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Skills في هذا المستودع
جمع SkillsMP عدد ٤٩٦ من skills من zja2004/BGI-CLI. افتح أي skill لمراجعة مصدره وتفاصيله.
zja2004/BGI-CLIعرض ٤٠ من أصل ٤٩٦ skills مجمعة.
Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration, diagnosing convergence issues, choosing line search vs trust region, and analyzing Jacobian quality.
لغة النص الأصلي: الإنجليزية
Select and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances, adapting time steps, diagnosing integration accuracy, planning IMEX splitting, or handling stiff/non-stiff coupled…
لغة النص الأصلي: الإنجليزية
Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diagnosing numerical blow-up, checking CFL/Fourier criteria, von Neumann analysis, matrix conditioning, or detecting…
لغة النص الأصلي: الإنجليزية
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
لغة النص الأصلي: الإنجليزية
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, understanding class relationships, finding properties for a given class, or searching for ontology terms related to a…
لغة النص الأصلي: الإنجليزية
Map materials science terms, crystal structures, and sample descriptions to ontology classes and properties. Supports any ontology registered in ontology_registry.json. Use when translating natural-language material descriptions to ontology terms, annotating…
لغة النص الأصلي: الإنجليزية
Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, verifying that required properties are present, or validating that object property relationships have consistent domain…
لغة النص الأصلي: الإنجليزية
Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating…
لغة النص الأصلي: الإنجليزية
Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or…
لغة النص الأصلي: الإنجليزية
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
لغة النص الأصلي: الإنجليزية
Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows.
لغة النص الأصلي: الإنجليزية
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper…
لغة النص الأصلي: الإنجليزية
Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection. Use for calibration, uncertainty studies, parameter sweeps, LHS sampling, Sobol analysis, surrogate modeling, or Bayesian optimization…
لغة النص الأصلي: الإنجليزية
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus…
لغة النص الأصلي: الإنجليزية
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
لغة النص الأصلي: الإنجليزية
Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in production environments, processing large volumes of PDFs, or requiring robust error handling and validation.
لغة النص الأصلي: الإنجليزية
Extract text and tables from PDF files, fill forms, merge documents. Use when working with PDF files or when the user mentions PDFs, forms, or document extraction.
لغة النص الأصلي: الإنجليزية
Identify computational bottlenecks, analyze scaling behavior, estimate memory requirements, and receive optimization recommendations for any computational simulation. Use when simulations are slow, investigating parallel efficiency, planning resource…
لغة النص الأصلي: الإنجليزية
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with…
لغة النص الأصلي: الإنجليزية
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
لغة النص الأصلي: الإنجليزية
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and…
لغة النص الأصلي: الإنجليزية
Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.
لغة النص الأصلي: الإنجليزية
Extract, analyze, and visualize simulation output data. Use for field extraction, time series analysis, line profiles, statistical summaries, derived quantity computation, result comparison to references, and automated report generation from simulation…
لغة النص الأصلي: الإنجليزية
Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based…
لغة النص الأصلي: الإنجليزية
Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
لغة النص الأصلي: الإنجليزية
End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5)…
لغة النص الأصلي: الإنجليزية
Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines,…
لغة النص الأصلي: الإنجليزية
Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for…
لغة النص الأصلي: الإنجليزية
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize…
لغة النص الأصلي: الإنجليزية
Analyzes events through psychological lens using cognitive psychology, social psychology, developmental psychology, clinical psychology, and neuroscience. Provides insights on behavior, cognition, emotion, motivation, group dynamics, decision-making biases,…
لغة النص الأصلي: لغات متعددة
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
لغة النص الأصلي: الإنجليزية
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
لغة النص الأصلي: الإنجليزية
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
لغة النص الأصلي: الإنجليزية
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound),…
لغة النص الأصلي: الإنجليزية
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug…
لغة النص الأصلي: الإنجليزية
Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment. Use this skill when automating laboratory workflows, programming liquid handling robots (Hamilton STAR,…
لغة النص الأصلي: الإنجليزية
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
لغة النص الأصلي: الإنجليزية
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide…
لغة النص الأصلي: الإنجليزية
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
لغة النص الأصلي: الإنجليزية
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
لغة النص الأصلي: الإنجليزية