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Science Comp.

Simulation and numerical analysis.

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scientific-computing

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lifesciences-graph-builder

Orchestrates life sciences APIs to build knowledge graphs using the Fuzzy-to-Fact protocol, combining MCPs for nodes and curl for edges, then persisting to Graphiti. This skill should be used when the user asks to "build knowledge graphs", "find biological connections", "explore drug repurposing", "validate drug targets", or mentions traversing gene→protein→pathway→drug→disease paths, multi-API orchestration, or graph persistence workflows.

donbr

research

scientific-computing

4

orcaflex-batch-manager

Manage large-scale OrcaFlex batch processing with parallel execution, adaptive worker scaling, memory optimization, and progress tracking for efficient simulation campaigns.

vamseeachanta

research

scientific-computing

4

research

Research topics by verifying actual source content. Use when asked to research or study links and documentation.

spences10

research

scientific-computing

4

lifesciences-clinical

Queries clinical databases (Open Targets, ClinicalTrials.gov) via curl for target-disease associations, target tractability assessment, and clinical trial discovery. This skill should be used when the user asks to "validate drug targets", "find clinical trials", "assess target tractability", "discover disease associations", or mentions Open Targets scores, NCT identifiers, target-disease evidence, druggability assessment, or translational research workflows.

donbr

research

scientific-computing

4

paper-implementation

Implement research papers from arxiv. Use when the user provides an arxiv link, asks to implement a paper, or wants to reproduce research results.

Infatoshi

research

scientific-computing

4

lifesciences-crispr

Validates synthetic lethality claims from CRISPR knockout screens using BioGRID ORCS 5-phase workflow. This skill should be used when the user asks to "validate synthetic lethality", "query CRISPR essentiality data", "find gene dependencies", "compare cell line screens", or mentions BioGRID ORCS, gene knockout data, essentiality scores (CERES, MAGeCK, BAGEL), or asks to validate claims from published CRISPR papers.

donbr

research

scientific-computing

4

lifesciences-proteomics

Queries protein databases (UniProt, STRING, BioGRID) via curl for protein lookups, protein-protein interactions, functional enrichment analysis, and cross-database ID mapping. This skill should be used when the user asks to "find protein interactions", "analyze interaction networks", "perform GO enrichment", "map protein IDs", or mentions PPI networks, UniProt accessions, STRING scores, BioGRID interactions, or protein ID conversion between databases.

donbr

research

scientific-computing

4

lifesciences-genomics

Queries genomic databases (Ensembl, NCBI, HGNC) via curl for gene lookup, variant annotation, orthology, and cross-database ID resolution. This skill should be used when the user asks to "annotate variants", "find orthologs", "map gene IDs", "analyze linkage disequilibrium", or mentions gene symbols, ENSG IDs, HGNC identifiers, VEP annotation, LD analysis, HGVS notation, or DNA sequences.

donbr

research

scientific-computing

4

orcaflex-results-comparison

Compare results across multiple OrcaFlex simulations for design verification, sensitivity studies, and configuration comparison. Includes pretension, stiffness, and force distribution analysis.

vamseeachanta

research

scientific-computing

4

lifesciences-pharmacology

Queries pharmacology databases (ChEMBL, PubChem, DrugBank, IUPHAR) via curl for drug mechanisms, target identification, bioactivity profiling, and indication discovery. This skill should be used when the user asks to "find drug mechanisms", "identify drug targets", "analyze bioactivity data", "discover drug indications", or mentions ChEMBL IDs, mechanisms of action, IC50/Ki values, drug-target relationships, or compound similarity searches.

donbr

research

scientific-computing

4

gmsh-meshing

Specialized AI agent for finite element mesh generation and manipulation using GMSH. Use for 1D/2D/3D mesh generation, geometry processing, quality assessment, optimization, and integration with OrcaFlex, ANSYS, and OpenFOAM.

vamseeachanta

research

scientific-computing

4

bsee-sodir-extraction

Extract and process energy data from BSEE (Gulf of Mexico) and SODIR (Norway) regulatory databases

vamseeachanta

research

scientific-computing

3

power-analysis

Calculate statistical power and required sample sizes for research studies. Use when: (1) Designing experiments to determine sample size, (2) Justifying sample size for grant proposals or protocols, (3) Evaluating adequacy of existing studies, (4) Meeting NIH rigor standards for pre-registration, (5) Conducting retrospective power analysis to interpret null results.

astoreyai

research

scientific-computing

3

perplexity-researcher-pro

Complex research requiring deeper analysis, multi-step reasoning, and sophisticated source evaluation for technical, academic, or specialized domain queries needing expert-level analysis, high-stakes decisions, or multi-layered problem solving.

d-o-hub

research

scientific-computing

3

hic-compartment-shift

This skill performs A/B compartment shift analysis between two Hi-C samples.

BIsnake2001

research

scientific-computing

3

hic-compartments-calling

This skill performs PCA-based A/B compartments calling on Hi-C .mcool datasets using pre-defined MCP tools from the cooler-tools, cooltools-tools, and plot-hic-tools servers.

BIsnake2001

research

scientific-computing

3

alignment-level-qc

Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read group data using samtools and Picard.Use this skill to check "how well the reads mapped" or to validate BAM formatting/sorting before further processing. Do NOT use this skill for biological signal validation (like checking for peaks or open chromatin) or for filtering/removing reads.

BIsnake2001

research

scientific-computing

3

atomic-thought

INVOKE for research tasks and multi-source understanding. Produces visible dependency graphs and contracted answers. Use during research phase of workflow. Triggers: researching topics, gathering information before building, combining facts from multiple independent areas.

bnadlerjr

research

scientific-computing

3

chipseq-qc

Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics.

BIsnake2001

research

scientific-computing

3

functional-enrichment

Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform GO and KEGG functional enrichment using HOMER from genomic regions or just want to link genomic region to genes.

BIsnake2001

research

scientific-computing

3

arxiv-research

Use when searching academic papers on arXiv, understanding research content, building literature reviews, or generating citations for academic writing

Ray0907

research

scientific-computing

3

researcher

Researches topics in-depth and generates comprehensive summaries and references. Use when trying to deeply understand a topic or use a new framework.

MykalMachon

research

scientific-computing

3

research

Deep research using web, docs, and code search. Triggers on: "research", "look into", "what's the best", "how should I", evaluating libraries, unfamiliar patterns, state of the art.

nijaru

research

scientific-computing

3

particles-physics

Physics simulation for particle systems—forces (gravity, wind, drag), attractors/repulsors, velocity fields, turbulence, and collision. Use when particles need realistic or artistic motion, swarm behavior, or field-based animation.

Bbeierle12

research

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