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Science Comp.

Simulation and numerical analysis.

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scientific-computing

9

dynamo-preprocess

Run or adapt dynamo preprocessing with `dynamo.preprocessing.Preprocessor`, including the `recipe` branches `monocle`, `seurat`, `sctransform`, `pearson_residuals`, and `monocle_pearson_residuals`. Use when converting or reproducing `docs/tutorials/notebooks/100_tutorial_preprocess.ipynb`, preprocessing an `AnnData` object for downstream dynamo analysis, customizing preprocessing kwargs, or translating notebook-level preprocessing into a reusable agent workflow.

aristoteleo

research

scientific-computing

9

analyze-diffusion-dynamics

Analysieren the dynamics of diffusion processes using stochastic differential equations, Fokker-Planck equations, first-passage time distributions, and parameter sensitivity analysis. Verwenden wenn deriving probability density evolution for a continuous-time diffusion process, computing mean first-passage times for bounded diffusion, analyzing how drift and diffusion parameters affect process behavior, or validating closed-form solutions gegen stochastic simulation.

pjt222

research

scientific-computing

9

pymatgen-core

Use for pymatgen core objects and structure manipulation: Element/Specie/Composition, Lattice/Site/Structure/Molecule, oxidation states, structure edits, transformations, and serialization.

Hongyu-yu

research

scientific-computing

9

analyze-diffusion-dynamics

Analyze the dynamics of diffusion processes using stochastic differential equations, Fokker-Planck equations, first-passage time distributions, and parameter sensitivity analysis. Use when deriving probability density evolution for a continuous-time diffusion process, computing mean first-passage times for bounded diffusion, analyzing how drift and diffusion parameters affect process behavior, or validating closed-form solutions against stochastic simulation.

pjt222

research

scientific-computing

8

regulatory-drafter

Drafts regulatory documents (FDA, EMA) with audit trails and specific "Thinking Block" reasoning. Use for high-stakes compliance writing.

mdbabumiamssm

research

scientific-computing

8

research-web

Deep web research with parallel investigators, multi-wave exploration, and structured synthesis. Spawns multiple web-researcher agents to explore different facets of a topic simultaneously, launches additional waves when gaps are identified, then synthesizes findings. Use when asked to research, investigate, compare options, find best practices, or gather comprehensive information from the web.\n\nThoroughness: quick for factual lookups | medium for focused topics | thorough for comparisons/evaluations (waves continue while critical gaps remain) | very-thorough for comprehensive research (waves continue until satisficed). Auto-selects if not specified.

doodledood

research

scientific-computing

8

clinical-trial-matcher

Matches patient profiles to open clinical trials using vector similarity and inclusion/exclusion criteria. Use when a user provides patient data and asks for relevant trials.

mdbabumiamssm

research

scientific-computing

8

chemcrow-tools

A production-grade cheminformatics toolkit for analyzing molecular properties, toxicity, and synthetic accessibility.

mdbabumiamssm

research

scientific-computing

8

protein-structure-prediction

Predicts 3D protein structures from amino acid sequences using ESMFold or AlphaFold3 (mock).

mdbabumiamssm

research

scientific-computing

8

crispr-designer

Designs guide RNA (gRNA) sequences for CRISPR-Cas9 editing, including off-target analysis. Use when a user needs to edit a gene or asks for gRNA sequences.

mdbabumiamssm

research

scientific-computing

7

deep-researcher

Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources. Use when the user needs thorough investigation, market research, technical deep-dives, due diligence, or comprehensive analysis on any subject.

Karanjot786

research

scientific-computing

7

m4-research

Start a structured clinical research session. Triggers on "/research", "start research", "new study", "analyze cohort", "investigate hypothesis", "research question", or when users describe clinical research goals. Interviews the user, then produces a rigorous research plan.

hannesill

research

scientific-computing

7

m4-api

Use the M4 Python API to query clinical datasets (MIMIC-IV, eICU) programmatically. Triggers on "M4 API", "query MIMIC with Python", "clinical data analysis", "EHR data", "execute SQL on MIMIC", or when writing code to access clinical databases.

hannesill

research

scientific-computing

7

research-workflow

Guide agents through structured research including planning, multi-query execution, source analysis, and synthesis. Use for comprehensive topic research, deep investigation, or creating research reports. Keywords: research, investigate, deep dive, comprehensive, analysis, synthesis, report.

jwynia

research

scientific-computing

7

research

Diagnose research quality and guide systematic query expansion. Use when starting research on any topic, when stuck in research, or when unsure if research is complete.

jwynia

research

scientific-computing

7

mimic-eicu-mapping

Map equivalent concepts between MIMIC-IV and eICU databases. Use for multi-database studies, external validation, or understanding structural differences between databases.

hannesill

research

scientific-computing

7

numerical-stability

Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diagnosing numerical blow-up, or checking CFL/Fourier criteria for advection/diffusion/reaction problems.

HeshamFS

research

scientific-computing

7

differentiation-schemes

Select and apply numerical differentiation schemes for PDE/ODE discretization. Use when choosing finite difference/volume/spectral schemes, building stencils, handling boundaries, or estimating truncation error and dispersion.

HeshamFS

research

scientific-computing

7

numerical-integration

Select and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances, adapting time steps, or diagnosing integration accuracy and stability issues.

HeshamFS

research

scientific-computing

7

clinical-research-pitfalls

Avoid common methodological mistakes in clinical research with MIMIC-IV and eICU databases. Covers immortal time bias, information leakage, selection bias, and other critical pitfalls.

hannesill

research

scientific-computing

7

suspicion-of-infection

Identify suspected infection events in MIMIC-IV using antibiotic administration plus culture timing. Use as a component of Sepsis-3 definition or for infection research.

hannesill

research

scientific-computing

7

mesh-generation

Plan and evaluate mesh generation for numerical simulations. Use when choosing grid resolution, checking aspect ratios/skewness, or estimating mesh quality constraints for PDE discretization.

HeshamFS

research

scientific-computing

7

time-stepping

Plan and control time-step policies for simulations. Use when coupling CFL/physics limits with adaptive stepping, ramping initial transients, or scheduling outputs/checkpoints for long runs.

HeshamFS

research

scientific-computing

6

geniml

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

jackspace

research

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