis
+**Skills:** astropy, matplotlib, scientific-visualization, sympy **[needs files]**
+
+Analyze gravitational lensing in the uploaded data. (1) Identify lensed features (arcs, multiple images, distortions), (2) Model the mass distribution of the lens ({lens_type}), (3) Reconstruct the source morphology, (4) Estimate the lens mass and mass-to-light ratio, (5) Constrain dark matter distribution, (6) Visualize the lensing geometry and mass model.
+
+### Dark Matter Constraints
+**Skills:** astropy, pymc, matplotlib, scientific-visualization **[needs files]**
+
+Derive dark matter constraints from the uploaded data ({data_type}). (1) Fit dark matter halo models ({profile}) to the data, (2) Compare with baryon-only predictions, (3) Estimate dark matter mass and concentration, (4) Place upper limits on dark matter cross-section or decay rate, (5) Compare with existing constraints from other experiments, (6) Visualize exclusion limits in parameter space.
+
+### Solar Activity Analysis
+**Skills:** astropy, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze solar activity from the uploaded data. (1) Identify and catalog solar events (flares: {flare_class}, CMEs, sunspots), (2) Analyze the solar cycle phase, (3) Compute flare frequency-energy distributions, (4) Analyze geomagnetic indices (Kp, Dst) correlation with solar events, (5) Assess space weather impacts, (6) Generate a solar activity summary dashboard.
+
+### Cosmic Ray Analysis
+**Skills:** astropy, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded cosmic ray data. (1) Reconstruct primary particle energy and direction, (2) Determine chemical composition from shower observables, (3) Compute energy spectrum and compare with known models, (4) Search for anisotropy in arrival directions, (5) Analyze temporal variations and correlation with solar activity, (6) Compare with theoretical predictions and other experiments.
+
+## Cell Biology and Single-Cell
+
+### scRNA-seq Clustering
+**Skills:** scanpy, anndata, scientific-visualization, umap-learn **[needs files]**
+
+Perform clustering analysis on the uploaded scRNA-seq data. (1) Apply Leiden/Louvain clustering at multiple resolutions, (2) Evaluate cluster stability and optimal resolution, (3) Identify marker genes per cluster (Wilcoxon rank-sum test), (4) Annotate clusters using {reference} markers, (5) Visualize on UMAP with marker expression, (6) Report cluster proportions and key distinguishing features.
+
+### Cell Type Annotation
+**Skills:** scvi-tools, scanpy, cellxgene-census, anndata **[needs files]**
+
+Annotate cell types in the uploaded scRNA-seq dataset. (1) Use automated annotation tools (scvi-tools, CellTypist) against reference atlases, (2) Validate with known marker genes for {tissue}, (3) Resolve ambiguous annotations using subclustering, (4) Generate annotation confidence scores, (5) Visualize annotated UMAP and dotplots of markers, (6) Report cell type proportions.
+
+### Trajectory / Pseudotime Analysis
+**Skills:** scanpy, scvelo, scientific-visualization, anndata **[needs files]**
+
+Perform trajectory analysis on the uploaded scRNA-seq data. (1) Identify root cell population based on {root}, (2) Compute diffusion pseudotime or PAGA connectivity, (3) Order cells along developmental trajectories, (4) Identify genes that change along pseudotime (trajectory-associated genes), (5) Detect branch points and fate decisions, (6) Visualize trajectory on UMAP and gene expression trends along pseudotime.
+
+### Flow Cytometry Analysis
+**Skills:** flowio, scientific-visualization, statistical-analysis, umap-learn **[needs files]**
+
+Analyze the uploaded flow cytometry data (FCS files). (1) Compensation and quality control, (2) Automatic gating or reproduce manual gating strategy: {gating}, (3) Dimensionality reduction (UMAP) of marker expression, (4) FlowSOM or Phenograph clustering, (5) Quantify cell population frequencies, (6) Compare populations between {comparison}. Generate publication-quality dot plots and histograms.
+
+### Cell-Cell Communication
+**Skills:** scanpy, anndata, networkx, scientific-visualization **[needs files]**
+
+Infer cell-cell communication networks from the uploaded scRNA-seq data. (1) Identify ligand-receptor pairs between cell types, (2) Score interaction strength using CellChat or similar, (3) Identify dominant signaling pathways, (4) Detect outgoing and incoming signals per cell type, (5) Visualize communication networks (chord diagrams, dot plots), (6) Compare signaling between {comparison} if multiple conditions.
+
+### Multi-Omics Integration
+**Skills:** scvi-tools, anndata, scanpy, scientific-visualization **[needs files]**
+
+Integrate the uploaded multi-omics datasets ({modalities}). (1) Harmonize features across modalities, (2) Apply integration methods (MOFA+, WNN, or scVI multi-modal), (3) Generate a joint embedding, (4) Identify features driving cross-modality variation, (5) Discover multi-omic cell states or subtypes, (6) Validate with modality-specific markers.
+
+### Cell Cycle Analysis
+**Skills:** scanpy, anndata, scientific-visualization **[needs files]**
+
+Perform cell cycle analysis on the uploaded scRNA-seq data. (1) Score G1, S, and G2M phases using standard gene sets, (2) Visualize cell cycle distribution across clusters, (3) Test whether cell cycle drives clustering, (4) Regress out cell cycle effects if confounding, (5) Compare cell cycle distribution between {comparison}, (6) Identify cell cycle-regulated genes specific to each cell type.
+
+### Perturbation / CRISPR Screen Analysis
+**Skills:** scanpy, anndata, depmap, scientific-visualization **[needs files]**
+
+Analyze the uploaded perturbation screen data ({screen_type}). (1) QC: assess guide RNA coverage and cell numbers per perturbation, (2) Identify differentially expressed genes per perturbation vs non-targeting controls, (3) Score perturbation effects on gene programs, (4) Cluster perturbations by transcriptional similarity, (5) Identify genetic interactions or epistasis, (6) Prioritize hits for validation.
+
+### Immune Cell Profiling
+**Skills:** scanpy, anndata, scientific-visualization, statistical-analysis **[needs files]**
+
+Perform immune cell profiling from the uploaded data ({data_type}). (1) Identify major immune populations (T cells, B cells, NK, myeloid, DCs), (2) Subtype each population (CD4/CD8, naive/memory/effector), (3) Score activation, exhaustion, and cytotoxicity signatures, (4) Quantify clonal expansion from TCR/BCR if available, (5) Compare immune composition between {comparison}, (6) Generate a comprehensive immune landscape report.
+
+### Lineage Tracing Analysis
+**Skills:** scanpy, anndata, etetoolkit, scientific-visualization **[needs files]**
+
+Analyze lineage tracing data from the uploaded dataset. (1) Process barcode or mutation data for lineage reconstruction, (2) Build lineage trees using neighbor-joining or Bayesian methods, (3) Map cell types onto the lineage tree, (4) Identify lineage-biased progenitors, (5) Quantify fate probabilities for each progenitor class, (6) Visualize lineage trees annotated with cell types and pseudotime.
+
+### Spatial Cell Analysis
+**Skills:** scanpy, scientific-visualization, geopandas **[needs files]**
+
+Analyze spatial cell organization in the uploaded data ({platform}). (1) Segment cells and quantify marker expression, (2) Classify cell types, (3) Identify spatial neighborhoods and niches, (4) Compute spatial statistics (co-localization, exclusion, clustering), (5) Detect tissue microenvironments, (6) Correlate spatial patterns with {outcome} if available.
+
+### Metabolic Flux Analysis
+**Skills:** cobrapy, kegg-database, scientific-visualization, matplotlib
+
+Perform metabolic flux analysis on {organism} using constraint-based modeling. (1) Load or construct a genome-scale metabolic model (GEM), (2) Define media conditions: {media}, (3) Run flux balance analysis (FBA) to predict growth rate and fluxes, (4) Perform flux variability analysis (FVA), (5) Simulate gene knockouts and predict essential genes, (6) Visualize metabolic flux maps on pathway diagrams.
+
+### Glycan Engineering & Analysis
+**Skills:** glycoengineering, biopython, scientific-visualization, matplotlib **[needs files]**
+
+Analyze glycosylation patterns from the uploaded data. (1) Identify N-linked and O-linked glycan structures, (2) Quantify glycoform distributions, (3) Map glycosylation sites on the protein, (4) Compare glycoprofiles between {comparison}, (5) Predict the impact of glycosylation on protein function and immunogenicity, (6) Suggest glycoengineering strategies to optimize the glycoprofile.
+
+## Chemistry and Cheminformatics
+
+### Molecular Property Prediction
+**Skills:** rdkit, datamol, molfeat, deepchem **[needs files]**
+
+Predict properties of the uploaded molecules (SMILES or SDF). Properties to predict: {properties}. (1) Calculate molecular descriptors (MW, LogP, TPSA, HBD/HBA, rotatable bonds), (2) Apply ML models for property prediction, (3) Assess drug-likeness (Lipinski, Veber, Ghose rules), (4) Generate a property dashboard for each molecule, (5) Flag outliers or unusual structures, (6) Export results as a table.
+
+### Chemical Reaction Prediction
+**Skills:** rdkit, deepchem, scientific-writing
+
+Predict the products and conditions for the reaction: {reaction}. (1) Identify the reaction type and mechanism, (2) Predict major and minor products, (3) Estimate regioselectivity and stereoselectivity, (4) Suggest optimal reaction conditions (solvent, temperature, catalyst), (5) Predict expected yield range, (6) Flag potential side reactions or safety concerns.
+
+### Retrosynthesis Planning
+**Skills:** rdkit, pubchem-database, deepchem, research-lookup
+
+Plan a retrosynthetic route to: {target}. (1) Identify strategic disconnections, (2) Propose multiple synthetic routes (3-5 routes), (3) Evaluate each route: number of steps, reagent availability, expected yields, (4) Check literature for precedent reactions, (5) Rank routes by practicality, (6) Provide a detailed forward synthesis plan for the top route with specific reagents and conditions.
+
+### Conformer Generation & Analysis
+**Skills:** rdkit, datamol, rowan
+
+Generate and analyze conformers for: {molecule}. (1) Generate a diverse conformer ensemble (ETKDG or similar), (2) Optimize geometries with a force field, (3) Rank conformers by energy, (4) Analyze the conformational landscape (torsion angles, RMSD clustering), (5) Identify the global minimum and key metastable states, (6) Visualize the low-energy conformers.
+
+### QSAR Modeling
+**Skills:** rdkit, molfeat, deepchem, scikit-learn **[needs files]**
+
+Build a QSAR model for {target_property} using the uploaded molecular dataset. (1) Calculate molecular descriptors and fingerprints, (2) Split data into training/test sets with scaffold splitting, (3) Train multiple models (random forest, gradient boosting, neural network), (4) Evaluate with cross-validation (R², RMSE, MAE), (5) Analyze feature importance and applicability domain, (6) Predict {target_property} for new molecules if provided.
+
+### Chemical Space Exploration
+**Skills:** rdkit, molfeat, umap-learn, scientific-visualization **[needs files]**
+
+Explore the chemical space of the uploaded compound library. (1) Calculate molecular fingerprints for all compounds, (2) Reduce to 2D/3D using t-SNE and UMAP, (3) Color by {property} if available, (4) Identify clusters and outliers, (5) Compare with known drug space (DrugBank), (6) Identify underexplored regions, (7) Report diversity metrics (scaffold diversity, property coverage).
+
+### NMR Spectral Analysis
+**Skills:** rdkit, scientific-visualization, matplotlib **[needs files]**
+
+Analyze the uploaded NMR spectrum ({nmr_type}) for: {compound}. (1) Identify all peaks and their chemical shifts, (2) Assign peaks to structural features, (3) Analyze multiplicity patterns (1H) or DEPT data (13C), (4) Determine connectivity from 2D experiments if provided (COSY, HSQC, HMBC), (5) Confirm or propose the molecular structure, (6) Report complete assignments table.
+
+### Mass Spectrometry Analysis
+**Skills:** matchms, pyopenms, scientific-visualization, rdkit **[needs files]**
+
+Analyze the uploaded mass spectrometry data ({ms_type}). (1) Identify molecular ion peak and calculate molecular formula, (2) Interpret fragmentation pattern, (3) Match fragments against spectral libraries, (4) Propose structural fragments for unknown peaks, (5) Quantify target compounds if standards provided, (6) Generate annotated spectrum visualization.
+
+### Thermodynamics Calculation
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Calculate thermodynamic properties for: {system}. (1) Compute standard enthalpies, entropies, and Gibbs free energies, (2) Determine equilibrium constants at {temperature}, (3) Generate van't Hoff plots across temperature range, (4) Calculate reaction spontaneity and feasibility, (5) Estimate activation energy if kinetic data provided, (6) Compare with experimental values from literature.
+
+### pKa Prediction
+**Skills:** rdkit, datamol, medchem
+
+Predict pKa values for: {molecule}. (1) Identify all ionizable groups, (2) Predict microscopic pKa for each site, (3) Determine the dominant protonation state at pH {ph}, (4) Generate a microspeciation diagram, (5) Compare with experimental pKa values if available, (6) Analyze the effect of pH on charge state and solubility.
+
+### Solubility Prediction
+**Skills:** rdkit, datamol, medchem, deepchem
+
+Predict the aqueous solubility of: {molecules}. (1) Calculate LogS using multiple methods (ESOL, AqSolPred, group contribution), (2) Predict intrinsic and pH-dependent solubility, (3) Analyze structural features affecting solubility, (4) Suggest salt forms or co-crystal strategies to improve solubility if needed, (5) Compare with experimental data if available, (6) Report BCS classification.
+
+### Reaction Optimization
+**Skills:** rdkit, pymoo, scientific-visualization, statistical-analysis
+
+Design an optimization campaign for the reaction: {reaction}. (1) Identify key variables (temperature, solvent, catalyst loading, concentration, time), (2) Design a DoE (Design of Experiments) plan — factorial or Bayesian optimization, (3) Suggest the initial screening set, (4) Define the objective function and constraints, (5) Propose an iterative optimization strategy, (6) Estimate the number of experiments needed.
+
+### Polymer Design & Analysis
+**Skills:** rdkit, research-lookup, scientific-writing, deepchem
+
+Design or analyze a polymer for {application}. Target properties: {properties}. (1) Identify candidate monomer structures, (2) Predict key polymer properties (Tg, Tm, mechanical strength, solubility), (3) Evaluate sustainability and processability, (4) Compare with existing polymers in the literature, (5) Suggest synthesis routes, (6) Recommend characterization experiments.
+
+### Catalyst Design
+**Skills:** rdkit, research-lookup, deepchem, scientific-writing
+
+Design a catalyst for: {reaction}. (1) Analyze the reaction mechanism and identify the rate-determining step, (2) Propose candidate catalyst scaffolds (metal-organic, enzymatic, organocatalytic), (3) Predict activity trends using descriptors, (4) Screen candidates computationally, (5) Compare with known catalysts in the literature, (6) Recommend top candidates for experimental testing.
+
+### Chemical Safety Assessment
+**Skills:** rdkit, pubchem-database, research-lookup
+
+Perform a safety assessment of: {chemicals}. (1) Look up GHS classification and hazard statements, (2) Predict toxicity endpoints (LD50, LC50, mutagenicity), (3) Assess environmental fate (biodegradation, bioaccumulation), (4) Check regulatory status (REACH, TSCA), (5) Identify incompatibilities and storage requirements, (6) Generate a safety data summary.
+
+### Metabolite Identification
+**Skills:** matchms, hmdb-database, metabolomics-workbench-database, kegg-database **[needs files]**
+
+Identify metabolites from the uploaded {data_type} data. (1) Process and align spectral features, (2) Match against spectral databases (HMDB, MassBank, METLIN), (3) Predict metabolite identities from accurate mass and fragmentation, (4) Score confidence levels (identified, putative, unknown), (5) Map identified metabolites to metabolic pathways, (6) Report a ranked candidate list for each feature.
+
+### Synthetic Accessibility Score
+**Skills:** rdkit, datamol, zinc-database, medchem **[needs files]**
+
+Evaluate the synthetic accessibility of the uploaded molecules. (1) Calculate SA scores for each compound, (2) Identify challenging structural motifs (strained rings, stereocenters, rare functional groups), (3) Estimate the number of synthetic steps, (4) Flag commercially available building blocks, (5) Rank compounds by ease of synthesis, (6) Suggest simplifications for hard-to-synthesize compounds.
+
+### Metabolomics Data Analysis
+**Skills:** hmdb-database, metabolomics-workbench-database, kegg-database, scientific-visualization **[needs files]**
+
+Analyze the uploaded metabolomics dataset ({platform}). (1) Preprocess: peak picking, alignment, normalization, (2) Quality control (QC sample analysis, batch correction), (3) Statistical analysis: PCA, PLS-DA between {comparison}, (4) Identify significant metabolites (fold change > {fc}, FDR < 0.05), (5) Pathway enrichment via KEGG and MetaboAnalyst, (6) Generate volcano plot, pathway impact plot, and metabolite heatmap.
+
+## Clinical Research and Medicine
+
+### Clinical Trial Analysis
+**Skills:** statistical-analysis, scikit-survival, scientific-visualization, statsmodels **[needs files]**
+
+Analyze the uploaded clinical trial data. (1) Describe the study population (demographics, baseline characteristics), (2) Analyze the primary endpoint: {endpoint}, (3) Perform intention-to-treat and per-protocol analyses, (4) Generate Kaplan-Meier curves for time-to-event endpoints, (5) Run subgroup analyses, (6) Report adverse events. Follow CONSORT reporting guidelines.
+
+### Clinical Survival Analysis
+**Skills:** scikit-survival, statistical-analysis, scientific-visualization, matplotlib **[needs files]**
+
+Perform survival analysis on the uploaded clinical data. Outcome: {outcome}, follow-up time in {time_unit}. (1) Kaplan-Meier estimates for overall and subgroup survival, (2) Log-rank tests comparing {groups}, (3) Multivariable Cox regression adjusting for {covariates}, (4) Check proportional hazards assumption, (5) Generate forest plot of hazard ratios, (6) Report median survival and 5-year rates.
+
+### Epidemiological Study Design
+**Skills:** statistical-analysis, scientific-writing, research-lookup, statsmodels
+
+Design an epidemiological study to investigate: {question}. Study type: {study_type}. (1) Define the study population and sampling strategy, (2) Specify exposure and outcome definitions, (3) Identify confounders and effect modifiers, (4) Calculate required sample size, (5) Plan the statistical analysis (OR, RR, hazard ratios), (6) Describe methods to address bias (selection, information, confounding).
+
+### Medical Image Analysis
+**Skills:** pydicom, pathml, imaging-data-commons, pytorch-lightning **[needs files]**
+
+Analyze the uploaded medical images ({modality}). (1) Preprocess images (normalization, artifact removal), (2) Apply segmentation for {target_structure}, (3) Extract quantitative features (shape, texture, intensity), (4) Classify findings using ML models if applicable, (5) Generate annotated output images, (6) Report findings in standard radiological/pathological format.
+
+### Diagnostic Test Accuracy
+**Skills:** statistical-analysis, scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Evaluate the diagnostic accuracy of {test} for {condition} using the uploaded data. (1) Calculate sensitivity and specificity, (2) Compute PPV and NPV at prevalence = {prevalence}, (3) Generate ROC curve with AUC, (4) Determine optimal cutoff (Youden's index), (5) Calculate likelihood ratios, (6) Report results following STARD guidelines.
+
+### Treatment Comparison
+**Skills:** statistical-analysis, scikit-survival, scientific-visualization, statsmodels **[needs files]**
+
+Compare treatment outcomes between {treatments} using the uploaded clinical data. (1) Check baseline balance between groups, (2) Analyze primary outcome with appropriate tests, (3) Adjust for confounders using {method}, (4) Perform NNT (number needed to treat) calculation, (5) Analyze secondary outcomes, (6) Run sensitivity analyses. Report effect sizes with confidence intervals.
+
+### Clinical Risk Prediction Model
+**Skills:** pyhealth, scikit-learn, scikit-survival, scientific-visualization **[needs files]**
+
+Build a clinical risk prediction model for: {outcome}. (1) Select candidate predictors from the uploaded data, (2) Handle missing data (multiple imputation), (3) Fit logistic regression and ML models, (4) Internal validation with bootstrapping, (5) Assess calibration (calibration plot) and discrimination (C-statistic/AUC), (6) Create a nomogram or risk calculator. Follow TRIPOD guidelines.
+
+### Adverse Event Analysis
+**Skills:** statistical-analysis, clinical-reports, scientific-visualization, matplotlib **[needs files]**
+
+Analyze adverse events from the uploaded clinical safety data. (1) Tabulate AE frequencies by system organ class and preferred term, (2) Compare AE rates between {groups} (risk difference, risk ratio), (3) Identify dose-dependent AEs, (4) Analyze time-to-onset distributions, (5) Flag serious adverse events (SAEs), (6) Generate standardized safety tables and forest plots following ICH E3 guidelines.
+
+### Cost-Effectiveness Analysis
+**Skills:** pymc, simpy, scientific-visualization, statistical-analysis
+
+Perform a cost-effectiveness analysis comparing {interventions} for {condition}. (1) Define the model structure (decision tree or Markov), (2) Populate with clinical effectiveness data, (3) Assign costs from {perspective} perspective, (4) Calculate ICERs (incremental cost-effectiveness ratios), (5) Run probabilistic sensitivity analysis (1000 iterations), (6) Generate cost-effectiveness plane and acceptability curves.
+
+### Patient Cohort Study
+**Skills:** statistical-analysis, scikit-survival, scientific-visualization, statsmodels **[needs files]**
+
+Analyze the uploaded patient cohort data (n={sample_size} patients). (1) Describe demographics and clinical characteristics, (2) Analyze the primary outcome: {outcome}, (3) Perform multivariable analysis adjusting for confounders, (4) Run subgroup analyses by: {subgroups}, (5) Check for interaction effects, (6) Generate a comprehensive results table (Table 1) and key figures.
+
+### Clinical Systematic Review
+**Skills:** pubmed-database, literature-review, statistical-analysis, scientific-writing
+
+Conduct a systematic review on: {question}. (1) Define PICO criteria, (2) Search PubMed, Cochrane, and Embase with structured queries, (3) Screen titles/abstracts against inclusion criteria, (4) Extract data from included studies, (5) Assess risk of bias (Cochrane RoB 2.0), (6) Perform meta-analysis if appropriate, (7) Generate PRISMA flow diagram and evidence summary tables.
+
+### Clinical Guideline Summary
+**Skills:** research-lookup, clinical-decision-support, scientific-writing
+
+Summarize clinical practice guidelines for: {condition}. (1) Identify current guidelines from major societies ({societies}), (2) Compare recommendations across guidelines, (3) Note the strength of evidence behind each recommendation, (4) Highlight areas of agreement and disagreement, (5) Create a quick-reference comparison table, (6) Identify gaps where evidence is lacking.
+
+### Quality Improvement Analysis
+**Skills:** statistical-analysis, scientific-visualization, matplotlib, clinical-reports
+
+Analyze healthcare quality data for: {initiative}. (1) Define quality metrics and benchmarks, (2) Create control charts (SPC) to assess process stability, (3) Identify special-cause variation, (4) Perform pre/post intervention comparison, (5) Calculate process capability indices, (6) Recommend next steps for sustained improvement. Follow IHI Model for Improvement.
+
+### Health Equity Analysis
+**Skills:** statistical-analysis, datacommons-client, scientific-visualization, statsmodels **[needs files]**
+
+Analyze health equity in the uploaded data. Outcome: {outcome}. (1) Stratify outcomes by {demographics}, (2) Calculate absolute and relative disparities, (3) Apply decomposition methods to identify drivers, (4) Adjust for socioeconomic confounders, (5) Map geographic variations if data available, (6) Recommend targeted interventions to reduce disparities.
+
+### EHR Data Analysis
+**Skills:** pyhealth, polars, statistical-analysis, scikit-learn **[needs files]**
+
+Analyze the uploaded EHR dataset. (1) Clean and harmonize clinical codes (ICD, CPT, LOINC), (2) Define the study cohort using inclusion criteria: {criteria}, (3) Extract clinical features (diagnoses, labs, medications, vitals), (4) Handle temporal data and create time windows, (5) Analyze: {analysis_goal}, (6) Address missingness and potential biases in EHR data.
+
+### Longitudinal Data Analysis
+**Skills:** statsmodels, statistical-analysis, scientific-visualization, matplotlib **[needs files]**
+
+Analyze the uploaded longitudinal data. Outcome: {outcome}, measured at {timepoints} timepoints. (1) Visualize individual trajectories and group means, (2) Fit mixed-effects models (random intercepts and slopes), (3) Test group × time interactions for {groups}, (4) Handle missing data (MAR assumption, multiple imputation), (5) Check model assumptions, (6) Report trajectory plots and model estimates.
+
+### Population Health Assessment
+**Skills:** datacommons-client, statistical-analysis, scientific-visualization, research-lookup
+
+Conduct a population health assessment for: {population}. (1) Compile demographic and socioeconomic profile, (2) Analyze leading causes of morbidity and mortality, (3) Assess healthcare access and utilization, (4) Identify health risk factors and social determinants, (5) Compare with state/national benchmarks, (6) Prioritize health needs and recommend interventions.
+
+### Case-Control Analysis
+**Skills:** statistical-analysis, statsmodels, scientific-visualization **[needs files]**
+
+Analyze the uploaded case-control study data. Cases: {cases}, Controls: {controls}. (1) Compare baseline characteristics, (2) Calculate crude and adjusted odds ratios, (3) Perform conditional logistic regression for matched designs, (4) Check for confounding and effect modification, (5) Assess dose-response if applicable, (6) Report with forest plots and summary tables.
+
+### Digital Pathology Analysis
+**Skills:** pathml, histolab, pytorch-lightning, scientific-visualization **[needs files]**
+
+Analyze the uploaded whole-slide image ({stain}). (1) Tissue detection and artifact removal, (2) Tile extraction at {magnification}x magnification, (3) Cell segmentation and classification, (4) Quantify: {metrics}, (5) Spatial analysis of cell distributions, (6) Generate heatmaps overlaid on the tissue. Report findings in standard pathology format.
+
+## Data Analysis
+
+### Explore My Data
+**Skills:** exploratory-data-analysis, scientific-visualization, polars **[needs files]**
+
+Perform exploratory data analysis on the uploaded dataset. Summarize the structure (rows, columns, types), check for missing values, compute descriptive statistics, visualize distributions of key variables, examine correlations, and flag any anomalies or patterns. Generate clear summary visualizations.
+
+### Statistical Analysis
+**Skills:** statistical-analysis, statsmodels, scikit-learn **[needs files]**
+
+Run appropriate statistical analyses on the uploaded data. For each analysis: (1) state the hypothesis, (2) check test assumptions, (3) run the appropriate test, (4) report test statistics, p-values, confidence intervals, and effect sizes, (5) interpret the results. {instructions}
+
+### Reproduce an Analysis
+**Skills:** statistical-analysis, scientific-critical-thinking **[needs files]**
+
+Reproduce the analysis described in the uploaded paper using the provided data. Follow the methods section step by step, implement the same statistical tests and procedures, and compare your results with the reported findings. Document any discrepancies.
+
+### Clean & Transform Data
+**Skills:** polars, exploratory-data-analysis **[needs files]**
+
+Clean and transform the uploaded dataset into an analysis-ready format. Handle missing values, fix data types, remove duplicates, standardize column names, deal with outliers, and apply any necessary transformations. Document every step taken and save the cleaned dataset.
+
+### Build a Predictive Model
+**Skills:** scikit-learn, shap, exploratory-data-analysis **[needs files]**
+
+Build a predictive model on the uploaded data. Target variable: {target}. (1) Explore and preprocess the data, (2) Select and train appropriate models, (3) Evaluate with cross-validation, (4) Report metrics (accuracy, AUC, RMSE as appropriate), (5) Interpret feature importance, (6) Save the best model.
+
+### Time Series Analysis
+**Skills:** timesfm-forecasting, statsmodels, scientific-visualization, matplotlib **[needs files]**
+
+Analyze the uploaded time series data. (1) Visualize the series and check for trends, seasonality, and stationarity, (2) Decompose into trend/seasonal/residual components, (3) Fit appropriate models (ARIMA, Prophet, or ML-based), (4) Generate forecasts for {horizon}, (5) Detect anomalies, (6) Report confidence intervals.
+
+### Survival Analysis
+**Skills:** scikit-survival, statistical-analysis, scientific-visualization, statsmodels **[needs files]**
+
+Perform survival analysis on the uploaded data. (1) Generate Kaplan-Meier curves for key groups, (2) Run log-rank tests for group comparisons, (3) Fit a Cox proportional hazards model with covariates: {covariates}, (4) Check proportional hazards assumption, (5) Report hazard ratios with 95% CI, (6) Create forest plots.
+
+### Meta-Analysis
+**Skills:** statistical-analysis, statsmodels, scientific-visualization, matplotlib **[needs files]**
+
+Conduct a meta-analysis using the uploaded study data. (1) Extract or verify effect sizes and standard errors, (2) Run fixed-effects and random-effects models, (3) Assess heterogeneity (I², Q statistic, tau²), (4) Generate a forest plot, (5) Create a funnel plot to assess publication bias, (6) Run sensitivity and subgroup analyses.
+
+### Power Analysis
+**Skills:** statistical-analysis, statsmodels, scientific-visualization
+
+Perform a power analysis for a {study_design}. Parameters: expected effect size = {effect_size}, significance level = {alpha}. (1) Calculate the required sample size for 80% and 90% power, (2) Generate power curves across a range of effect sizes, (3) Account for multiple comparisons if applicable, (4) Provide recommendations for the study design.
+
+### Bayesian Analysis
+**Skills:** pymc, statistical-analysis, scientific-visualization, matplotlib **[needs files]**
+
+Perform Bayesian analysis on the uploaded data. (1) Define the model and priors for {parameters}, (2) Run MCMC sampling (NUTS/HMC), (3) Check convergence (R-hat, trace plots, ESS), (4) Report posterior distributions and 95% credible intervals, (5) Compute Bayes factors if comparing models, (6) Generate posterior predictive checks.
+
+### Dimensionality Reduction
+**Skills:** umap-learn, scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Apply dimensionality reduction to the uploaded high-dimensional dataset. (1) Run PCA and report variance explained, (2) Apply t-SNE and UMAP with optimized parameters, (3) Color points by {label} if available, (4) Compare methods side by side, (5) Identify clusters or outlier groups, (6) Save reduced coordinates.
+
+### Clustering Analysis
+**Skills:** scikit-learn, umap-learn, scientific-visualization, seaborn **[needs files]**
+
+Perform clustering analysis on the uploaded dataset. (1) Preprocess and scale features, (2) Determine optimal cluster count (elbow method, silhouette, gap statistic), (3) Apply k-means, hierarchical, and DBSCAN, (4) Compare results and select the best method, (5) Characterize each cluster by key features, (6) Visualize with UMAP/t-SNE.
+
+### Regression Analysis
+**Skills:** statsmodels, statistical-analysis, scientific-visualization **[needs files]**
+
+Fit a {regression_type} regression model on the uploaded data. Outcome: {outcome}, predictors: {predictors}. (1) Check assumptions (linearity, normality, homoscedasticity, multicollinearity), (2) Fit the model, (3) Report coefficients with CIs and p-values, (4) Assess model fit (R², AIC, BIC), (5) Generate diagnostic plots, (6) Interpret key findings.
+
+### ANOVA / Group Comparisons
+**Skills:** statistical-analysis, statsmodels, scientific-visualization, matplotlib **[needs files]**
+
+Perform ANOVA on the uploaded data. Factor(s): {factors}, outcome: {outcome}. (1) Check assumptions (normality, homogeneity of variance), (2) Run the appropriate ANOVA (one-way, two-way, repeated measures), (3) Report F-statistics and p-values, (4) Run post-hoc pairwise comparisons with correction, (5) Calculate effect sizes (eta²), (6) Create bar/box plots with significance markers.
+
+### Correlation Network
+**Skills:** networkx, scientific-visualization, statsmodels, plotly **[needs files]**
+
+Build a correlation network from the uploaded dataset. (1) Calculate pairwise correlations (Pearson, Spearman, or partial), (2) Apply significance threshold (p < {threshold}), (3) Construct a network graph, (4) Identify hubs and communities, (5) Visualize with node sizes proportional to connectivity, (6) Report key network statistics (density, modularity, clustering coefficient).
+
+## Drug Discovery and Pharmacology
+
+### Drug Target Identification
+**Skills:** opentargets-database, gene-database, drugbank-database, primekg
+
+Identify potential drug targets for: {disease}. (1) Query disease-gene associations from OpenTargets, OMIM, and GWAS catalog, (2) Prioritize targets by genetic evidence, expression, and druggability, (3) Check existing drugs against each target, (4) Assess target tractability (structure availability, assayability), (5) Evaluate safety liabilities (tissue expression, mouse KO phenotypes), (6) Recommend top 5-10 targets with rationale.
+
+### Virtual Screening
+**Skills:** diffdock, rdkit, zinc-database, medchem **[needs files]**
+
+Perform virtual screening against {target}. (1) Prepare the target structure (PDB: {pdb_id}), (2) Define the binding site, (3) Screen the uploaded compound library or ZINC subset ({library_size} compounds), (4) Rank compounds by docking score, (5) Apply ADMET filters, (6) Cluster top hits by scaffold, (7) Select diverse top 50 candidates for experimental testing.
+
+### ADMET Prediction
+**Skills:** rdkit, medchem, pytdc, deepchem **[needs files]**
+
+Predict ADMET properties for the uploaded compounds. (1) Absorption: Caco-2 permeability, oral bioavailability, P-gp substrate, (2) Distribution: plasma protein binding, VDss, BBB penetration, (3) Metabolism: CYP inhibition/induction (1A2, 2C9, 2C19, 2D6, 3A4), metabolic stability, (4) Excretion: clearance, half-life, (5) Toxicity: hERG, AMES, hepatotoxicity, (6) Generate a traffic-light summary dashboard.
+
+### Lead Optimization
+**Skills:** rdkit, medchem, molfeat, deepchem **[needs files]**
+
+Optimize the lead compound: {compound} for {target}. (1) Analyze the SAR from the uploaded data, (2) Identify key pharmacophore features, (3) Propose structural modifications to improve {property}, (4) Predict ADMET for proposed analogs, (5) Rank modifications by predicted improvement, (6) Design a focused library of 20-50 analogs for synthesis.
+
+### Drug Repurposing
+**Skills:** primekg, drugbank-database, clinicaltrials-database, opentargets-database
+
+Identify drug repurposing candidates for: {disease}. (1) Query drug-disease associations from knowledge graphs (PrimeKG), (2) Identify approved drugs targeting related pathways, (3) Check clinical trials for off-label use, (4) Predict drug-target interactions computationally, (5) Assess safety profile from existing clinical data, (6) Rank candidates by evidence strength and feasibility.
+
+### PK Modeling
+**Skills:** statsmodels, scientific-visualization, matplotlib, statistical-analysis **[needs files]**
+
+Build a pharmacokinetic model for {drug} using the uploaded PK data. (1) Fit compartmental models (1-compartment, 2-compartment), (2) Estimate PK parameters (Cmax, Tmax, AUC, half-life, clearance, Vd), (3) Test for dose linearity, (4) Simulate concentration-time profiles at different doses: {doses}, (5) Predict steady-state concentrations for repeated dosing, (6) Generate PK profile plots.
+
+### Dose-Response Analysis
+**Skills:** statistical-analysis, statsmodels, scientific-visualization, matplotlib **[needs files]**
+
+Analyze the uploaded dose-response data. (1) Fit a 4-parameter logistic (Hill) curve to each compound, (2) Calculate EC50/IC50 with 95% confidence intervals, (3) Determine Hill coefficient and maximal response, (4) Compare potency across compounds, (5) Assess curve quality (R², residual plots), (6) Generate publication-quality dose-response plots with error bars.
+
+### Drug Interaction Prediction
+**Skills:** drugbank-database, rdkit, medchem, clinical-decision-support
+
+Predict drug-drug interactions for: {drugs}. (1) Check for known interactions in DrugBank, (2) Predict CYP-mediated metabolic interactions (inhibition, induction), (3) Check for transporter-mediated interactions (P-gp, OATP, BCRP), (4) Assess pharmacodynamic interactions (additive, synergistic, antagonistic), (5) Evaluate clinical significance, (6) Generate an interaction matrix.
+
+### Clinical Trial Design
+**Skills:** clinicaltrials-database, statistical-analysis, scientific-writing, writing
+
+Design a clinical trial for {drug} in {indication}. (1) Define primary and secondary endpoints, (2) Calculate sample size with power analysis, (3) Describe study design (parallel, crossover, adaptive), (4) Define inclusion/exclusion criteria, (5) Plan dosing regimen and schedule, (6) Describe safety monitoring plan, (7) Outline statistical analysis plan. Follow ICH-GCP guidelines.
+
+### Biomarker Discovery
+**Skills:** scikit-learn, shap, scientific-visualization, statistical-analysis **[needs files]**
+
+Discover biomarkers for {condition} from the uploaded {data_type} data. (1) Differential analysis between groups, (2) Feature selection (LASSO, random forest importance, mutual information), (3) Build a multi-marker panel classifier, (4) Evaluate with ROC curves and cross-validation, (5) Validate with independent data if available, (6) Assess biological plausibility of top markers via pathway analysis.
+
+### Toxicity Prediction
+**Skills:** rdkit, deepchem, pytdc, medchem **[needs files]**
+
+Predict toxicity for the uploaded compounds. (1) AMES mutagenicity, (2) hERG channel inhibition (cardiac toxicity), (3) Hepatotoxicity (DILI risk), (4) Skin sensitization, (5) Acute oral toxicity (LD50), (6) Carcinogenicity prediction, (7) Endocrine disruption potential. Generate a traffic-light safety dashboard with confidence scores for each endpoint.
+
+### Pharmacogenomics Analysis
+**Skills:** clinpgx-database, drugbank-database, clinvar-database, gene-database
+
+Perform pharmacogenomics analysis for {drug}. (1) Identify pharmacogenomic variants from ClinPGx and PharmGKB, (2) Assess how {genotype} variants affect drug metabolism, efficacy, and toxicity, (3) Review FDA pharmacogenomic labels, (4) Predict metabolizer status (poor, intermediate, extensive, ultra-rapid), (5) Recommend dosing adjustments, (6) Generate a clinical PGx report.
+
+### Drug-Target Interaction Network
+**Skills:** chembl-database, drugbank-database, bindingdb-database, networkx
+
+Build a drug-target interaction network for: {compounds}. (1) Query known targets from ChEMBL, DrugBank, and BindingDB, (2) Predict additional targets computationally, (3) Construct the drug-target network, (4) Identify off-target effects and polypharmacology, (5) Enrich targets with pathway information, (6) Visualize the network and identify therapeutic vs safety-relevant targets.
+
+### Pharma Competitive Landscape
+**Skills:** clinicaltrials-database, drugbank-database, fda-database, market-research-reports
+
+Analyze the competitive landscape for {indication}. (1) Map all drugs in development (preclinical through Phase 3) from ClinicalTrials.gov, (2) Categorize by mechanism of action, (3) Identify the most advanced programs, (4) Analyze patent expiry timelines, (5) Assess market size and pricing, (6) Identify white space opportunities and unmet needs.
+
+### Side Effect Prediction
+**Skills:** rdkit, drugbank-database, medchem, pytdc
+
+Predict potential side effects for: {compound}. (1) Query known side effects for structurally similar drugs, (2) Predict off-target activity against safety panels, (3) Analyze structural alerts for reactive metabolites, (4) Predict organ-specific toxicity (liver, kidney, heart, CNS), (5) Compare risk profile with drugs in the same class, (6) Generate a side effect risk report with confidence scores.
+
+### Formulation Optimization
+**Skills:** rdkit, medchem, scientific-writing
+
+Optimize the formulation of {compound} for {route} administration. (1) Analyze physicochemical properties (solubility, stability, LogP, pKa), (2) Evaluate BCS classification, (3) Screen formulation strategies (salt form, amorphous solid dispersion, nanoparticles, cyclodextrins), (4) Predict dissolution profiles, (5) Recommend excipient selection, (6) Design stability testing plan.
+
+## Ecology and Environmental Science
+
+### Species Distribution Model
+**Skills:** geopandas, scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Build a species distribution model for: {species}. (1) Compile occurrence records from GBIF or uploaded data, (2) Extract environmental variables (bioclim, land cover, elevation), (3) Fit MaxEnt or random forest SDM, (4) Evaluate model (AUC, TSS), (5) Generate habitat suitability map, (6) Project under future climate scenarios ({scenario}) if requested.
+
+### Biodiversity Assessment
+**Skills:** scikit-bio, scientific-visualization, statistical-analysis, matplotlib **[needs files]**
+
+Perform a biodiversity assessment on the uploaded community data. (1) Calculate species richness and rarefaction curves, (2) Compute diversity indices (Shannon, Simpson, Fisher's alpha), (3) Analyze species abundance distributions, (4) Compare communities between {sites} using beta diversity (Bray-Curtis, Jaccard), (5) Ordination (NMDS, PCoA), (6) Test for significant differences (PERMANOVA).
+
+### Population Dynamics Modeling
+**Skills:** sympy, matplotlib, scientific-visualization, statsmodels **[needs files]**
+
+Model population dynamics for: {system}. (1) Define the model structure ({model_type}), (2) Estimate parameters from the uploaded data, (3) Simulate population trajectories, (4) Analyze equilibria and stability, (5) Perform sensitivity analysis on key parameters, (6) Generate phase portraits and time series plots. {scenario}
+
+### Climate Data Analysis
+**Skills:** geopandas, geomaster, scientific-visualization, statistical-analysis
+
+Analyze climate data for: {region}. (1) Compute trends in temperature and precipitation over {period}, (2) Detect changepoints and regime shifts, (3) Analyze seasonal patterns and anomalies, (4) Compare with climate model projections, (5) Calculate extreme event frequencies (heat waves, droughts, floods), (6) Generate trend maps and time series visualizations.
+
+### Remote Sensing Analysis
+**Skills:** geopandas, geomaster, scientific-visualization, scikit-learn **[needs files]**
+
+Analyze the uploaded satellite imagery ({sensor}). (1) Preprocess (atmospheric correction, cloud masking), (2) Calculate relevant indices: {indices}, (3) Perform land cover classification, (4) Detect changes between time periods, (5) Quantify area statistics per class, (6) Generate publication-quality maps with legends and scale bars.
+
+### Phylogeographic Analysis
+**Skills:** phylogenetics, biopython, geopandas, etetoolkit **[needs files]**
+
+Perform a phylogeographic analysis for: {taxon}. (1) Build a phylogenetic tree from the uploaded sequences, (2) Map haplotypes to geographic locations, (3) Construct a haplotype network, (4) Test for isolation by distance, (5) Infer ancestral areas and dispersal routes, (6) Analyze demographic history (Bayesian skyline plot). Visualize on maps.
+
+### Ecological Network Analysis
+**Skills:** networkx, scientific-visualization, matplotlib, statistical-analysis **[needs files]**
+
+Analyze the uploaded ecological interaction network ({network_type}). (1) Compute network metrics (connectance, nestedness, modularity), (2) Identify keystone species (high centrality), (3) Analyze network robustness to species loss, (4) Detect modules and their composition, (5) Compare with null models, (6) Visualize the network with nodes sized by importance.
+
+### Conservation Prioritization
+**Skills:** geopandas, geomaster, scientific-visualization, research-lookup
+
+Perform conservation prioritization for {target} in {region}. (1) Compile species occurrence and threat status data, (2) Map areas of high biodiversity value, (3) Overlay with threat layers (deforestation, urbanization, climate change), (4) Run systematic conservation planning (complementarity analysis), (5) Identify priority areas that maximize species representation, (6) Assess protection gap (currently protected vs needed).
+
+### Water Quality Analysis
+**Skills:** exploratory-data-analysis, scientific-visualization, statistical-analysis, matplotlib **[needs files]**
+
+Analyze the uploaded water quality dataset. (1) Summarize key parameters (pH, DO, turbidity, nutrients, heavy metals), (2) Compare against regulatory standards ({standards}), (3) Analyze spatial patterns across sampling sites, (4) Detect temporal trends, (5) Perform water quality index calculation, (6) Identify pollution sources using multivariate analysis. Flag exceedances.
+
+### Carbon Footprint Analysis
+**Skills:** exploratory-data-analysis, scientific-visualization, research-lookup, xlsx **[needs files]**
+
+Calculate the carbon footprint for: {entity}. (1) Define system boundaries and scope (1, 2, 3), (2) Collect activity data from uploaded records, (3) Apply emission factors from IPCC/EPA databases, (4) Calculate total CO2-equivalent emissions by category, (5) Identify emission hotspots, (6) Benchmark against industry averages, (7) Recommend reduction strategies with estimated impact.
+
+### Environmental Impact Assessment
+**Skills:** research-lookup, scientific-writing, writing, geopandas
+
+Conduct an environmental impact assessment for: {project}. (1) Describe the project and its setting, (2) Identify potential impacts on air, water, soil, biodiversity, (3) Assess impact magnitude and significance, (4) Propose mitigation measures for each significant impact, (5) Develop a monitoring plan, (6) Summarize in an impact matrix. Follow {framework} framework.
+
+### Habitat Suitability Analysis
+**Skills:** geopandas, geomaster, scientific-visualization, research-lookup
+
+Assess habitat suitability for {species} in {region}. (1) Define habitat requirements from literature, (2) Compile environmental layers (vegetation, elevation, hydrology, temperature), (3) Score each cell by habitat suitability criteria, (4) Classify habitat quality (optimal, suitable, marginal, unsuitable), (5) Calculate total suitable habitat area, (6) Map habitat suitability and identify corridors.
+
+### Microbial Community Ecology
+**Skills:** scikit-bio, pydeseq2, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded 16S/ITS amplicon data. (1) Process sequences (quality filter, denoise with DADA2), (2) Taxonomic assignment against {database}, (3) Alpha diversity (observed, Shannon, Faith's PD), (4) Beta diversity (UniFrac, Bray-Curtis), (5) Differential abundance between {comparison} (DESeq2/ANCOM), (6) Core microbiome analysis, (7) Visualize community composition and diversity.
+
+### Invasive Species Risk Assessment
+**Skills:** geopandas, research-lookup, scientific-writing, scientific-visualization
+
+Assess the invasion risk of {species} in {region}. (1) Characterize the species' native range and environmental tolerances, (2) Model potential distribution in the target region, (3) Assess introduction pathways and propagule pressure, (4) Evaluate potential ecological and economic impacts, (5) Assess management feasibility, (6) Assign an overall risk score. Provide management recommendations.
+
+## Engineering and Simulation
+
+### CFD Simulation
+**Skills:** fluidsim, matplotlib, scientific-visualization
+
+Set up and run a CFD simulation for: {geometry}. (1) Define the geometry and meshing strategy, (2) Set boundary conditions: {conditions}, (3) Select turbulence model (k-ε, k-ω SST, LES), (4) Run the simulation to convergence, (5) Post-process: velocity fields, pressure distribution, drag/lift coefficients, (6) Visualize streamlines and contour plots.
+
+### Signal Processing
+**Skills:** matplotlib, scientific-visualization, neurokit2, statistical-analysis **[needs files]**
+
+Process the uploaded signal data. (1) Characterize the signal (sample rate, duration, channels), (2) Apply filtering: {filter_spec}, (3) Compute FFT and power spectral density, (4) Perform time-frequency analysis (STFT, wavelet transform), (5) Extract features: {features}, (6) Detect events or anomalies, (7) Compare before/after processing.
+
+### Control System Design
+**Skills:** sympy, matlab, matplotlib, scientific-visualization
+
+Design a control system for: {plant}. Requirements: {specs}. (1) Model the plant dynamics (transfer function or state-space), (2) Analyze open-loop stability and performance, (3) Design a {controller_type} controller, (4) Tune controller parameters, (5) Analyze closed-loop: step response, Bode plot, root locus, (6) Verify robustness to model uncertainty and disturbances.
+
+### Heat Transfer Analysis
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Analyze heat transfer in: {system}. (1) Define the geometry, materials, and thermal boundary conditions, (2) Set up the heat equation (conduction, convection coefficients, radiation), (3) Solve for temperature distribution (analytical or FEM), (4) Calculate heat flux and total heat transfer rate, (5) Analyze thermal resistance network, (6) Visualize temperature contours and heat flow paths.
+
+### Vibration Analysis
+**Skills:** matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze vibrations in the uploaded data or system: {system}. (1) Compute frequency spectrum (FFT), (2) Identify natural frequencies and mode shapes, (3) Calculate damping ratios, (4) Perform order tracking if rotating machinery, (5) Compare with operational limits and standards ({standard}), (6) Identify fault signatures if diagnostic. Generate waterfall and Campbell diagrams.
+
+### Process Simulation
+**Skills:** simpy, sympy, matplotlib, scientific-visualization
+
+Simulate the process: {process}. (1) Define the process flow diagram and unit operations, (2) Specify feed compositions and operating conditions, (3) Simulate using discrete event or continuous simulation, (4) Calculate mass and energy balances, (5) Optimize for {objective}, (6) Perform sensitivity analysis on key parameters. Report yields, throughputs, and utility consumption.
+
+### Reliability Analysis
+**Skills:** scikit-survival, statistical-analysis, scientific-visualization, matplotlib
+
+Perform reliability analysis for: {system}. (1) Fit failure time distributions (Weibull, exponential, lognormal), (2) Estimate MTTF/MTBF and failure rates, (3) Construct reliability block diagram or fault tree, (4) Calculate system-level reliability and availability, (5) Perform failure mode analysis (FMEA), (6) Recommend optimal maintenance intervals.
+
+### Sensor / IoT Data Analysis
+**Skills:** polars, scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Analyze the uploaded sensor/IoT data ({sensors}). (1) Clean and synchronize multi-sensor streams, (2) Detect and handle missing data and outliers, (3) Extract statistical and frequency-domain features, (4) Correlate sensor readings with {events}, (5) Build anomaly detection models for predictive maintenance, (6) Create a monitoring dashboard visualization.
+
+### Robot Path Planning
+**Skills:** matplotlib, scientific-visualization, pymoo **[needs files]**
+
+Plan a path for a {robot_type} robot in the uploaded environment. (1) Define the configuration space and obstacles, (2) Apply {algorithm} path planning, (3) Optimize for {objective}, (4) Smooth the path for physical feasibility, (5) Verify collision-free traversal, (6) Visualize the planned path in 2D/3D with obstacles. Report path length and computation time.
+
+### Structural Analysis
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Perform structural analysis on: {structure}. Loads: {loads}. (1) Define the structural model (beams, frames, plates), (2) Apply material properties and boundary conditions, (3) Solve for reactions, internal forces, and displacements, (4) Check stresses against material limits (safety factor = {sf}), (5) Analyze buckling if applicable, (6) Visualize deformed shape and stress distribution.
+
+### Finite Element Analysis
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Perform finite element analysis for: {problem}. (1) Define the geometry and create the mesh, (2) Assign material properties, (3) Apply boundary conditions and loads: {conditions}, (4) Solve the FEM problem, (5) Post-process: stress/strain fields, displacement, temperature, (6) Check convergence with mesh refinement, (7) Visualize results with contour plots.
+
+### Circuit Simulation
+**Skills:** sympy, matlab, matplotlib, scientific-visualization
+
+Simulate the electronic circuit: {circuit}. (1) Define the circuit topology and component values, (2) Run DC operating point analysis, (3) Run AC frequency response (Bode plot), (4) Run transient analysis with input: {input_signal}, (5) Analyze: gain, bandwidth, phase margin, power consumption, (6) Optimize component values for {objective}.
+
+## Finance and Economics
+
+### Stock Market Analysis
+**Skills:** alpha-vantage, scientific-visualization, matplotlib, statistical-analysis
+
+Analyze {ticker} stock performance. (1) Plot price history and volume over {period}, (2) Calculate technical indicators (SMA, EMA, RSI, MACD, Bollinger Bands), (3) Identify support/resistance levels, (4) Analyze fundamental ratios (P/E, P/B, EV/EBITDA), (5) Compare with sector peers, (6) Perform correlation analysis with market indices. Generate a comprehensive analysis report.
+
+### Portfolio Optimization
+**Skills:** alpha-vantage, pymoo, scientific-visualization, statistical-analysis **[needs files]**
+
+Optimize a portfolio from the uploaded asset returns data. (1) Calculate expected returns and covariance matrix, (2) Generate the efficient frontier, (3) Find the tangency (maximum Sharpe) portfolio, (4) Calculate minimum variance portfolio, (5) Apply constraints: {constraints}, (6) Backtest optimal portfolio over {period}, (7) Report allocation weights, expected return, volatility, and Sharpe ratio.
+
+### Financial Risk Assessment
+**Skills:** alpha-vantage, statistical-analysis, scientific-visualization, pymc **[needs files]**
+
+Perform risk assessment on the uploaded portfolio data. (1) Calculate Value at Risk (VaR) at 95% and 99% confidence using historical, parametric, and Monte Carlo methods, (2) Compute Conditional VaR (Expected Shortfall), (3) Perform stress testing with scenarios: {scenarios}, (4) Analyze drawdown history, (5) Calculate risk-adjusted performance metrics, (6) Generate a risk dashboard.
+
+### Economic Indicator Analysis
+**Skills:** fred-economic-data, datacommons-client, scientific-visualization, statistical-analysis
+
+Analyze economic indicators for {country}. (1) Pull data from FRED/World Bank for: {indicators}, (2) Plot trends over {period}, (3) Analyze correlations between indicators, (4) Identify leading vs lagging relationships, (5) Compare with {benchmark} countries, (6) Generate economic outlook summary with key risks and opportunities.
+
+### Financial Statement Analysis
+**Skills:** edgartools, xlsx, scientific-visualization, statistical-analysis
+
+Analyze the financial statements of {company}. (1) Parse income statement, balance sheet, and cash flow, (2) Calculate key ratios (profitability, liquidity, leverage, efficiency), (3) Perform DuPont decomposition of ROE, (4) Analyze trends over {years} years, (5) Compare with industry peers, (6) Identify red flags or strengths, (7) Provide a financial health assessment.
+
+### Hedge Fund Analysis
+**Skills:** hedgefundmonitor, alpha-vantage, scientific-visualization, statistical-analysis
+
+Analyze hedge fund performance for: {fund}. (1) Calculate returns, alpha, beta, and Sharpe ratio, (2) Decompose returns by factor exposure (Fama-French, momentum), (3) Analyze drawdowns and recovery periods, (4) Assess strategy consistency and style drift, (5) Compare with benchmark and peer funds, (6) Evaluate risk-adjusted performance across market regimes.
+
+### Cryptocurrency Analysis
+**Skills:** alpha-vantage, scientific-visualization, statistical-analysis, matplotlib
+
+Analyze {crypto} cryptocurrency. (1) Plot price and volume history, (2) Calculate volatility and drawdown metrics, (3) Analyze correlation with BTC, ETH, and traditional assets, (4) Compute technical indicators, (5) Analyze on-chain metrics if available (active addresses, hash rate, NVT), (6) Compare with top {n} cryptocurrencies by market cap.
+
+### Financial Time Series Forecasting
+**Skills:** timesfm-forecasting, statsmodels, scientific-visualization, scikit-learn **[needs files]**
+
+Forecast the uploaded financial time series ({series_type}) for the next {horizon}. (1) Analyze stationarity (ADF test), (2) Fit ARIMA/GARCH models, (3) Fit ML models (XGBoost, LSTM), (4) Compare forecast accuracy (RMSE, MAPE, Diebold-Mariano test), (5) Generate prediction intervals, (6) Backtest forecasting performance over a rolling window.
+
+### Credit Risk Model
+**Skills:** scikit-learn, shap, scientific-visualization, statistical-analysis **[needs files]**
+
+Build a credit risk model using the uploaded loan/credit data. (1) EDA: analyze default rates, feature distributions, (2) Engineer credit features (utilization, payment history, DTI), (3) Train models (logistic regression, gradient boosting), (4) Evaluate: AUC, KS statistic, Gini coefficient, (5) Calibrate predicted probabilities, (6) Create scorecard with point allocation, (7) Analyze model fairness across demographic groups.
+
+### Market Sentiment Analysis
+**Skills:** transformers, scientific-visualization, statistical-analysis, research-lookup
+
+Analyze market sentiment for {asset_or_sector}. (1) Collect and process text data from {sources}, (2) Apply NLP sentiment scoring (FinBERT or similar), (3) Track sentiment over time, (4) Correlate sentiment with price movements, (5) Identify sentiment-driven events, (6) Generate a sentiment dashboard with bull/bear indicators.
+
+### Econometric Modeling
+**Skills:** statsmodels, statistical-analysis, scientific-visualization, fred-economic-data
+
+Build an econometric model to estimate: {relationship}. (1) Specify the model (OLS, IV, panel, difference-in-differences), (2) Check for endogeneity and propose instruments if needed, (3) Test assumptions (heteroskedasticity, autocorrelation, multicollinearity), (4) Estimate with robust standard errors, (5) Report marginal effects and elasticities, (6) Interpret results and discuss policy implications.
+
+### Fiscal Policy Analysis
+**Skills:** usfiscaldata, fred-economic-data, scientific-visualization, statistical-analysis
+
+Analyze fiscal policy for {country}. (1) Compile revenue and expenditure data from {source}, (2) Analyze budget balance trends, (3) Decompose debt dynamics (primary balance, interest rate, growth rate), (4) Project debt-to-GDP ratio under baseline and stress scenarios, (5) Assess fiscal sustainability, (6) Compare with peer countries and IMF thresholds.
+
+### Real Estate Market Analysis
+**Skills:** scikit-learn, scientific-visualization, statistical-analysis, geopandas
+
+Analyze the real estate market in {location}. (1) Compile price data and transaction volumes, (2) Analyze price trends and seasonality, (3) Calculate cap rates and yield metrics, (4) Compare neighborhoods/submarkets, (5) Build a price prediction model using features: {features}, (6) Identify undervalued areas and investment opportunities.
+
+### Startup Valuation
+**Skills:** xlsx, scientific-visualization, what-if-oracle, market-research-reports **[needs files]**
+
+Value the startup: {company}. (1) Analyze financials from the uploaded data, (2) Apply DCF model with {growth} revenue growth scenarios, (3) Apply comparable company multiples (revenue, EBITDA), (4) Apply comparable transaction multiples, (5) Score using the Scorecard/Berkus method for early stage, (6) Provide a valuation range with justification for each method.
+
+### ESG Analysis
+**Skills:** edgartools, research-lookup, scientific-visualization, xlsx
+
+Perform ESG analysis for {company}. (1) Compile ESG metrics from sustainability reports and databases, (2) Score E (carbon, water, waste), S (labor, diversity, community), G (board, ethics, transparency), (3) Compare with industry peers, (4) Identify material ESG risks, (5) Analyze ESG trajectory over time, (6) Assess regulatory compliance and disclosure quality.
+
+### Trade Flow Analysis
+**Skills:** datacommons-client, scientific-visualization, geopandas, statistical-analysis **[needs files]**
+
+Analyze trade flows for {country} in {sector}. (1) Compile import/export data from UN Comtrade or uploaded data, (2) Identify top trading partners, (3) Analyze trade balance trends, (4) Calculate revealed comparative advantage (RCA), (5) Visualize trade flows with Sankey diagrams, (6) Assess impact of tariffs or trade agreements on flows.
+
+### VC Deal Screening
+**Skills:** market-research-reports, research-lookup, edgartools, scientific-visualization **[needs files]**
+
+Screen {company} as a potential venture investment. (1) Analyze the business model, value proposition, and defensibility, (2) Size the TAM/SAM/SOM for {market}, (3) Evaluate the founding team's background and track record, (4) Assess competitive landscape and differentiation, (5) Analyze unit economics (CAC, LTV, gross margin, burn rate) from uploaded financials, (6) Identify key risks (market, technical, regulatory, execution), (7) Compare with analogous companies at the same stage, (8) Prov...
+
+### VC Fund Benchmarking
+**Skills:** scientific-visualization, matplotlib, statistical-analysis, xlsx **[needs files]**
+
+Benchmark the uploaded fund data against the VC industry. (1) Calculate fund-level metrics: TVPI, DPI, RVPI, net IRR, (2) Compare against Cambridge Associates / PitchBook benchmarks for {vintage} vintage, (3) Analyze the J-curve and cash flow profile, (4) Break down returns by sector, stage, and geography, (5) Assess portfolio concentration and diversification, (6) Model scenarios for unrealized portfolio, (7) Generate a GP-quality fund performance tear sheet.
+
+### Cap Table Modeling
+**Skills:** scientific-visualization, matplotlib, xlsx, what-if-oracle **[needs files]**
+
+Build a cap table model for {company}. (1) Set up the current ownership structure from the uploaded data, (2) Model the next round: {round_details}, (3) Calculate dilution impact on each stakeholder (founders, employees, existing investors), (4) Build a liquidation waterfall for exit at {exit_values} valuations, (5) Model the option pool expansion, (6) Calculate returns multiples and IRR for each investor class, (7) Visualize ownership evolution across rounds.
+
+### Market Sizing (TAM/SAM/SOM)
+**Skills:** market-research-reports, research-lookup, scientific-visualization, datacommons-client
+
+Size the market for {market}. (1) Top-down: start from the broadest addressable market and apply segmentation filters, (2) Bottom-up: estimate from unit economics × addressable customers, (3) Cross-validate both approaches, (4) Analyze market growth rate and key drivers, (5) Map the competitive landscape and market share distribution, (6) Project market size for the next {years} years under base and bull scenarios. Cite all data sources.
+
+### DCF Valuation Model
+**Skills:** xlsx, scientific-visualization, what-if-oracle, statistical-analysis
+
+Build a DCF valuation for {company}. (1) Project revenue for {years} years using growth assumptions: {growth}, (2) Model operating expenses, EBITDA margins, capex, and working capital, (3) Calculate unlevered free cash flows, (4) Determine WACC (cost of equity via CAPM, cost of debt from comparables), (5) Compute terminal value (perpetuity growth and exit multiple methods), (6) Discount to present value, (7) Run sensitivity tables on WACC vs growth rate and WACC vs exit multiple, (8) Report i...
+
+### Comparable Company Analysis
+**Skills:** edgartools, xlsx, scientific-visualization, alpha-vantage
+
+Perform a comparable company analysis for {company}. Peer set: {peers}. (1) Pull financial data for each company (revenue, EBITDA, net income, growth rates), (2) Calculate valuation multiples (EV/Revenue, EV/EBITDA, P/E, PEG, EV/FCF), (3) Analyze operating metrics (margins, ROIC, revenue per employee), (4) Compute mean/median multiples and implied valuation range for {company}, (5) Create a football field valuation chart, (6) Identify outliers and explain premium/discount drivers.
+
+### M&A Deal Analysis
+**Skills:** edgartools, xlsx, scientific-visualization, what-if-oracle
+
+Analyze the potential acquisition of {target} by {acquirer}. Deal terms: {terms}. (1) Value the target standalone (DCF + comps), (2) Estimate revenue and cost synergies, (3) Model the pro-forma combined entity, (4) Run accretion/dilution analysis on EPS, (5) Analyze financing scenarios (cash, stock, debt mix), (6) Assess goodwill and intangible asset implications, (7) Compare with precedent M&A transactions in the space, (8) Evaluate strategic rationale and integration risks.
+
+### LBO Model
+**Skills:** xlsx, scientific-visualization, what-if-oracle, statistical-analysis
+
+Build an LBO model for {company}. Entry: {entry_terms}. (1) Set up the sources and uses of funds, (2) Build a 5-year operating model with revenue growth: {growth} and margin expansion assumptions, (3) Construct the debt schedule (senior, mezzanine, revolver) with amortization and cash sweep, (4) Model credit metrics (leverage ratio, interest coverage, FCCR) each year, (5) Calculate exit returns at {exit_multiples} EV/EBITDA multiples, (6) Run sensitivity on entry multiple, leverage, and growt...
+
+### PE / VC Due Diligence Report
+**Skills:** edgartools, market-research-reports, research-lookup, xlsx
+
+Conduct due diligence on {company} for a potential {deal_type} investment. (1) Financial DD: analyze 3-5 years of financials — revenue quality, margin trends, working capital cycles, capex requirements, (2) Commercial DD: market position, customer concentration, competitive moats, TAM analysis, (3) Operational DD: management team assessment, key person risk, scalability of operations, (4) Legal/regulatory: flag potential risks in the sector, (5) Technology DD if relevant: IP, tech stack, tech...
+
+### Startup Data Room Due Diligence
+**Skills:** edgartools, market-research-reports, research-lookup, xlsx, scientific-visualization **[needs files]**
+
+Conduct comprehensive investment due diligence on {company} by analyzing the uploaded data room files. Work through each file systematically. (1) Financial DD: parse and analyze historical P&L, balance sheet, and cash flow statements — assess revenue quality, burn rate, runway, unit economics, and working capital trends, (2) Commercial DD: review customer data (concentration, retention cohorts, NPS scores, pipeline) and validate TAM/SAM claims against uploaded market data, (3) Legal DD: revie...
+
+### Pitch Deck Teardown
+**Skills:** market-research-reports, research-lookup, scientific-critical-thinking **[needs files]**
+
+Analyze the uploaded pitch deck for {company}. Score each section (1-10) and provide feedback: (1) Problem statement — is it compelling and real? (2) Solution — does it clearly solve the problem? (3) Market size — is the TAM/SAM credible? (4) Business model — are unit economics attractive? (5) Traction — what evidence of product-market fit? (6) Team — relevant experience and completeness? (7) Competition — honest assessment of landscape? (8) Financials — are projections realistic? (9) Ask — i...
+
+### Industry Deep Dive
+**Skills:** market-research-reports, research-lookup, edgartools, scientific-visualization
+
+Conduct an industry deep dive on {industry}. (1) Define the industry value chain and key segments, (2) Analyze market size, growth trajectory, and cyclicality, (3) Map the competitive landscape (Porter's Five Forces), (4) Identify secular tailwinds and headwinds, (5) Profile the top {n} public and private companies with financials, (6) Analyze recent M&A activity and deal multiples, (7) Identify emerging disruptors and technology shifts, (8) Develop an investment thesis with specific opportun...
+
+### Write an Investment Memo
+**Skills:** scientific-writing, writing, market-research-reports, research-lookup
+
+Write a formal investment memo for {company}. Structure: (1) Executive summary and recommendation, (2) Company overview (product, business model, stage), (3) Market opportunity (TAM, growth, dynamics), (4) Competitive positioning and moats, (5) Financial analysis (historical performance, projections, unit economics), (6) Valuation and proposed terms: {terms}, (7) Key risks and mitigants, (8) Value creation levers and exit scenarios, (9) Appendix with supporting data. Write in a professional t...
+
+### Equity Research Report
+**Skills:** edgartools, alpha-vantage, scientific-visualization, xlsx
+
+Write an equity research report on {ticker}. (1) Company overview and business segments, (2) Industry analysis and competitive positioning, (3) Financial analysis: revenue decomposition, margin analysis, balance sheet health, (4) Build a 3-year financial model with quarterly estimates, (5) Valuation: DCF, trading comps, and sum-of-the-parts, (6) Derive a 12-month price target, (7) Rate as Buy/Hold/Sell with upside/downside to target, (8) Identify catalysts and risks. Follow sell-side research...
+
+### Fund-of-Funds Portfolio Analysis
+**Skills:** scientific-visualization, matplotlib, statistical-analysis, xlsx **[needs files]**
+
+Analyze the uploaded fund-of-funds portfolio. (1) Calculate portfolio-level returns (net IRR, TVPI, DPI), (2) Break down by strategy (venture, growth, buyout), vintage, and geography, (3) Assess manager concentration and diversification, (4) Analyze cash flow pacing and unfunded commitments, (5) Benchmark each fund against its peer quartile, (6) Model future cash flows and NAV projections for the next {years} years, (7) Identify re-up candidates vs underperformers, (8) Generate an LP portfoli...
+
+### Scenario & Sensitivity Modeling
+**Skills:** pymc, scientific-visualization, what-if-oracle, xlsx
+
+Build a multi-scenario model for {company}. (1) Define base, bull, and bear case assumptions for: {variables}, (2) Build a 3-statement financial model for each scenario, (3) Create tornado charts showing sensitivity of valuation to each variable, (4) Run a Monte Carlo simulation ({n_sims} iterations) sampling from distributions around key assumptions, (5) Plot the probability distribution of outcomes (revenue, EBITDA, valuation), (6) Calculate probability-weighted expected value and confidenc...
+
+### Convertible Note / SAFE Analysis
+**Skills:** scientific-visualization, matplotlib, xlsx, what-if-oracle
+
+Model conversion scenarios for the following convertible instruments: {instruments}. (1) Detail each instrument's terms (cap, discount, interest rate, maturity), (2) Model conversion at various Series A valuations: {valuations}, (3) Calculate the effective price per share for each instrument at each valuation, (4) Compare investor ownership percentages vs a priced round, (5) Analyze the total dilution to founders, (6) Model MFN and pro-rata scenarios if applicable, (7) Visualize ownership sta...
+
+### Cohort & Revenue Quality Analysis
+**Skills:** scientific-visualization, matplotlib, statistical-analysis, polars **[needs files]**
+
+Analyze revenue quality from the uploaded cohort data for {company}. (1) Build a cohort retention matrix (logo and revenue retention), (2) Calculate net dollar retention (NDR) and gross retention by cohort, (3) Decompose revenue into new, expansion, contraction, and churn, (4) Analyze LTV/CAC ratio by acquisition channel and cohort, (5) Calculate payback period, (6) Plot NDR trends and revenue bridge waterfall, (7) Identify the strongest and weakest cohorts and explain drivers.
+
+### Secondaries Pricing Analysis
+**Skills:** scientific-visualization, what-if-oracle, xlsx, statistical-analysis
+
+Price a secondary transaction for {asset}. (1) Analyze the current portfolio composition and NAV, (2) Apply appropriate discounts/premiums by segment (early-stage: steeper discount, late-stage/PE: tighter), (3) Model the remaining value creation potential, (4) Estimate future distributions and cash flow timeline, (5) Compare with recent secondary market pricing data, (6) Calculate buyer IRR and MOIC at various discount levels ({discounts} of NAV), (7) Recommend a bid range with rationale.
+
+### Factor Analysis & Attribution
+**Skills:** alpha-vantage, statsmodels, scientific-visualization, statistical-analysis **[needs files]**
+
+Perform factor analysis on the uploaded portfolio returns data. (1) Regress returns against Fama-French 5 factors (market, size, value, profitability, investment), (2) Add momentum and quality factors, (3) Calculate factor exposures (betas) and their statistical significance, (4) Decompose returns into factor-driven and alpha components, (5) Run rolling-window analysis to detect factor timing or drift, (6) Perform Brinson attribution by sector and geography if holdings available, (7) Visualiz...
+
+### Venture Market Map
+**Skills:** market-research-reports, research-lookup, scientific-visualization, markdown-mermaid-writing
+
+Create a venture market map for the {sector} sector. (1) Identify all notable startups (seed through late-stage), (2) Categorize by sub-segment and value chain position, (3) Map total funding raised and latest valuation for each, (4) Identify the most active investors in the space, (5) Analyze recent deal flow trends (deal count, round sizes, valuations by stage), (6) Spot white spaces and emerging sub-segments, (7) Create a visual market map organized by category with company logos/names.
+
+### Options Strategy Analysis
+**Skills:** alpha-vantage, scientific-visualization, matplotlib, sympy
+
+Analyze an options strategy for {underlying}. Strategy: {strategy}. (1) Price each leg using Black-Scholes with current implied volatility, (2) Generate the payoff diagram at expiration, (3) Calculate max profit, max loss, and breakeven points, (4) Compute the Greeks (delta, gamma, theta, vega, rho) for the combined position, (5) Model P&L across a range of underlying prices and dates to expiration, (6) Compare with alternative strategies for the same thesis, (7) Assess the risk/reward profil...
+
+### Debt & Credit Analysis
+**Skills:** edgartools, xlsx, scientific-visualization, statistical-analysis
+
+Perform a credit analysis on {company}. (1) Analyze the capital structure (all debt tranches, maturity profile, interest rates), (2) Calculate credit metrics: net debt/EBITDA, interest coverage, FCCR, (3) Assess free cash flow generation and debt service capacity, (4) Review covenant compliance and headroom, (5) Compare with credit rating agency criteria (Moody's/S&P), (6) Analyze refinancing risk and maturity wall, (7) Model stress scenarios for a {stress} downturn, (8) Assign a shadow credi...
+
+### Activist Investor Campaign Analysis
+**Skills:** edgartools, alpha-vantage, research-lookup, scientific-visualization
+
+Analyze the activist campaign at {company} by {activist}. (1) Summarize the activist's stated thesis and demands, (2) Analyze the company's operational and financial underperformance vs peers, (3) Evaluate the proposed changes (board seats, M&A, capital allocation, management), (4) Model the financial impact of each proposed action, (5) Assess the likelihood of success based on ownership stake and board dynamics, (6) Analyze the stock price reaction and implied market expectations, (7) Recomm...
+
+### Fund Economics & Formation Modeling
+**Skills:** scientific-visualization, xlsx, what-if-oracle, matplotlib
+
+Model the economics of a {fund_type} fund. Fund size: {fund_size}. (1) Set up the fee structure: management fee ({mgmt_fee}), carried interest ({carry}), preferred return ({pref}), (2) Model the GP commitment and fee offsets, (3) Project management fee income over the fund life, (4) Model carry distribution under European and American waterfall, (5) Calculate GP economics at various fund-level return scenarios (0.5x to 5x MOIC), (6) Analyze the breakeven for the GP, (7) Compare with market-st...
+
+## Genomics and Transcriptomics
+
+### Bulk RNA-seq Analysis
+**Skills:** pydeseq2, scientific-visualization, kegg-database, reactome-database **[needs files]**
+
+Analyze the uploaded RNA-seq count matrix. Perform: (1) Quality control and filtering of low-count genes, (2) Normalization with DESeq2, (3) Differential expression analysis between {comparison}, (4) Volcano plot and MA plot, (5) Gene ontology and pathway enrichment analysis via KEGG and Reactome, (6) Heatmap of top 50 differentially expressed genes. Save all results and figures.
+
+### Single-Cell RNA-seq Pipeline
+**Skills:** scanpy, anndata, scientific-visualization, umap-learn **[needs files]**
+
+Run a complete single-cell RNA-seq analysis pipeline on the uploaded count matrix. (1) QC filtering (mitochondrial %, gene counts, UMIs), (2) Normalization and log-transformation, (3) Highly variable gene selection, (4) PCA and batch correction if needed, (5) UMAP embedding, (6) Leiden clustering, (7) Marker gene identification, (8) Cell type annotation using known markers for {tissue}. Save the annotated AnnData object.
+
+### Variant Calling & Annotation
+**Skills:** pysam, gnomad-database, clinvar-database, ensembl-database **[needs files]**
+
+Process the uploaded sequencing data for variant calling. (1) Align reads to {reference} reference genome, (2) Call SNPs and indels, (3) Filter variants by quality metrics (QUAL, DP, GQ), (4) Annotate variants with gene names, functional impact, and population frequencies from gnomAD, (5) Flag clinically relevant variants using ClinVar, (6) Generate a summary report.
+
+### GWAS Analysis
+**Skills:** gwas-database, polars-bio, scientific-visualization, matplotlib **[needs files]**
+
+Perform a genome-wide association study analysis on the uploaded genotype and phenotype data. (1) QC: filter by MAF > {maf}, call rate, HWE, (2) Population stratification analysis with PCA, (3) Run association tests (logistic or linear regression) with covariates, (4) Generate Manhattan and QQ plots, (5) Identify significant loci (p < 5e-8), (6) Annotate lead SNPs with nearby genes and known associations.
+
+### ChIP-seq Peak Calling
+**Skills:** deeptools, jaspar-database, ensembl-database, scientific-visualization **[needs files]**
+
+Analyze the uploaded ChIP-seq data for {factor}. (1) Assess read quality and mapping statistics, (2) Call peaks with appropriate parameters for {peak_type} peaks, (3) Annotate peaks relative to genomic features (promoters, enhancers, gene bodies), (4) Run motif enrichment analysis, (5) Generate coverage tracks and peak visualizations, (6) Identify target genes.
+
+### ATAC-seq Chromatin Accessibility
+**Skills:** deeptools, jaspar-database, scientific-visualization, pysam **[needs files]**
+
+Analyze the uploaded ATAC-seq data. (1) QC: check fragment size distribution and TSS enrichment, (2) Call accessibility peaks, (3) Perform differential accessibility analysis between {comparison}, (4) Footprint analysis for transcription factor binding, (5) Annotate peaks with genomic features, (6) Integrate with gene expression data if provided, (7) Visualize genome browser tracks.
+
+### DNA Methylation Analysis
+**Skills:** scientific-visualization, statistical-analysis, ensembl-database, matplotlib **[needs files]**
+
+Analyze the uploaded DNA methylation data ({data_type}). (1) QC and normalization, (2) Identify differentially methylated positions (DMPs) and regions (DMRs) between {comparison}, (3) Annotate DMRs with genes and CpG islands, (4) Perform pathway enrichment on associated genes, (5) Visualize methylation patterns across key regions, (6) Correlate with gene expression if available.
+
+### Gene Set Enrichment Analysis
+**Skills:** kegg-database, reactome-database, gget, scientific-visualization **[needs files]**
+
+Perform gene set enrichment analysis on the uploaded gene list or ranked gene data. (1) Run over-representation analysis (ORA) against GO, KEGG, Reactome, (2) Run GSEA with ranked gene list if fold-changes provided, (3) Report enriched pathways with FDR-adjusted p-values, (4) Create dot plots and enrichment maps, (5) Identify key driver genes, (6) Summarize biological themes.
+
+### Gene Regulatory Network
+**Skills:** arboreto, networkx, jaspar-database, scientific-visualization **[needs files]**
+
+Infer a gene regulatory network from the uploaded expression data. (1) Select candidate regulators (transcription factors from {organism}), (2) Apply network inference algorithms (GRNBoost2/GENIE3), (3) Score and threshold regulatory interactions, (4) Identify key hub regulators, (5) Validate against known interactions in the literature, (6) Visualize the top regulatory subnetwork.
+
+### Genome Annotation
+**Skills:** biopython, interpro-database, ensembl-database, scikit-bio **[needs files]**
+
+Annotate the uploaded genome assembly. (1) Predict protein-coding genes with ab initio and homology-based methods, (2) Identify non-coding RNAs (tRNA, rRNA, miRNA), (3) Annotate repetitive elements, (4) Perform functional annotation with InterPro and GO, (5) Generate GFF3/GTF annotation files, (6) Compute assembly statistics (N50, BUSCO completeness).
+
+### Comparative Genomics
+**Skills:** biopython, etetoolkit, phylogenetics, ensembl-database
+
+Perform comparative genomics analysis between {species}. (1) Identify orthologous genes, (2) Compute dN/dS ratios to detect positive selection, (3) Identify lineage-specific gene gains and losses, (4) Analyze synteny blocks, (5) Build a phylogenetic tree from conserved genes, (6) Identify rapidly evolving gene families. Visualize key results.
+
+### Metagenomics Analysis
+**Skills:** scikit-bio, kegg-database, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded metagenomic sequencing data. (1) QC and host read removal, (2) Taxonomic classification and profiling, (3) Alpha diversity (Shannon, Chao1) and beta diversity (Bray-Curtis, UniFrac), (4) Differential abundance testing between {comparison}, (5) Functional profiling (KEGG pathways, CAZymes), (6) Visualize community composition and diversity.
+
+### RNA Velocity Analysis
+**Skills:** scvelo, scanpy, scientific-visualization, anndata **[needs files]**
+
+Perform RNA velocity analysis on the uploaded single-cell data. (1) Quantify spliced and unspliced counts, (2) Fit RNA velocity models (stochastic or dynamical), (3) Project velocity vectors onto the UMAP embedding, (4) Identify root and terminal cell states, (5) Compute latent time, (6) Identify driver genes for each lineage transition.
+
+### Spatial Transcriptomics
+**Skills:** scanpy, anndata, scientific-visualization, geopandas **[needs files]**
+
+Analyze the uploaded spatial transcriptomics data ({platform}). (1) QC and normalization, (2) Identify spatially variable genes, (3) Cluster spots/cells and annotate tissue regions, (4) Map cell types using reference scRNA-seq if available, (5) Analyze spatial co-localization and communication patterns, (6) Visualize gene expression overlaid on tissue images.
+
+### Variant Annotation & Interpretation
+**Skills:** clinvar-database, gnomad-database, ensembl-database, gene-database **[needs files]**
+
+Annotate and interpret the uploaded variant list (VCF or table). (1) Add functional annotations (missense, nonsense, splice-site), (2) Query population frequency from gnomAD, (3) Check ClinVar for known pathogenic variants, (4) Predict functional impact (CADD, PolyPhen, SIFT scores), (5) Flag variants in ACMG-actionable genes, (6) Prioritize variants relevant to {phenotype}.
+
+### Phylogenetic Analysis
+**Skills:** phylogenetics, biopython, etetoolkit **[needs files]**
+
+Perform a phylogenetic analysis on the uploaded sequences. (1) Align sequences with an appropriate method, (2) Select the best evolutionary model, (3) Build a phylogenetic tree (ML or Bayesian), (4) Assess branch support (bootstrap), (5) Visualize and annotate the tree. Interpret the key evolutionary relationships.
+
+### Gene Expression Atlas
+**Skills:** gtex-database, geo-database, gget, scientific-visualization
+
+Create a gene expression atlas for: {genes}. (1) Query GTEx for tissue-level expression patterns, (2) Query GEO/ArrayExpress for condition-specific data, (3) Generate tissue expression heatmaps, (4) Compare expression between {conditions} if specified, (5) Identify tissue-specific and ubiquitous genes, (6) Report isoform-level expression differences.
+
+## Grant Writing
+
+### Write a Specific Aim
+**Skills:** scientific-writing, research-grants, writing
+
+Draft a Specific Aim page for a grant proposal on: {topic}. Include: (1) opening paragraph establishing significance and knowledge gap, (2) overall objective and central hypothesis, (3) 2-3 specific aims with brief rationale and approach for each, (4) closing statement on expected impact. Target agency: {agency}
+
+### Write a Research Plan
+**Skills:** scientific-writing, research-grants, writing
+
+Create a detailed research plan for investigating: {topic}. Include: (1) Background and rationale, (2) Specific hypotheses, (3) Experimental design and methods, (4) Expected outcomes and alternatives, (5) Timeline with milestones, (6) Required resources and personnel.
+
+### Draft a Budget Justification
+**Skills:** research-grants, writing
+
+Draft a budget justification narrative for a grant proposal on: {topic}. Cover personnel (PI, postdocs, students), equipment, supplies, travel, and other costs. Justify each line item in terms of the proposed research. Total budget target: {budget}
+
+### Write a Biosketch
+**Skills:** research-grants, writing, scientific-writing
+
+Draft a biosketch for {name} in the context of a {agency} proposal on {topic}. Include: (1) Personal statement connecting expertise to the project, (2) Positions, scientific appointments, and honors, (3) Contributions to science (up to 5 key accomplishments with up to 4 publications each), (4) Research support (current and completed). Follow {agency} format guidelines.
+
+### Write Significance Section
+**Skills:** scientific-writing, research-grants, literature-review, writing
+
+Write the Significance section for a grant proposal on: {topic}. (1) Establish the burden/importance of the problem, (2) Explain how the proposed research will fill a critical gap, (3) Describe the expected impact on the field, (4) Cite key statistics and prior findings that motivate the work. Write persuasively and cite evidence.
+
+### Write Innovation Section
+**Skills:** scientific-writing, research-grants, writing
+
+Write the Innovation section for a grant proposal on: {topic}. Describe: (1) How the approach differs from existing methods, (2) New technologies or techniques being applied, (3) Novel conceptual framework or hypothesis, (4) Why this innovation matters for advancing the field. Be specific and avoid generic claims.
+
+### Write Research Strategy / Approach
+**Skills:** scientific-writing, research-grants, writing
+
+Write the Approach/Research Strategy section for a grant on: {topic}. For each aim: (1) Rationale, (2) Preliminary data supporting feasibility, (3) Detailed experimental design, (4) Expected results and interpretation, (5) Potential pitfalls and alternative approaches, (6) Timeline. Write for {agency} format.
+
+### Create a Project Timeline
+**Skills:** scientific-visualization, matplotlib, markdown-mermaid-writing
+
+Create a detailed project timeline for a {duration} project on: {topic}. Include: (1) Gantt chart showing all tasks across aims, (2) Milestones and deliverables, (3) Go/no-go decision points, (4) Personnel assignments, (5) Dependencies between tasks. Visualize as a Gantt chart.
+
+### Write a Data Management Plan
+**Skills:** scientific-writing, research-grants, writing
+
+Write a Data Management Plan for a {agency} grant on: {topic}. Cover: (1) Types of data generated, (2) Data standards and formats, (3) Access and sharing policies, (4) Archiving and preservation plan, (5) Privacy and security considerations, (6) Roles and responsibilities. Follow {agency} DMS policy requirements.
+
+### Write Broader Impacts
+**Skills:** scientific-writing, research-grants, writing
+
+Write a Broader Impacts section (NSF) or Dissemination Plan for a proposal on: {topic}. Include: (1) Educational and training activities, (2) Plans for broadening participation (underrepresented groups), (3) Public engagement and outreach, (4) Potential societal benefits, (5) Plans for open-access publication and data sharing.
+
+### Risk Mitigation Plan
+**Skills:** scientific-writing, what-if-oracle, writing
+
+Create a risk mitigation plan for a research project on: {topic}. (1) Identify key scientific and technical risks for each aim, (2) Rate each risk by likelihood and impact, (3) Describe mitigation strategies and alternative approaches, (4) Identify early indicators of problems, (5) Create a risk matrix visualization.
+
+### Facilities & Equipment
+**Skills:** research-grants, writing
+
+Write a Facilities, Equipment, and Other Resources section for a grant on: {topic} at {institution}. Describe: (1) Laboratory space and equipment, (2) Computational resources, (3) Core facilities and shared instruments, (4) Animal/clinical facilities if applicable, (5) Institutional support and collaborations, (6) Office space and meeting rooms.
+
+## Literature and Search
+
+### Literature Search
+**Skills:** literature-review, research-lookup, openalex-database
+
+Search the literature on the topic: {topic}. Find the most relevant and highly cited papers, summarize key findings from each, identify major themes and consensus, note any controversies, and highlight gaps in the current knowledge. Provide a structured bibliography.
+
+### Summarize a Paper
+**Skills:** scientific-critical-thinking **[needs files]**
+
+Provide a structured summary of the uploaded paper: (1) Research objective and hypothesis, (2) Study design and methods, (3) Key findings and results, (4) Limitations acknowledged, (5) Conclusions and significance, (6) How this fits into the broader field. Keep it concise but thorough.
+
+### Compare Papers
+**Skills:** scientific-critical-thinking, peer-review **[needs files]**
+
+Compare and contrast the uploaded papers. Create a structured comparison covering: (1) Research questions and objectives, (2) Methodological approaches, (3) Key findings — agreements and contradictions, (4) Strengths and weaknesses of each, (5) Which provides stronger evidence and why. Present as a comparative table where appropriate.
+
+### Research Landscape Map
+**Skills:** literature-review, research-lookup, markdown-mermaid-writing, openalex-database
+
+Create a research landscape map for the field of: {topic}. Identify the major research themes, key research groups and labs, landmark papers, current trends, emerging directions, and funding patterns. Visualize the landscape as a structured diagram or concept map.
+
+### Systematic Review Protocol
+**Skills:** literature-review, pubmed-database, scientific-writing, writing
+
+Design a systematic review protocol for: {question}. (1) Formulate the PICO question, (2) Define inclusion/exclusion criteria, (3) Create search strategies for PubMed, Web of Science, and Scopus, (4) Describe screening and data extraction procedures, (5) Plan quality assessment (e.g., Cochrane RoB, Newcastle-Ottawa), (6) Outline the analysis plan. Follow PRISMA guidelines.
+
+### Citation Analysis
+**Skills:** openalex-database, scholar-evaluation, research-lookup, networkx
+
+Perform a citation analysis on the topic: {topic}. (1) Identify the most cited papers and their citation trajectories, (2) Map citation networks between key papers, (3) Identify citation bursts (rapidly emerging topics), (4) Calculate h-index and other metrics for key authors, (5) Visualize the citation network.
+
+### Find Public Datasets
+**Skills:** research-lookup, get-available-resources, geo-database
+
+Find publicly available datasets relevant to: {topic}. Search across major repositories (GEO, ArrayExpress, TCGA, UK Biobank, Data Commons, Zenodo, Figshare, etc.). For each dataset: (1) describe its contents, (2) report sample size, (3) note the data format, (4) provide access URL, (5) list any usage restrictions.
+
+### Track Research Trends
+**Skills:** openalex-database, research-lookup, scientific-visualization, matplotlib
+
+Analyze research trends in the field of: {field}. (1) Plot publication volume over the past {years} years, (2) Identify the fastest-growing subtopics, (3) Map geographic distribution of research output, (4) Identify top-publishing institutions and authors, (5) Highlight emerging methodologies, (6) Project near-future trends.
+
+### Find Recent Preprints
+**Skills:** biorxiv-database, arxiv-database, research-lookup
+
+Search for recent preprints on: {topic}. Check bioRxiv, medRxiv, arXiv, and other relevant preprint servers. (1) List the most relevant preprints from the past {months} months, (2) Summarize each paper's main finding in 2-3 sentences, (3) Note which have been peer-reviewed or published, (4) Highlight any contradictory findings.
+
+### Patent Landscape
+**Skills:** uspto-database, research-lookup, market-research-reports
+
+Analyze the patent landscape for: {technology}. (1) Search USPTO and major patent databases, (2) Identify key patent holders and filing trends, (3) Map patent families and citations, (4) Identify freedom-to-operate concerns, (5) Highlight recent filings and emerging IP areas, (6) Summarize the competitive IP landscape.
+
+### Compare Methods
+**Skills:** literature-review, research-lookup, scientific-critical-thinking
+
+Systematically compare methods for: {task}. (1) Identify the main methods used in the literature, (2) Compare on criteria: accuracy, computational cost, ease of use, assumptions, sample size requirements, (3) Summarize which method is best under which conditions, (4) Create a comparison table, (5) Provide recommendations.
+
+## Machine Learning and AI
+
+### Build a Classifier
+**Skills:** scikit-learn, shap, scientific-visualization, exploratory-data-analysis **[needs files]**
+
+Build a classification model to predict {target} from the uploaded data. (1) EDA and class balance analysis, (2) Feature engineering and selection, (3) Train multiple models (logistic regression, random forest, XGBoost, SVM), (4) Evaluate: accuracy, precision, recall, F1, AUC-ROC, (5) Analyze with SHAP for interpretability, (6) Tune the best model and report final performance.
+
+### NLP Text Analysis
+**Skills:** transformers, scikit-learn, scientific-visualization, pytorch-lightning **[needs files]**
+
+Perform NLP analysis on the uploaded text data. Task: {task}. (1) Preprocess text (tokenize, clean, handle encoding), (2) Apply {task}: train a fine-tuned model or use pretrained transformers, (3) Evaluate on held-out test set, (4) Analyze errors and edge cases, (5) Visualize results (confusion matrix, attention maps, embedding clusters), (6) Export predictions.
+
+### Image Classification
+**Skills:** pytorch-lightning, scikit-learn, scientific-visualization **[needs files]**
+
+Build an image classifier for: {classes} using the uploaded image dataset. (1) Explore and augment the dataset, (2) Apply transfer learning from {backbone}, (3) Fine-tune with appropriate learning rate schedule, (4) Evaluate: accuracy, per-class precision/recall, confusion matrix, (5) Visualize Grad-CAM attention maps, (6) Report performance and failure cases.
+
+### Anomaly Detection
+**Skills:** scikit-learn, scientific-visualization, exploratory-data-analysis, pytorch-lightning **[needs files]**
+
+Build an anomaly detection system for the uploaded data. (1) Visualize data distribution, (2) Apply multiple methods (Isolation Forest, Local Outlier Factor, Autoencoder, DBSCAN), (3) Compare detected anomalies across methods, (4) Analyze the characteristics of anomalous points, (5) Tune detection thresholds based on {constraint}, (6) Report anomaly scores and flagged records.
+
+### Feature Engineering
+**Skills:** scikit-learn, shap, exploratory-data-analysis, polars **[needs files]**
+
+Perform feature engineering on the uploaded dataset for predicting {target}. (1) Analyze existing features (distributions, correlations, mutual information), (2) Create interaction features, polynomial features, and domain-specific features, (3) Handle categorical variables (encoding strategies), (4) Apply dimensionality reduction if high-dimensional, (5) Select top features using multiple methods (LASSO, RF importance, Boruta), (6) Report feature importance rankings.
+
+### Hyperparameter Tuning
+**Skills:** scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Optimize hyperparameters for the {model} model on the uploaded data. (1) Define the search space for key hyperparameters, (2) Run {method} with {n_trials} trials, (3) Use {n_folds}-fold cross-validation for evaluation, (4) Analyze hyperparameter importance and interactions, (5) Report the optimal configuration and its performance, (6) Visualize the optimization landscape.
+
+### Model Interpretability
+**Skills:** shap, scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Interpret the uploaded trained model's predictions. (1) Compute global SHAP values for all features, (2) Generate SHAP summary, dependence, and force plots, (3) Apply LIME to {n_samples} individual predictions, (4) Create partial dependence plots for top features, (5) Analyze feature interactions, (6) Identify prediction patterns and potential biases. Report key insights.
+
+### Transfer Learning
+**Skills:** pytorch-lightning, transformers, scikit-learn, scientific-visualization
+
+Apply transfer learning for: {task} using {source_model}. (1) Load the pretrained model and analyze layer representations, (2) Freeze appropriate layers, (3) Add task-specific head for {task}, (4) Fine-tune with learning rate warmup and decay, (5) Evaluate on the target domain vs training from scratch, (6) Analyze where transfer helps and where it hurts.
+
+### Graph Neural Network
+**Skills:** torch-geometric, pytorch-lightning, scientific-visualization, networkx **[needs files]**
+
+Build a graph neural network for: {task} on the uploaded graph data. (1) Construct the graph from the data, (2) Select GNN architecture (GCN, GAT, GraphSAGE, GIN), (3) Train with appropriate loss function, (4) Evaluate: {metrics}, (5) Analyze learned node embeddings, (6) Visualize attention weights or message passing. Compare with non-graph baselines.
+
+### Build a Generative Model
+**Skills:** pytorch-lightning, scientific-visualization, matplotlib
+
+Build a generative model to generate: {data_type}. (1) Analyze the training data distribution, (2) Choose architecture: {architecture}, (3) Train with appropriate loss and regularization, (4) Evaluate generation quality (FID, IS, or domain-specific metrics), (5) Generate {n_samples} samples, (6) Analyze interpolation in latent space and mode coverage.
+
+### Reinforcement Learning
+**Skills:** stable-baselines3, pufferlib, scientific-visualization, matplotlib
+
+Train an RL agent for: {environment}. (1) Define the state space, action space, and reward function, (2) Select algorithm: {algorithm}, (3) Train with appropriate hyperparameters, (4) Plot learning curves (reward, episode length), (5) Evaluate the trained policy, (6) Visualize the agent's behavior and decision-making.
+
+### Model Comparison & Selection
+**Skills:** scikit-learn, scientific-visualization, shap, statistical-analysis **[needs files]**
+
+Compare ML models for predicting {target} from the uploaded data. Models to compare: {models}. (1) Apply identical preprocessing and splits, (2) Train all models with cross-validation, (3) Compare on multiple metrics (accuracy, AUC, F1, calibration), (4) Statistical comparison (paired t-test, Friedman), (5) Analyze computational cost, (6) Generate a comprehensive comparison table and recommend the best model.
+
+### Dataset & Model Bias Audit
+**Skills:** scikit-learn, shap, scientific-visualization, statistical-analysis **[needs files]**
+
+Audit the uploaded dataset and model for bias and fairness. Protected attributes: {attributes}. (1) Analyze representation in training data, (2) Compute demographic parity and equalized odds, (3) Calculate disparate impact ratio, (4) Analyze prediction errors by subgroup, (5) Apply bias mitigation (reweighting, adversarial debiasing) if needed, (6) Report fairness metrics before and after mitigation.
+
+### Build a Recommendation System
+**Skills:** scikit-learn, pytorch-lightning, scientific-visualization, polars **[needs files]**
+
+Build a recommendation system from the uploaded {data_type} data. (1) EDA: analyze user-item interaction patterns, (2) Implement {approach} approach, (3) Handle cold-start problem, (4) Evaluate: precision@k, recall@k, NDCG, MAP, (5) Analyze recommendation diversity and coverage, (6) Generate top-N recommendations for sample users.
+
+### Federated Learning Design
+**Skills:** pytorch-lightning, scikit-learn, scientific-visualization
+
+Design a federated learning system for: {task}. (1) Define the data partitioning strategy ({partition}), (2) Select the FL algorithm (FedAvg, FedProx, FedBN), (3) Design the aggregation protocol, (4) Add privacy mechanisms (differential privacy with epsilon = {epsilon}), (5) Simulate training across {n_clients} clients, (6) Compare with centralized training baseline. Report convergence and accuracy.
+
+## Materials Science
+
+### Crystal Structure Prediction
+**Skills:** pymatgen, scientific-visualization, matplotlib
+
+Predict crystal structures for: {composition}. (1) Search existing structures in materials databases, (2) Generate candidate structures using substitution and prototype methods, (3) Optimize structures with DFT, (4) Evaluate formation energies and thermodynamic stability, (5) Construct the convex hull, (6) Identify the ground-state and low-energy polymorphs. Report space groups and lattice parameters.
+
+### Phase Diagram Analysis
+**Skills:** pymatgen, sympy, matplotlib, scientific-visualization
+
+Construct a phase diagram for the {system} system. (1) Collect thermodynamic data from literature and databases, (2) Calculate phase boundaries using Gibbs energy models, (3) Identify single-phase and multi-phase regions, (4) Mark invariant reactions (eutectic, peritectic, eutectoid), (5) Overlay experimental data if provided, (6) Visualize the complete phase diagram with labels.
+
+### Mechanical Property Prediction
+**Skills:** pymatgen, scientific-visualization, matplotlib
+
+Predict the mechanical properties of: {material}. (1) Calculate elastic constants (C_ij tensor), (2) Derive bulk modulus, shear modulus, and Young's modulus, (3) Estimate Vickers hardness, (4) Analyze anisotropy (Zener ratio), (5) Compare with known materials of similar composition, (6) Assess Pugh's ratio (ductile vs brittle behavior).
+
+### High-Throughput Materials Screening
+**Skills:** pymatgen, pymoo, scientific-visualization, research-lookup
+
+Screen materials for: {application}. Target properties: {properties}. (1) Query materials databases (Materials Project, AFLOW, OQMD), (2) Filter by target property ranges, (3) Rank candidates by a multi-objective score, (4) Check stability (formation energy, hull distance), (5) Assess synthesizability from literature, (6) Report top 20 candidates with all relevant properties.
+
+### Defect Analysis
+**Skills:** pymatgen, sympy, matplotlib, scientific-visualization
+
+Analyze defects in: {material}. (1) Calculate formation energies for common point defects (vacancies, interstitials, antisites), (2) Determine charge state transition levels, (3) Compute defect concentrations at {temperature}, (4) Analyze defect migration barriers, (5) Predict the dominant defect type under various chemical potentials, (6) Discuss implications for material properties.
+
+### Alloy Design
+**Skills:** pymatgen, research-lookup, scientific-writing, what-if-oracle
+
+Design an alloy for: {application}. Requirements: {requirements}. (1) Propose candidate composition ranges based on CALPHAD and literature, (2) Predict phase stability and microstructure, (3) Estimate mechanical properties (yield strength, hardness, ductility), (4) Assess corrosion resistance, (5) Check processability (castability, weldability), (6) Recommend top 3 compositions for experimental validation.
+
+### Battery Material Analysis
+**Skills:** pymatgen, scientific-visualization, matplotlib, research-lookup
+
+Evaluate {material} as a {component} for batteries. (1) Calculate voltage profile and theoretical capacity, (2) Analyze structural stability during cycling (volume change), (3) Compute ion migration barriers, (4) Assess electronic conductivity, (5) Compare with state-of-the-art materials, (6) Identify potential degradation mechanisms. Report all relevant electrochemical properties.
+
+### Thermal Conductivity Modeling
+**Skills:** pymatgen, sympy, matplotlib, scientific-visualization
+
+Model the thermal conductivity of: {material}. (1) Calculate phonon dispersion relations, (2) Compute phonon density of states, (3) Estimate lattice thermal conductivity using Boltzmann transport, (4) Analyze phonon scattering mechanisms, (5) Predict temperature dependence from {t_min} to {t_max} K, (6) Compare with experimental data if available.
+
+### Surface Energy Analysis
+**Skills:** pymatgen, matplotlib, scientific-visualization
+
+Calculate surface energies for: {material}. (1) Identify low-index surfaces, (2) Construct surface slab models, (3) Calculate surface energy for each facet, (4) Construct Wulff shape (equilibrium crystal morphology), (5) Analyze surface terminations and reconstructions, (6) Predict adsorption energies for {adsorbate} if specified.
+
+### Polymer Property Prediction
+**Skills:** rdkit, research-lookup, scientific-visualization, deepchem
+
+Predict properties for the polymer: {polymer}. (1) Calculate glass transition temperature (Tg), (2) Predict thermal decomposition temperature, (3) Estimate mechanical properties (modulus, tensile strength), (4) Predict gas permeability (O2, N2, CO2), (5) Assess solubility parameters, (6) Compare with experimental data and similar polymers in the literature.
+
+### Electronic Band Structure
+**Skills:** pymatgen, matplotlib, scientific-visualization
+
+Calculate the electronic band structure for: {material}. (1) Optimize the crystal structure, (2) Compute bands along the standard high-symmetry k-path, (3) Calculate total and projected density of states, (4) Determine band gap (direct/indirect), (5) Analyze orbital character of bands near the Fermi level, (6) Compute effective masses if semiconducting.
+
+### Materials Science Literature Review
+**Skills:** literature-review, research-lookup, scientific-writing, openalex-database
+
+Conduct a comprehensive literature review on: {topic} in materials science. (1) Search recent publications (last {years} years), (2) Identify key synthesis methods and characterization techniques, (3) Compile reported property values in a comparison table, (4) Identify trends and discrepancies between studies, (5) Highlight open challenges, (6) Suggest promising research directions.
+
+## Mathematics and Optimization
+
+### Solve Differential Equations
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Solve the differential equation(s): {equation}. (1) Classify the equation (ODE/PDE, order, linearity), (2) Attempt analytical solution if possible, (3) Implement numerical solution with appropriate methods, (4) Apply boundary/initial conditions: {conditions}, (5) Analyze solution stability and behavior, (6) Visualize the solution space and phase portraits.
+
+### Solve an Optimization Problem
+**Skills:** pymoo, sympy, scientific-visualization, matplotlib
+
+Solve the optimization problem: {objective} subject to constraints: {constraints}. (1) Classify the problem (LP, QP, MILP, nonlinear, multi-objective), (2) Select appropriate solver, (3) Find the optimal solution, (4) Perform sensitivity analysis on key parameters, (5) Analyze the Pareto front if multi-objective, (6) Visualize the feasible region and optimal point.
+
+### Bayesian Inference
+**Skills:** pymc, scientific-visualization, matplotlib, statsmodels
+
+Perform Bayesian inference for: {model}. Prior assumptions: {priors}. (1) Specify the generative model and likelihood, (2) Define prior distributions, (3) Run MCMC sampling (NUTS), (4) Check convergence (trace plots, R-hat, ESS), (5) Report posterior distributions and 95% HDIs, (6) Compare models using WAIC/LOO, (7) Generate posterior predictive checks.
+
+### Monte Carlo Simulation
+**Skills:** pymc, matplotlib, scientific-visualization, statistical-analysis
+
+Design and run a Monte Carlo simulation for: {problem}. (1) Define the random variables and their distributions, (2) Specify the model/function to evaluate, (3) Run {n_samples} samples, (4) Estimate the quantity of interest with confidence intervals, (5) Analyze convergence rate, (6) Perform variance reduction if needed (importance sampling, antithetic variables). Visualize the distribution of results.
+
+### Graph Theory Analysis
+**Skills:** networkx, scientific-visualization, matplotlib, plotly **[needs files]**
+
+Analyze the uploaded graph/network. (1) Compute basic properties (|V|, |E|, density, diameter), (2) Run graph algorithms: {algorithms}, (3) Detect communities/components, (4) Calculate centrality measures, (5) Test graph properties (planarity, bipartiteness, connectivity), (6) Solve optimization problems on the graph if specified. Visualize with appropriate layout.
+
+### Symbolic Computation
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Perform symbolic computation for: {expression}. (1) Simplify the expression, (2) Perform requested operations: {operations}, (3) Verify results numerically, (4) Provide step-by-step derivation, (5) Generate LaTeX output, (6) Plot symbolic functions if they represent curves or surfaces.
+
+### Numerical Methods Implementation
+**Skills:** sympy, matplotlib, scientific-visualization, matlab
+
+Implement numerical methods for: {problem}. (1) Implement {methods} algorithms, (2) Analyze convergence rate and order, (3) Compare accuracy vs computational cost, (4) Test on benchmark problems, (5) Analyze stability and error propagation, (6) Visualize convergence and error plots. Provide clean, documented code.
+
+### Stochastic Process Modeling
+**Skills:** pymc, sympy, matplotlib, scientific-visualization
+
+Model the stochastic process: {process}. (1) Define the state space and transition rules, (2) Derive key properties analytically (mean, variance, stationary distribution), (3) Simulate sample paths, (4) Estimate parameters from data if provided, (5) Compute hitting times and absorption probabilities, (6) Visualize sample paths and probability distributions.
+
+### Game Theory Analysis
+**Skills:** sympy, scientific-visualization, matplotlib
+
+Analyze the game: {game}. (1) Model as a normal-form or extensive-form game, (2) Find all pure strategy Nash equilibria, (3) Find mixed strategy Nash equilibria, (4) Analyze dominated strategies, (5) Compute Shapley values if coalitional game, (6) Simulate repeated play dynamics. Interpret the equilibria in context.
+
+### Topological Data Analysis
+**Skills:** scikit-learn, scientific-visualization, matplotlib **[needs files]**
+
+Apply topological data analysis to the uploaded dataset. (1) Build a filtration (Vietoris-Rips or alpha complex), (2) Compute persistent homology (H0, H1, H2), (3) Generate persistence diagrams and barcodes, (4) Identify significant topological features (loops, voids, connected components), (5) Compare persistence landscapes between groups if applicable, (6) Interpret topological features in the data context.
+
+### Fourier Analysis
+**Skills:** matplotlib, scientific-visualization, sympy **[needs files]**
+
+Perform Fourier analysis on the uploaded signal/data. (1) Compute the FFT and power spectrum, (2) Identify dominant frequencies and their amplitudes, (3) Apply windowing (Hann, Hamming) to reduce spectral leakage, (4) Generate spectrogram for time-frequency analysis, (5) Filter the signal: {filter_spec}, (6) Compare original and filtered signals. Report all significant frequency components.
+
+### Dynamical Systems Analysis
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Analyze the dynamical system: {system}. (1) Find all equilibrium points, (2) Linearize and classify stability (eigenvalue analysis), (3) Generate phase portraits, (4) Identify bifurcations as {parameter} varies, (5) Construct bifurcation diagrams, (6) Compute Lyapunov exponents to detect chaos, (7) Visualize attractors and basins of attraction.
+
+## Neuroscience
+
+### EEG Signal Analysis
+**Skills:** neurokit2, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded EEG data. (1) Preprocess: filter ({freq_range} Hz), re-reference, artifact rejection (ICA for eye/muscle), (2) Compute power spectral density for standard bands (delta, theta, alpha, beta, gamma), (3) Analyze event-related potentials (ERPs) for {events}, (4) Compute topographic maps, (5) Perform time-frequency analysis, (6) Run statistical comparisons between conditions.
+
+### fMRI Analysis Pipeline
+**Skills:** pydicom, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded fMRI data. (1) Preprocessing: motion correction, slice timing, spatial normalization to MNI, smoothing ({fwhm} mm FWHM), (2) First-level GLM for task contrasts: {contrasts}, (3) Group-level analysis (one-sample or two-sample t-test), (4) Cluster-level thresholding (p < 0.001 voxel, p < 0.05 cluster), (5) Report activated regions with MNI coordinates, (6) Visualize activations on brain templates.
+
+### Spike Sorting
+**Skills:** neuropixels-analysis, scientific-visualization, matplotlib **[needs files]**
+
+Perform spike sorting on the uploaded electrophysiology data ({recording_type}). (1) Bandpass filter (300-3000 Hz) for spike band, (2) Detect spikes using threshold-based methods, (3) Extract waveform features (PCA), (4) Cluster spikes into putative single units, (5) Assess unit quality (ISI violations, SNR, isolation distance), (6) Visualize sorted units with average waveforms and autocorrelograms.
+
+### Neural Decoding
+**Skills:** scikit-learn, pytorch-lightning, scientific-visualization, matplotlib **[needs files]**
+
+Build a neural decoder to predict {variable} from the uploaded neural data. (1) Preprocess neural data (binning, smoothing, z-scoring), (2) Split data into training/test sets (preserving temporal structure), (3) Train decoders (logistic regression, SVM, LSTM), (4) Evaluate accuracy with cross-validation, (5) Analyze which neurons contribute most to decoding, (6) Generate confusion matrices and decoding accuracy over time.
+
+### Brain Connectivity Analysis
+**Skills:** networkx, scientific-visualization, matplotlib, statistical-analysis **[needs files]**
+
+Perform brain connectivity analysis on the uploaded data ({modality}). (1) Parcellate the brain using {atlas}, (2) Compute connectivity matrix (functional: correlation/coherence, structural: streamline counts), (3) Threshold and binarize the network, (4) Calculate graph metrics (degree, clustering, modularity, efficiency), (5) Identify hub regions, (6) Compare connectivity between {groups}. Visualize the connectome.
+
+### Behavioral Data Analysis
+**Skills:** statistical-analysis, pymc, scientific-visualization, statsmodels **[needs files]**
+
+Analyze the uploaded behavioral data from a {task_type} task. (1) Compute summary statistics per condition (accuracy, RT), (2) Fit reaction time distributions (ex-Gaussian, drift diffusion), (3) Analyze learning curves if applicable, (4) Fit computational models: {models}, (5) Compare models using AIC/BIC, (6) Correlate model parameters with {neural_data} if available.
+
+### Calcium Imaging Analysis
+**Skills:** scientific-visualization, matplotlib, scikit-learn, statistical-analysis **[needs files]**
+
+Analyze the uploaded calcium imaging data. (1) Motion correction and registration, (2) ROI segmentation (CNMF or Suite2p approach), (3) Extract fluorescence traces and deconvolve to estimate spike rates, (4) Identify place cells, time cells, or task-modulated neurons for {task}, (5) Compute tuning curves and selectivity indices, (6) Analyze population dynamics with dimensionality reduction.
+
+### Neuropixels Data Processing
+**Skills:** neuropixels-analysis, scientific-visualization, matplotlib **[needs files]**
+
+Process the uploaded Neuropixels recording. (1) Apply preprocessing (common average reference, bandpass filter), (2) Run Kilosort or spike sorting, (3) Curate sorted units (merge, split, remove noise), (4) Compute unit quality metrics (ISI violations, presence ratio, amplitude cutoff), (5) Extract good single units and multi-units, (6) Align spikes to behavioral events and compute PSTHs for {events}.
+
+### Brain Atlas Mapping
+**Skills:** scientific-visualization, matplotlib, geopandas **[needs files]**
+
+Map the uploaded neural recording locations or imaging data onto the {atlas} brain atlas. (1) Register electrode positions or imaging coordinates to atlas space, (2) Identify the brain region for each recording site, (3) Summarize data by brain region, (4) Create publication-quality brain maps showing: {data_type}, (5) Generate tables of region assignments, (6) Visualize on 2D flatmaps or 3D renderings.
+
+### Computational Neuron Model
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Build a computational model of a {neuron_type} neuron. (1) Define the morphology (single-compartment or multi-compartment), (2) Set ion channel conductances based on {species} data, (3) Simulate responses to current injection ({protocol}), (4) Characterize firing properties (threshold, F-I curve, adaptation), (5) Analyze the contribution of each conductance, (6) Compare with experimental electrophysiology data if available.
+
+### Psychophysics Analysis
+**Skills:** pymc, statistical-analysis, scientific-visualization, matplotlib **[needs files]**
+
+Analyze the uploaded psychophysics data from a {task} task. (1) Fit psychometric functions (cumulative Gaussian, Weibull) to {conditions}, (2) Extract thresholds and slopes, (3) Compare thresholds across conditions using bootstrap, (4) Analyze response bias (criterion in SDT), (5) Compute d-prime and ROC if detection task, (6) Generate publication-quality psychometric curves with confidence intervals.
+
+### Compare Neural & Artificial Networks
+**Skills:** pytorch-lightning, scikit-learn, scientific-visualization, matplotlib
+
+Compare neural representations with deep network representations. (1) Extract neural population activity for {stimuli}, (2) Extract activations from {model} at multiple layers, (3) Compute representational similarity matrices (RSMs) for both, (4) Compare RSMs using RSA (Spearman correlation), (5) Identify which layer best matches neural data, (6) Analyze what stimulus features drive the match/mismatch.
+
+## Paper and Manuscript
+
+### Review a Paper
+**Skills:** peer-review, scientific-critical-thinking **[needs files]**
+
+Review the uploaded paper. Provide a structured critical review covering: (1) Summary of key findings, (2) Methodology assessment, (3) Statistical rigor, (4) Strengths, (5) Limitations and weaknesses, (6) Constructive suggestions for improvement. Be thorough but fair.
+
+### Write a Paper
+**Skills:** scientific-writing, writing, citation-management **[needs files]**
+
+Using the uploaded data and results, draft a scientific manuscript with the following sections: Abstract, Introduction, Methods, Results, Discussion, and References. Follow standard scientific writing conventions. The paper should be on the topic of: {topic}
+
+### Write a Review Article
+**Skills:** literature-review, scientific-writing, writing, research-lookup
+
+Write a comprehensive review article on the topic: {topic}. Search the literature thoroughly, synthesize key findings across studies, identify consensus and controversies, highlight research gaps, and suggest future directions. Structure with clear thematic sections.
+
+### Edit / Rewrite Manuscript
+**Skills:** scientific-writing, writing **[needs files]**
+
+Improve the writing quality of the uploaded manuscript. Fix grammar and spelling, improve sentence clarity, strengthen transitions between sections, ensure consistent scientific tone, and tighten verbose passages. Preserve the original meaning and technical accuracy. Output the revised manuscript in full.
+
+### Write a Rebuttal
+**Skills:** scientific-writing, writing, peer-review **[needs files]**
+
+Draft a point-by-point rebuttal letter addressing the reviewer comments provided in the uploaded document. For each comment: (1) restate the reviewer's concern, (2) provide a respectful and detailed response, (3) describe any changes made to the manuscript. Be professional and thorough.
+
+### Format for Journal
+**Skills:** scientific-writing, venue-templates, citation-management **[needs files]**
+
+Reformat the uploaded manuscript to match the submission guidelines of {journal}. Adjust sections, headings, reference style, figure/table formatting, word limits, and any other journal-specific requirements. Look up the journal's author guidelines to ensure compliance.
+
+### Write an Abstract
+**Skills:** scientific-writing, writing **[needs files]**
+
+Write a structured abstract for the uploaded manuscript or based on these details: {details}. Include: (1) Background/objective (1-2 sentences), (2) Methods (2-3 sentences), (3) Results (2-3 sentences), (4) Conclusions (1-2 sentences). Keep within {word_limit} words. Ensure it stands alone and conveys the key message.
+
+### Write a Cover Letter
+**Skills:** scientific-writing, writing, venue-templates **[needs files]**
+
+Write a cover letter for submitting the uploaded manuscript to {journal}. Include: (1) brief summary of the study, (2) key findings and their significance, (3) why this journal is the right venue, (4) statement of originality and no concurrent submission, (5) suggested reviewers if applicable. Address to the editor-in-chief.
+
+### Write a Methods Section
+**Skills:** scientific-writing, writing, protocolsio-integration **[needs files]**
+
+Based on the uploaded protocol, data, or experimental notes, write a detailed Methods section suitable for a journal manuscript. Include: (1) Study design, (2) Materials and reagents, (3) Experimental procedures, (4) Data collection methods, (5) Statistical analysis approach. Ensure sufficient detail for reproducibility.
+
+### Write a Results Section
+**Skills:** scientific-writing, writing, statistical-analysis **[needs files]**
+
+Write a Results section based on the uploaded data, figures, and statistical outputs. Present findings in logical order without interpretation. For each result: (1) state the finding clearly, (2) reference the relevant figure/table, (3) report exact statistics (test statistic, p-value, CI, effect size). {focus}
+
+### Write a Discussion Section
+**Skills:** scientific-writing, writing, literature-review, research-lookup **[needs files]**
+
+Write a Discussion section for the uploaded manuscript or these results: {findings}. (1) Summarize main findings, (2) Interpret in context of existing literature, (3) Discuss mechanisms and implications, (4) Acknowledge limitations, (5) Suggest future directions. Search the literature to support interpretive claims.
+
+### Write an Introduction
+**Skills:** scientific-writing, writing, literature-review, research-lookup
+
+Write an Introduction section for a paper on: {topic}. Structure as: (1) Broad context and significance of the field, (2) Review of key prior work (cite real papers), (3) Identify the gap or unanswered question, (4) State the objective and approach of the current study, (5) Brief overview of what follows. Search the literature for accurate citations.
+
+### Translate Manuscript
+**Skills:** scientific-writing, writing **[needs files]**
+
+Translate the uploaded scientific manuscript from {source_lang} to {target_lang}. Preserve all technical terminology, maintain scientific precision, keep formatting and reference numbers intact, and ensure the translation reads naturally to a native speaker in the target language. Flag any terms where translation is ambiguous.
+
+### Write Supplementary Materials
+**Skills:** scientific-writing, writing, scientific-visualization **[needs files]**
+
+Prepare supplementary materials for the uploaded manuscript. Include: (1) Detailed methods not in the main text, (2) Supplementary figures with captions, (3) Supplementary tables, (4) Additional statistical analyses, (5) Raw data summaries. Number all items (Fig. S1, Table S1, etc.) and reference them from the main text.
+
+### Check & Fix References
+**Skills:** citation-management, pyzotero, scientific-writing **[needs files]**
+
+Review the references in the uploaded manuscript. (1) Verify each citation exists and is correctly attributed, (2) Fix formatting inconsistencies, (3) Identify claims in the text that need citations but lack them, (4) Suggest more recent or more relevant references where appropriate, (5) Ensure reference style matches {style} format.
+
+## Physics and Quantum Computing
+
+### Quantum Circuit Design
+**Skills:** qiskit, cirq, sympy
+
+Design a quantum circuit for: {algorithm}. (1) Define the problem Hamiltonian or target operation, (2) Decompose into elementary gates, (3) Optimize circuit depth and gate count, (4) Simulate the circuit on a noiseless backend, (5) Analyze the output state or measurement distribution, (6) Estimate resource requirements (qubits, gate depth) for real hardware.
+
+### Quantum System Simulation
+**Skills:** qutip, sympy, matplotlib, scientific-visualization
+
+Simulate the quantum system: {system}. (1) Define the Hamiltonian, (2) Choose the simulation method (exact diagonalization, tensor networks, Monte Carlo), (3) Compute ground state energy and wavefunction, (4) Calculate observables: {observables}, (5) Analyze phase transitions if relevant, (6) Visualize energy spectrum and correlation functions.
+
+### Quantum Machine Learning
+**Skills:** pennylane, qiskit, scikit-learn, pytorch-lightning
+
+Build a quantum machine learning model for: {task}. (1) Encode the data into quantum states (amplitude or angle encoding), (2) Design a parameterized quantum circuit (ansatz), (3) Train using a hybrid quantum-classical optimization loop, (4) Compare performance with classical ML baseline, (5) Analyze the expressibility and entanglement of the circuit, (6) Assess practical quantum advantage.
+
+### Classical Mechanics Simulation
+**Skills:** sympy, matplotlib, scientific-visualization, matlab
+
+Simulate the mechanical system: {system}. (1) Formulate the equations of motion (Newtonian or Lagrangian), (2) Set initial conditions: {conditions}, (3) Integrate using appropriate numerical methods (RK4, Verlet), (4) Visualize the trajectory and phase space, (5) Compute conserved quantities (energy, momentum, angular momentum), (6) Analyze stability and sensitivity to initial conditions.
+
+### Electromagnetic Simulation
+**Skills:** sympy, matlab, matplotlib, scientific-visualization
+
+Simulate the electromagnetic system: {system}. (1) Define the geometry, materials, and boundary conditions, (2) Choose the appropriate method (FDTD, FEM, MoM), (3) Solve for electric and magnetic fields, (4) Compute derived quantities (impedance, S-parameters, radiation pattern), (5) Visualize field distributions, (6) Analyze resonances and mode profiles.
+
+### Statistical Mechanics Simulation
+**Skills:** sympy, matplotlib, scientific-visualization, molecular-dynamics
+
+Perform a statistical mechanics simulation of: {system}. (1) Define the model Hamiltonian, (2) Implement Monte Carlo (Metropolis) or molecular dynamics simulation, (3) Equilibrate and sample the canonical/microcanonical ensemble at T = {temperature}, (4) Compute thermodynamic averages (energy, heat capacity, magnetization), (5) Analyze phase transitions and critical exponents, (6) Generate phase diagram if varying parameters.
+
+### Particle Physics Data Analysis
+**Skills:** statistical-analysis, matplotlib, scientific-visualization, sympy **[needs files]**
+
+Analyze the uploaded particle physics data. (1) Apply event selection cuts for {channel}, (2) Reconstruct invariant mass distributions, (3) Fit signal + background models, (4) Calculate signal significance, (5) Estimate cross-section or branching ratio, (6) Compare with Standard Model predictions, (7) Generate publication-quality plots with statistical uncertainties.
+
+### Band Structure Calculation
+**Skills:** pymatgen, matplotlib, scientific-visualization, sympy
+
+Calculate the electronic band structure for: {material}. (1) Set up the crystal structure and lattice parameters, (2) Choose the appropriate method (DFT, tight-binding), (3) Compute bands along high-symmetry paths in the Brillouin zone, (4) Calculate the density of states (DOS), (5) Identify band gap, Fermi level, and band character, (6) Visualize band structure and projected DOS.
+
+### Optics Simulation
+**Skills:** sympy, matplotlib, scientific-visualization, matlab
+
+Simulate the optical system: {system}. (1) Define the optical configuration and components, (2) Perform ray tracing or wave optics propagation, (3) Compute key metrics: {metrics}, (4) Analyze aberrations, diffraction, or interference patterns, (5) Optimize system parameters, (6) Visualize beam profiles and optical fields.
+
+### Thermodynamic Modeling
+**Skills:** sympy, matplotlib, scientific-visualization
+
+Model the thermodynamic system: {system}. (1) Define the working fluid and state points, (2) Calculate state properties at each point (T, P, h, s, v), (3) Compute cycle efficiency and work output, (4) Generate T-s and P-v diagrams, (5) Perform sensitivity analysis on key parameters, (6) Compare with ideal cycle performance. Report all energy balances.
+
+### Gravitational Wave Analysis
+**Skills:** astropy, matplotlib, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded gravitational wave data. (1) Apply bandpass filtering and noise whitening, (2) Compute spectrograms and Q-transforms, (3) Perform matched filtering against {templates}, (4) Estimate signal parameters (chirp mass, spin, distance), (5) Calculate signal-to-noise ratio, (6) Generate strain and spectrogram visualizations, (7) Compare with waveform templates.
+
+### Plasma Physics Simulation
+**Skills:** fluidsim, sympy, matplotlib, scientific-visualization
+
+Simulate the plasma system: {system}. (1) Define plasma parameters (density, temperature, magnetic field), (2) Choose the appropriate model (MHD, PIC, Vlasov), (3) Set boundary and initial conditions, (4) Evolve the system and track: {quantities}, (5) Analyze instabilities and wave modes, (6) Visualize density, field, and velocity distributions.
+
+### Quantum Error Correction
+**Skills:** qiskit, cirq, matplotlib, scientific-visualization
+
+Design a quantum error correction scheme for: {noise_model}. (1) Select an appropriate QEC code (surface code, Steane, Shor), (2) Implement encoding and syndrome measurement circuits, (3) Simulate logical error rates vs physical error rate, (4) Plot the error threshold diagram, (5) Analyze resource overhead (physical qubits per logical qubit), (6) Compare with alternative codes.
+
+### Nuclear Decay Analysis
+**Skills:** statistical-analysis, sympy, matplotlib, scientific-visualization
+
+Analyze the nuclear decay data for: {isotope}. (1) Fit exponential decay curves to determine half-life, (2) Identify decay products and branching ratios, (3) Construct the decay chain, (4) Calculate specific activity and dose rates, (5) Compare with literature values from nuclear databases, (6) Generate decay scheme diagrams.
+
+## Proteomics and Structural Biology
+
+### Protein Structure Analysis
+**Skills:** pdb-database, alphafold-database, biopython, esm
+
+Analyze the protein structure for: {protein}. (1) Retrieve the structure from PDB or AlphaFold, (2) Describe the overall fold and domains, (3) Identify active site residues and binding pockets, (4) Analyze secondary structure composition, (5) Visualize key structural features, (6) Compare with homologous structures if relevant.
+
+### Molecular Docking
+**Skills:** diffdock, rdkit, pdb-database
+
+Perform molecular docking of {ligand} against {target}. (1) Retrieve or prepare the protein structure, (2) Prepare the ligand, (3) Define the binding site, (4) Run docking simulations, (5) Analyze binding poses and scores, (6) Visualize the best binding mode. Report binding affinity and key interactions.
+
+### Mass Spectrometry Proteomics
+**Skills:** pyopenms, kegg-database, scientific-visualization, statistical-analysis **[needs files]**
+
+Analyze the uploaded mass spectrometry proteomics data. (1) Process raw spectra (peak picking, deconvolution), (2) Peptide-spectrum matching against {database} database, (3) Protein inference and FDR control, (4) Label-free or TMT quantification, (5) Differential expression analysis between {comparison}, (6) Pathway enrichment of significant proteins. Generate volcano plot and heatmap.
+
+### Protein-Protein Interaction Network
+**Skills:** string-database, networkx, scientific-visualization, kegg-database
+
+Construct a protein-protein interaction network for: {proteins}. (1) Query STRING database for known interactions, (2) Add predicted interactions from co-expression and text mining, (3) Build and visualize the network, (4) Identify hub proteins and clusters, (5) Perform GO enrichment on network modules, (6) Compare with {context} if relevant.
+
+### AlphaFold Structure Prediction
+**Skills:** alphafold-database, pdb-database, biopython, esm
+
+Obtain the AlphaFold-predicted structure for: {protein}. (1) Check the AlphaFold database for existing predictions, (2) Assess prediction confidence (pLDDT scores), (3) Identify well-predicted vs disordered regions, (4) Compare with experimental structures if available, (5) Analyze key structural features (domains, active sites, interfaces), (6) Visualize and annotate the structure.
+
+### Protein Engineering Design
+**Skills:** esm, adaptyv, alphafold-database, biopython
+
+Design protein engineering strategies for: {protein} to improve {property}. (1) Analyze the wild-type structure and active site, (2) Identify candidate positions for mutagenesis (conservation, structural context), (3) Predict effects of mutations using computational tools, (4) Rank mutations by predicted impact, (5) Suggest a focused library design, (6) Recommend experimental validation strategy.
+
+### Binding Site Analysis
+**Skills:** pdb-database, rdkit, diffdock, biopython
+
+Analyze the binding site(s) of: {protein}. (1) Identify all binding pockets using geometric and energy-based methods, (2) Characterize each pocket (volume, hydrophobicity, druggability score), (3) Identify key residues lining the binding site, (4) Map known ligands to binding sites, (5) Compare pocket conservation across homologs, (6) Assess druggability and suggest pharmacophore features.
+
+### Molecular Dynamics Simulation
+**Skills:** molecular-dynamics, rowan, pdb-database
+
+Set up and analyze a molecular dynamics simulation of: {system}. (1) Prepare the system (solvation, ionization, force field selection), (2) Energy minimization and equilibration protocol, (3) Production run setup ({duration}), (4) Analyze RMSD, RMSF, radius of gyration, (5) Identify key conformational changes, (6) Calculate binding free energy if ligand present.
+
+### Homology Modeling
+**Skills:** pdb-database, biopython, alphafold-database, esm
+
+Build a homology model for: {protein}. (1) Search for suitable template structures in PDB, (2) Perform sequence alignment with templates, (3) Build the 3D model using comparative modeling, (4) Refine loop regions and side chains, (5) Validate the model (Ramachandran plot, ERRAT, ProSA), (6) Compare with AlphaFold prediction if available.
+
+### Protein Function Prediction
+**Skills:** interpro-database, uniprot-database, biopython, esm
+
+Predict the function of: {protein}. (1) Run sequence similarity searches (BLAST, HMMer), (2) Identify conserved domains (InterPro, Pfam), (3) Predict subcellular localization, (4) Predict Gene Ontology terms from sequence and structure, (5) Check for signal peptides and transmembrane domains, (6) Integrate all evidence into a function prediction with confidence scores.
+
+### PTM Analysis
+**Skills:** uniprot-database, biopython, pdb-database
+
+Analyze post-translational modifications for: {protein}. (1) Query known PTMs from UniProt, (2) Predict phosphorylation, glycosylation, ubiquitination, and acetylation sites, (3) Map PTMs onto the 3D structure, (4) Assess structural and functional impact of each PTM, (5) Check for disease-associated PTM changes, (6) Compare PTM conservation across species.
+
+### Structural Alignment
+**Skills:** pdb-database, biopython, scientific-visualization
+
+Perform structural alignment between: {structures}. (1) Superimpose the structures using TM-align or similar, (2) Calculate RMSD and TM-score, (3) Identify conserved structural cores and variable regions, (4) Map sequence differences onto the structural alignment, (5) Highlight functional site differences, (6) Visualize the superposition with color-coded differences.
+
+### Epitope Prediction
+**Skills:** biopython, alphafold-database, esm, uniprot-database
+
+Predict epitopes for: {antigen}. (1) Predict linear B-cell epitopes (surface accessibility, hydrophilicity), (2) Predict conformational B-cell epitopes from 3D structure, (3) Predict MHC-I binding peptides for {hla_alleles}, (4) Predict MHC-II binding peptides, (5) Rank epitopes by predicted immunogenicity, (6) Map top epitopes onto the protein structure. Suggest candidates for vaccine design.
+
+## Science Communication
+
+### Plain Language Summary
+**Skills:** scientific-writing, writing **[needs files]**
+
+Rewrite the uploaded paper or abstract in plain language suitable for a non-specialist audience. Avoid jargon, use analogies where helpful, and convey the key findings and their significance in 2-3 paragraphs. This should be suitable for a press release or public-facing summary.
+
+### Write a Blog Post
+**Skills:** scientific-writing, writing **[needs files]**
+
+Write an engaging scientific blog post based on the uploaded paper or results. Use an accessible tone, hook the reader with a compelling opening, explain the science clearly with examples and analogies, and end with why this matters. Target length: 800-1200 words.
+
+### Draft a Protocol
+**Skills:** scientific-writing, writing, protocolsio-integration
+
+Write a detailed step-by-step protocol for: {procedure}. Include: (1) Overview and purpose, (2) Materials and reagents (with catalog numbers if applicable), (3) Equipment needed, (4) Numbered step-by-step procedure, (5) Expected results and troubleshooting tips, (6) Safety notes.
+
+### Write a Press Release
+**Skills:** scientific-writing, writing **[needs files]**
+
+Write an institutional press release about the uploaded research paper or findings. Include: (1) Attention-grabbing headline, (2) Lead paragraph with the key finding, (3) Context and significance, (4) Quotes from researchers, (5) Methods in plain language, (6) Future implications, (7) Contact information placeholder. Write at an 8th-grade reading level.
+
+### Social Media Post
+**Skills:** scientific-writing, writing **[needs files]**
+
+Create a social media thread (Twitter/X or LinkedIn) summarizing the uploaded paper or research finding. Write {num_posts} posts that: (1) Hook with the key finding, (2) Explain the context, (3) Describe the method simply, (4) Present the main result, (5) State why it matters, (6) Include relevant hashtags. Keep each post under 280 characters for Twitter.
+
+### Write a Podcast Script
+**Skills:** scientific-writing, writing, research-lookup
+
+Write a podcast script discussing: {topic}. Structure: (1) Engaging introduction with a hook, (2) Background context, (3) Main discussion points based on recent findings, (4) Interview-style questions and talking points, (5) Conclusion with key takeaways. Target length: {duration} minutes of speaking. Use conversational but accurate language.
+
+### Write a Policy Brief
+**Skills:** scientific-writing, writing, research-lookup
+
+Write a policy brief on: {topic}. Target audience: {audience}. Include: (1) Executive summary, (2) Problem statement with data, (3) Key research findings, (4) Policy options with pros/cons, (5) Recommended actions, (6) Implementation considerations. Keep to 2-4 pages and lead with actionable recommendations.
+
+### Patient Education Material
+**Skills:** scientific-writing, writing, clinical-decision-support
+
+Create patient education materials about: {condition}. Include: (1) What the condition is (plain language), (2) Causes and risk factors, (3) Signs and symptoms, (4) Diagnosis and treatment options, (5) What to expect, (6) When to seek help, (7) Frequently asked questions. Write at a 6th-grade reading level. Avoid medical jargon.
+
+### Write a Textbook Chapter
+**Skills:** scientific-writing, writing, research-lookup
+
+Write a textbook chapter on: {topic} for a {level} audience. Include: (1) Learning objectives, (2) Introduction with historical context, (3) Core concepts explained progressively, (4) Worked examples and case studies, (5) Key equations/formulas with derivations, (6) Summary and key takeaways, (7) Review questions. Target length: {length} words.
+
+### Write an Elevator Pitch
+**Skills:** scientific-writing, writing
+
+Write a compelling 30-60 second elevator pitch for the research project: {topic}. The pitch should: (1) Open with a relatable problem or striking fact, (2) Explain what you're doing in one sentence, (3) Describe the approach briefly, (4) State the potential impact, (5) End with a call to action or next step. Avoid all jargon. Write for a {audience} audience.
+
+## Social Science
+
+### Survey Data Analysis
+**Skills:** statistical-analysis, scientific-visualization, statsmodels, polars **[needs files]**
+
+Analyze the uploaded survey data (n={n} respondents). (1) Report response rates and check for non-response bias, (2) Descriptive statistics for all items, (3) Cross-tabulations with chi-square tests for key comparisons, (4) Likert scale analysis (means, medians, distributions), (5) Factor analysis or PCA if multiple scale items, (6) Regression models predicting {outcome}. Apply survey weights if provided.
+
+### Text Mining & NLP
+**Skills:** transformers, scientific-visualization, matplotlib, scikit-learn **[needs files]**
+
+Perform text mining on the uploaded corpus ({corpus_type}). (1) Preprocess: tokenize, remove stopwords, lemmatize, (2) Generate word frequency and TF-IDF analysis, (3) Run topic modeling (LDA) with {n_topics} topics, (4) Perform named entity recognition, (5) Analyze sentiment distribution, (6) Visualize with word clouds, topic networks, and temporal trends.
+
+### Demographic Analysis
+**Skills:** datacommons-client, scientific-visualization, statistical-analysis, matplotlib
+
+Perform a demographic analysis for: {population}. (1) Compile population data (age, sex, ethnicity, education, income), (2) Create population pyramids and distribution charts, (3) Analyze trends over {period}, (4) Compute dependency ratios and aging indicators, (5) Compare with national/regional benchmarks, (6) Project future demographics using cohort-component method.
+
+### Social Network Analysis
+**Skills:** networkx, scientific-visualization, matplotlib, plotly **[needs files]**
+
+Analyze the uploaded social network data. (1) Compute network statistics (size, density, diameter, clustering coefficient), (2) Calculate centrality measures (degree, betweenness, closeness, eigenvector), (3) Detect communities (Louvain algorithm), (4) Identify bridges and brokers, (5) Analyze information flow patterns, (6) Visualize the network with community coloring and centrality-based node sizing.
+
+### Social Media Sentiment Analysis
+**Skills:** transformers, scientific-visualization, statistical-analysis, matplotlib **[needs files]**
+
+Analyze sentiment in the uploaded social media data about: {topic}. (1) Classify posts as positive/negative/neutral using NLP, (2) Track sentiment over time, (3) Identify key themes driving positive and negative sentiment, (4) Analyze sentiment by demographic or geographic group if available, (5) Detect bot or inauthentic activity, (6) Generate a sentiment report with actionable insights.
+
+### Policy Impact Evaluation
+**Skills:** statsmodels, statistical-analysis, scientific-visualization, matplotlib
+
+Evaluate the impact of {policy} on {outcome}. (1) Define the treatment and control groups, (2) Apply the appropriate method: {method}, (3) Check parallel trends assumption (if DiD), (4) Estimate the treatment effect with confidence intervals, (5) Run robustness checks (placebo tests, alternative specifications), (6) Interpret findings and discuss policy implications.
+
+### Education Outcomes Analysis
+**Skills:** statistical-analysis, scikit-learn, scientific-visualization, statsmodels **[needs files]**
+
+Analyze education outcomes from the uploaded data. (1) Describe student demographics and performance distributions, (2) Compare outcomes between {groups}, (3) Analyze achievement gaps by subgroup, (4) Build a predictive model for {outcome}, (5) Identify key predictors of success, (6) Evaluate the effect of {intervention} if intervention data available. Control for SES and prior achievement.
+
+### Public Opinion Analysis
+**Skills:** statistical-analysis, scientific-visualization, matplotlib, statsmodels **[needs files]**
+
+Analyze public opinion on: {topic} from the uploaded polling data. (1) Weight responses for representativeness, (2) Calculate point estimates with margins of error, (3) Analyze trends over time, (4) Break down by demographics (age, gender, education, party, region), (5) Identify opinion drivers using regression, (6) Compare with historical polls and identify shifts.
+
+### Migration Analysis
+**Skills:** geopandas, datacommons-client, scientific-visualization, statsmodels **[needs files]**
+
+Analyze migration patterns for {region}. (1) Map migration flows (origin-destination) from the uploaded or public data, (2) Quantify net migration rates, (3) Analyze push and pull factors, (4) Model migration determinants using gravity models, (5) Assess demographic impact on sending and receiving regions, (6) Visualize flows on maps and chord diagrams.
+
+### Inequality Measurement
+**Skills:** statistical-analysis, scientific-visualization, matplotlib, datacommons-client **[needs files]**
+
+Measure inequality in {dimension} using the uploaded data. (1) Calculate Gini coefficient and Lorenz curve, (2) Compute percentile ratios (90/10, 80/20), (3) Decompose inequality by {subgroups}, (4) Analyze trends over time, (5) Compare with international benchmarks, (6) Identify key drivers using decomposition methods (Blinder-Oaxaca, Theil).
+
+### Behavioral Experiment Analysis
+**Skills:** statistical-analysis, statsmodels, scientific-visualization, pymc **[needs files]**
+
+Analyze data from the uploaded behavioral experiment ({design}). (1) Check randomization balance, (2) Analyze manipulation check, (3) Test main hypotheses using {analysis_type}, (4) Analyze moderators and mediators, (5) Calculate effect sizes (Cohen's d, partial eta-squared), (6) Check for demand effects and order effects, (7) Generate APA-formatted results with publication-quality figures.
+
+### Content Analysis
+**Skills:** transformers, scientific-visualization, statistical-analysis, matplotlib **[needs files]**
+
+Perform content analysis on the uploaded documents/media. (1) Develop a coding scheme for: {categories}, (2) Apply automated coding using NLP, (3) Calculate inter-rater reliability (Cohen's kappa) if human-coded, (4) Analyze frequency and co-occurrence of codes, (5) Compare content across {groups} or time periods, (6) Identify dominant frames and narratives.
+
+## Visualization and Figures
+
+### Create a Graphical Abstract
+**Skills:** generate-image, scientific-schematics, infographics **[needs files]**
+
+Create a graphical abstract summarizing the key findings of the uploaded paper or data. The graphic should be clear, visually appealing, and convey the main story in a single figure. Use a logical flow from left to right or top to bottom. Include minimal text labels.
+
+### Make a Publication Figure
+**Skills:** scientific-visualization, matplotlib, seaborn, plotly **[needs files]**
+
+Create publication-quality figures from the uploaded data. Choose appropriate plot types for the data, use clear axis labels and legends, apply a clean color palette, and ensure the figures are suitable for journal submission at high resolution. {instructions}
+
+### Build a Slide Deck
+**Skills:** scientific-slides, pptx **[needs files]**
+
+Create a scientific slide deck (PPTX) based on the uploaded paper or data. The presentation is for a {context}. Include a title slide, outline, background/motivation, methods overview, key results with figures, discussion points, and conclusions. Keep slides clean with minimal text.
+
+### Create a Conference Poster
+**Skills:** pptx-posters, latex-posters, scientific-visualization **[needs files]**
+
+Design a scientific conference poster based on the uploaded paper or results. Include: title and authors, introduction/background, methods, key results with figures, conclusions, and references. Use a clear visual hierarchy and clean layout.
+
+### Create an Infographic
+**Skills:** infographics, generate-image **[needs files]**
+
+Create an infographic that explains the key findings from the uploaded paper or data in a visually engaging way suitable for a broad audience. Use icons, simple charts, and minimal jargon. The infographic should tell a clear story.
+
+### Create a Scientific Schematic
+**Skills:** scientific-schematics, generate-image, markdown-mermaid-writing
+
+Create a scientific schematic diagram illustrating: {concept}. The diagram should clearly show the key components, their relationships, and the flow of the process. Use standard scientific conventions, clean lines, and appropriate labels. Make it suitable for inclusion in a journal manuscript.
+
+### Create a Flowchart
+**Skills:** markdown-mermaid-writing, scientific-schematics, generate-image
+
+Create a detailed flowchart for: {workflow}. Show all decision points, parallel processes, and outcomes. Use standard flowchart symbols (rectangles for processes, diamonds for decisions, ovals for start/end). Include color coding for different phases.
+
+### Create a Research Timeline
+**Skills:** scientific-visualization, matplotlib, markdown-mermaid-writing
+
+Create a visual research timeline for a project on: {project}. Total duration: {duration}. Show key milestones, deliverables, work packages, and dependencies. Use a Gantt-chart style with color-coded phases. Include go/no-go decision points.
+
+### Create a Heatmap
+**Skills:** scientific-visualization, seaborn, matplotlib, plotly **[needs files]**
+
+Create a publication-quality heatmap from the uploaded matrix data. (1) Apply appropriate clustering (hierarchical, k-means) to rows and columns if suitable, (2) Choose a perceptually uniform colormap, (3) Add dendrograms if clustered, (4) Label axes clearly, (5) Include a color bar with units. {instructions}
+
+### Create a Network Diagram
+**Skills:** scientific-visualization, networkx, plotly, matplotlib **[needs files]**
+
+Create a network visualization from the uploaded data. (1) Parse nodes and edges, (2) Choose an appropriate layout algorithm (force-directed, circular, hierarchical), (3) Size nodes by {metric}, (4) Color-code by community/cluster, (5) Label key nodes, (6) Include a legend. Make it publication-ready.
+
+### Create a Geographic Map
+**Skills:** geopandas, geomaster, scientific-visualization, matplotlib **[needs files]**
+
+Create a geographic visualization from the uploaded data. (1) Plot data points on an appropriate map projection, (2) Use color gradients or sized markers for quantitative values, (3) Add a legend and scale bar, (4) Include relevant geographic features (borders, coastlines, rivers), (5) Make it publication-ready.
+
+### Create an Interactive Dashboard
+**Skills:** plotly, exploratory-data-analysis, scientific-visualization **[needs files]**
+
+Create an interactive data dashboard from the uploaded dataset. Include: (1) Summary statistics panel, (2) Key distributions as interactive histograms, (3) Correlation scatter plots with hover details, (4) Filterable data table, (5) Time series if temporal data exists. Use Plotly for interactivity. Save as HTML.