computational-chemistry
538
mcmc-diagnostics
MCMC convergence diagnostics and analysis
a5c-ai
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
computational-chemistry
538
counterexample-generator
Automated search for counterexamples to mathematical conjectures
a5c-ai
research
computational-chemistry
538
surface-analysis
Skill for surface composition, chemical state, and topography analysis including XPS depth profiling, AFM imaging, and contact angle measurements
a5c-ai
research
computational-chemistry
538
polymer-characterization
Specialized skill for polymer materials analysis including molecular weight distribution, thermal transitions, crystallinity, and rheological properties
a5c-ai
research
computational-chemistry
538
rag-reranking
Cross-encoder reranking and MMR diversity filtering for improved retrieval quality
a5c-ai
research
computational-chemistry
538
niosh-lifting-calculator
NIOSH Lifting Equation calculator for manual material handling risk assessment.
a5c-ai
research
computational-chemistry
538
integer-program-solver
Integer and mixed-integer programming skill for combinatorial optimization problems with discrete decision variables.
a5c-ai
research
computational-chemistry
538
rag-hybrid-search
Hybrid search combining semantic and keyword retrieval for RAG pipelines. Implement BM25 + dense vector search with fusion strategies.
a5c-ai
research
computational-chemistry
538
screen-reader
Screen reader compatibility, testing, and optimization.
a5c-ai
research
computational-chemistry
538
binary-exploitation-skill
Advanced binary exploitation and mitigation bypass
a5c-ai
research
computational-chemistry
538
turing-machine-simulator
Simulate Turing machines for computability analysis and algorithm demonstration
a5c-ai
research
computational-chemistry
538
vehicle-physics
Vehicle simulation skill for wheel colliders, suspension, and aerodynamics.
a5c-ai
research
computational-chemistry
493
clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
jimmc414
research
computational-chemistry
492
patch-applier
Draft and apply small, atomic patches; always present a preview diff and appropriate verification commands.
pilinux
research
computational-chemistry
471
bioskills
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.
GPTomics
research
computational-chemistry
471
bio-reporting-rmarkdown-reports
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.
GPTomics
research
computational-chemistry
471
bio-rna-structure-secondary-structure-prediction
Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold). Computes base-pair probabilities, centroid structures, and consensus structures from alignments. Use when predicting RNA folding, evaluating structural stability, or comparing structures across homologs.
GPTomics
research
computational-chemistry
471
bio-rna-structure-ncrna-search
Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database. Identifies structured RNAs by sequence and secondary structure conservation. Use when querying sequences against Rfam, building custom covariance models for novel RNA families, or classifying non-coding transcripts by family.
GPTomics
research
computational-chemistry
471
bio-similarity-searching
Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules by structural similarity using Butina clustering. Use when finding analogs of a query compound or clustering chemical libraries.
GPTomics
research
computational-chemistry
471
bio-crispr-screens-jacks-analysis
JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.
GPTomics
research
computational-chemistry
471
bio-alignment-pairwise
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
GPTomics
research
computational-chemistry
471
bio-clip-seq-clip-peak-calling
Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads.
GPTomics
research
computational-chemistry
471
bio-clinical-databases-clinvar-lookup
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
GPTomics
research
computational-chemistry
471
bio-ribo-seq-ribosome-periodicity
Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determining read offsets for downstream analysis.
GPTomics
research