科學計算

Binary Analysis Patterns

Comprehensive patterns and techniques for analyzing compiled binaries, understanding assembly code, and reconstructing program logic.

sickn3333.8k

Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks.

sickn3333.8k

Hypothesis Generation

Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.

davila724.7k

Exploration

Systematic methodology for profiling datasets, assessing data quality, discovering patterns, and understanding schemas.

kortix-ai19.6k

Fluidsim

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.

Exploratory Data Analysis

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.

Database Lookup

Search 78 public scientific, biomedical, materials science, and economic databases via REST APIs. Covers physics/astronomy (NASA, NIST, SDSS, SIMBAD), earth/environment (USGS, NOAA, EPA), chemistry/drugs (PubChem, ChEMBL, DrugBank, FDA, KEGG, ZINC, BindingDB), materials (Materials Project, COD), biology/genomics (Reactome, UniProt, STRING, Ensembl, NCBI Gene, GEO, GTEx, PDB, AlphaFold, InterPro, BioGRID, Gene Ontology, dbSNP, gnomAD, ENCODE, Human Protein Atlas, Human Cell Atlas), disease/clinical (COSMIC, Open Targets, ClinicalTrials.gov, OMIM, ClinVar, GDC/TCGA, cBioPortal, DisGeNET, GWAS Catalog), regulatory (FDA, USPTO, SEC EDGAR), economics/finance (FRED, World Bank, US Treasury), demographics (US Census, Eurostat, WHO). Use when looking up compounds, genes, proteins, pathways, variants, clinical trials, patents, economic indicators, or any public database API query.

Biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

Cobrapy

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

Etetoolkit

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

Deeptools

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

Glycoengineering

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.

Flowio

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.

NeuroKit2

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

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

Primekg

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

Explain

Parse and interpret Z3 output for human consumption. Handles models, unsat cores, proofs, statistics, and error messages. Translates solver internals into plain-language explanations.

Z3Prover12.2k

Customization

Hypothesis-test-analyze cycles for systematic problem-solving — the meta-skill governing all others. Includes define goal, generate hypotheses, design experiment, measure results, analyze results, iterate, full cycle, quick diagnosis, and structured investigation. USE WHEN think about, figure out, try approaches, experiment with, iterate on, improve, optimize, define goal, generate hypotheses, design experiment, measure results, analyze results, full cycle, quick diagnosis, structured investigation, science, hypothesis.

danielmiessler11.6k

Dummy Dataset

Generate realistic dummy datasets for testing with customizable columns, constraints, and output formats (CSV, JSON, SQL, Python script). Use when creating test data, building mock datasets, or generating sample data for development and demos.

phuryn10.2k

Performing Malware Persistence Investigation

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

mukul9754.5k

Detecting T1055 Process Injection With Sysmon

Detect process injection techniques (T1055) including classic DLL injection, process hollowing, and APC injection by analyzing Sysmon events for cross-process memory operations, remote thread creation, and anomalous DLL loading patterns.

mukul9754.5k

Implementing Ot Network Traffic Analysis With Nozomi

Deploy Nozomi Networks Guardian sensors for passive OT network traffic analysis to achieve comprehensive asset visibility, real-time threat detection, and vulnerability assessment across industrial control systems without disrupting operations, leveraging behavioral anomaly detection and protocol-aware monitoring.

mukul9754.5k

Agente Biologia — A Vida como Algoritmo

Agente especialista em Biologia para FUVEST — 1ª fase. Biologia tem presença consistente nas 90 questões objetivas, especialmente Genética e Ecologia, que são os tópicos favoritos da FUVEST. Cobre: Citologia, Histologia, Fisiologia Humana, Genética (Mendel + Molecular), Evolução, Ecologia, Botânica e Zoologia. Entra no ciclo após Matemática, Português e Física consolidarem base. Opera em integração com vestibular-tutor, vestibular-srs e agente-quimica (bioquímica celular). Acionar quando Antonio mencionar qualquer tópico de biologia, células, genética, evolução, ecossistemas, ou o orchestrator abrir sessão de Biologia.

Biorxiv

Access bioRxiv preprint repository for biology preprints. Use for: (1) Fetching recent preprints from specific categories like bioinformatics, genomics, molecular-biology, etc., (2) Getting papers by date range, (3) Listing available subject collections, (4) Retrieving paper metadata including titles, authors, DOIs, dates, and categories. No authentication required.

Synthclaw

Render Blender files with agent-controlled procedural parameters for synthetic data generation. Use when generating training data with controlled variations, creating procedural image datasets, or automating Blender renders via natural language. Supports CYCLES (production) and EEVEE (fast testing) render engines.

Vestige

Cognitive memory system using FSRS-6 spaced repetition. Memories fade naturally like human memory. Use for persistent recall across sessions.

Automd Gromacs

AutoMD-GROMACS: Automated molecular dynamics simulation workflow - 13 Skills covering system setup, equilibration, production, analysis, free energy, ligand binding, membrane proteins, umbrella sampling, PCA, and workflows. Built-in auto-repair, 84.7% token savings. Part of the AutoMD series.

Research Automation

Automated web research for peptides, biohacking protocols, longevity science, and trending health topics. Use when you need to discover new information, track emerging trends, monitor scientific updates, or generate content ideas based on current research. Runs periodically via heartbeat or on-demand.

Experience Permafrost Blood Siberia

Feel awe uncovering ancient life frozen for millions of years as you join scientists in Siberia’s summer‑thawing permafrost. Experience the chill, the crack of ice, and the thrill of each fossil reveal. 12 steps • medium intensity • several hours. 感受古代化石的惊叹. asombro fósil.