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Skills في هذا المستودع
جمع SkillsMP عدد ٤٢٠ من skills من eightmm/codex-science. افتح أي skill لمراجعة مصدره وتفاصيله.
eightmm/codex-scienceعرض ٤٠ من أصل ٤٢٠ skills مجمعة.
Distills a completed user workflow or interaction into a reusable agent skill. Use when the user asks to turn their workflow, interaction, or multi-step process into a skill, or when they say "make this a skill", "create a skill from what we just did",…
لغة النص الأصلي: الإنجليزية
How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays,…
لغة النص الأصلي: الإنجليزية
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed…
لغة النص الأصلي: الإنجليزية
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for…
لغة النص الأصلي: الإنجليزية
Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize…
لغة النص الأصلي: الإنجليزية
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and…
لغة النص الأصلي: الإنجليزية
Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.
لغة النص الأصلي: الإنجليزية
Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks…
لغة النص الأصلي: الإنجليزية
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database…
لغة النص الأصلي: الإنجليزية
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression…
لغة النص الأصلي: الإنجليزية
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use…
لغة النص الأصلي: الإنجليزية
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
لغة النص الأصلي: الإنجليزية
Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a…
لغة النص الأصلي: الإنجليزية
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core…
لغة النص الأصلي: الإنجليزية
Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology…
لغة النص الأصلي: الإنجليزية
Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my…
لغة النص الأصلي: الإنجليزية
DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
لغة النص الأصلي: الإنجليزية
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
لغة النص الأصلي: الإنجليزية
Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.
لغة النص الأصلي: الإنجليزية
Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and…
لغة النص الأصلي: الإنجليزية
Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so the results will actually be interpretable. Use whenever someone is planning a study, asks how to assign…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits,…
لغة النص الأصلي: الإنجليزية
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based…
لغة النص الأصلي: الإنجليزية
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster…
لغة النص الأصلي: الإنجليزية
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations,…
لغة النص الأصلي: الإنجليزية
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine…
لغة النص الأصلي: الإنجليزية
Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, theorem proving,…
لغة النص الأصلي: الإنجليزية
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework.…
لغة النص الأصلي: الإنجليزية
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
لغة النص الأصلي: الإنجليزية
Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches,…
لغة النص الأصلي: الإنجليزية
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
لغة النص الأصلي: الإنجليزية
Local document and PDF parsing with spatial text and bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; OCR on scans; layout-preserved JSON for RAG; batch-ingesting paper folders; or page screenshots for multimodal agents —…
لغة النص الأصلي: الإنجليزية
Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24…
لغة النص الأصلي: الإنجليزية
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
لغة النص الأصلي: الإنجليزية