Scientific Computing

SourceK-Dense-AI/scientific-agent-skills/skills/deeptools/SKILL.md

Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Supports batch processing, custom molecular-biology pipelines, BLAST automation, structure analysis, and motif analysis.

deeptools

SourceK-Dense-AI/scientific-agent-skills/skills/glycoengineering/SKILL.md

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

glycoengineering

SourceK-Dense-AI/scientific-agent-skills/skills/hugging-science/SKILL.md

Analyzes and engineers protein glycosylation by scanning canonical N-glycosylation sequons, describing S/T-rich regions, checking curated glycan evidence, and preparing NetNGlyc, NetOGlyc and GlycoSHIELD workflows. Use for glycoprotein engineering, antibody Fc glycosylation, glycan shielding, and site-specific glycoproteomics interpretation.

hugging-science

SourceK-Dense-AI/scientific-agent-skills/skills/marine-carbonate-chemistry/SKILL.md

Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML resources in biology, chemistry, genomics, materials, climate, physics, astronomy, medicine, mathematics, protein design, single-cell analysis, or PDE modeling, and when checking their actual datasets, Transformers, native-runtime, Inference Providers, or Gradio interfaces.

marine-carbonate-chemistry

SourceK-Dense-AI/scientific-agent-skills/skills/matchms/SKILL.md

Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved inorganic carbon, pH, or seawater pCO2/fCO2 measurements; carbonate speciation; aragonite and calcite saturation; Revelle factors; lab-to-in-situ temperature and pressure corrections; and measurement uncertainty propagation. Applies to carbonate-system calculations, not general aqueous speciation or air-sea gas-flux estimation.

matchms

SourceK-Dense-AI/scientific-agent-skills/skills/pymatgen/SKILL.md

Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.

pymatgen

SourceK-Dense-AI/scientific-agent-skills/skills/pyopenms/SKILL.md

Analyzes, validates, converts, and transforms materials structures and computed materials data with pymatgen. Use for local phase diagrams, symmetry sensitivity, electronic-structure I/O, and bounded Materials Project queries.

pyopenms

SourceK-Dense-AI/scientific-agent-skills/skills/pysam/SKILL.md

Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.

pysam

SourceK-Dense-AI/scientific-agent-skills/skills/qiskit/SKILL.md

Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.

qiskit

SourceK-Dense-AI/scientific-agent-skills/skills/simpy/SKILL.md

Builds, simulates, transpiles, and executes quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem packages.

simpy

SourceK-Dense-AI/scientific-agent-skills/skills/vaex/SKILL.md

Builds, inspects, tests, and analyzes bounded process-based discrete-event simulations with SimPy. Use for event scheduling, resource queues, interrupts, monitoring, independent replications, warm-up, and reproducible output analysis.

vaex

Sourcevideojs/video.js/.agents/skills/create-spf-behavior/SKILL.md

Processes large tabular scientific datasets with Vaex expressions, filtered views, streamed statistics, binned visualizations, and file conversion. Use for larger-than-RAM HDF5, Arrow, CSV, or Parquet analysis, virtual feature engineering, or Vaex ML preprocessing; distinguishes these operations from estimators and conversions that materialize data.

create-spf-behavior

Updated2026-10-21

Create or extract one SPF playback-engine behavior. Use for a new atomic responsibility with signals, lifecycle, cleanup, composition, and tests.

detecting-stuxnet-style-attacks

Sourcemukul975/Anthropic-Cybersecurity-Skills/skills/detecting-stuxnet-style-attacks/SKILL.md

Sourcemukul975/Anthropic-Cybersecurity-Skills/skills/detecting-t1055-process-injection-with-sysmon/SKILL.md

Detects sophisticated cyber-physical attacks that follow the Stuxnet pattern of modifying PLC logic while spoofing sensor readings to hide the manipulation, using PLC logic integrity monitoring (Claroty xDome, Nozomi Guardian) and physics-based process anomaly detection. Use when hunting for IT-to-OT lateral movement or discrepancies between PLC program state and physical process behavior in ICS/SCADA environments.

detecting-t1055-process-injection-with-sysmon

Sourcemukul975/Anthropic-Cybersecurity-Skills/skills/performing-malware-persistence-investigation/SKILL.md

Detect process injection techniques (T1055) - including DLL injection, process hollowing, and APC injection - by analyzing Sysmon Event IDs 1, 7, 8, 10, and 25 for cross-process memory operations, remote thread creation, and anomalous DLL loads. Use when hunting defense-evasion activity that hides code inside legitimate processes, investigating an EDR alert on suspicious cross-process access, or validating Sysmon coverage for injection detection.

performing-malware-persistence-investigation

Sourcemukul975/Anthropic-Cybersecurity-Skills/skills/performing-static-malware-analysis-with-pe-studio/SKILL.md

Systematically investigate all persistence mechanisms on Windows and Linux systems to identify how malware survives reboots and maintains access.

performing-static-malware-analysis-with-pe-studio

Sourcedavila7/claude-code-templates/cli-tool/components/skills/ai-research/data-scientist/SKILL.md

Performs static analysis of Windows PE malware samples using PEStudio to examine file headers, imports, strings, and resources without executing the binary, identifying packing, anti-analysis tricks, and malicious imports. Use for pre-execution triage of a suspicious Windows executable before sandbox detonation.

data-scientist

Updated2026-10-24

Expert data scientist for advanced analytics, machine learning, and statistical modeling. Handles complex data analysis, predictive modeling, and business intelligence.

biopython

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/biopython/SKILL.md

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/cobrapy/SKILL.md

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

cobrapy

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/cosmic-database/SKILL.md

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

cosmic-database

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/deeptools/SKILL.md

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

deeptools

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/etetoolkit/SKILL.md

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

etetoolkit

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/exploratory-data-analysis/SKILL.md

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

exploratory-data-analysis

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/flowio/SKILL.md

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

flowio

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/fluidsim/SKILL.md

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

fluidsim

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/hmdb-database/SKILL.md

Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

hmdb-database

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/matchms/SKILL.md

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

matchms

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/neurokit2/SKILL.md

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

neurokit2

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/pymatgen/SKILL.md

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

pymatgen

Sourcedavila7/claude-code-templates/cli-tool/components/skills/scientific/pyopenms/SKILL.md

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

pyopenms