Lord1Egypt/ai-skillforge - Page 6

prometheus-metrics

Instrumenting system diagnostics, counting requests, and exporting metrics to Prometheus monitoring systems.

Langue du texte source : anglais

protein-structure-prediction

Protein structure prediction and analysis using AlphaFold2, ESMFold, RoseTTAFold, and ColabFold. Use for 3D structure prediction from amino acid sequences, structure quality assessment, binding site identification, and structural comparison. Best for proteins…

Langue du texte source : anglais

proteomics-analysis

Mass spectrometry-based proteomics data analysis with pyteomics, spectrum_utils, and MaxQuant/DIA-NN output processing. Use for peptide identification, protein quantification (LFQ, TMT, SILAC), differential expression, PTM analysis, and proteomics data…

Langue du texte source : anglais

protocolsio-integration

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…

Langue du texte source : anglais

pufferlib

High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups…

Langue du texte source : anglais

pydantic-settings

Managing environment variables, validating system configurations, and parsing .env configurations using Pydantic Settings.

Langue du texte source : anglais

pydantic-validation

Data validation, data parsing, configuration management, and type coercion using Pydantic.

Langue du texte source : anglais

pydeseq2

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.

Langue du texte source : anglais

pydicom

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),…

Langue du texte source : anglais

pyhealth

Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD…

Langue du texte source : anglais

pylabrobot

Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation.…

Langue du texte source : anglais

pymatgen

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

Langue du texte source : anglais

pymc

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Langue du texte source : anglais

pymoo

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Langue du texte source : anglais

pyopenms

Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS…

Langue du texte source : anglais

pysam

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Langue du texte source : anglais

pytdc

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

Langue du texte source : anglais

python-requests-client

Performing synchronous HTTP requests, managing sessions, passing headers, and query parameters using Requests.

Langue du texte source : anglais

python-unittest

Writing test cases, assertions, mocking API calls, and running test runner pipelines using unittest.

Langue du texte source : anglais

pytorch-lightning

Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard), distributed training (DDP, FSDP, DeepSpeed), for scalable neural…

Langue du texte source : anglais

pyzotero

Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically,…

Langue du texte source : anglais

qiskit

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For…

Langue du texte source : anglais

qutip

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based…

Langue du texte source : anglais

rag-vector-db

Retrieval-Augmented Generation implementation using vector databases, embedding models, and query routines.

Langue du texte source : anglais

rdkit

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper…

Langue du texte source : anglais

redis-caching

Distributed key-value caching, session storage, and rate limiting with Upstash or standard Redis.

Langue du texte source : anglais

regular-expressions

Designing, parsing, and searching string parameters using Python regular expressions.

Langue du texte source : anglais

research-grants

Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.

Langue du texte source : anglais

research-lookup

Look up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (deep research), or Perplexity sonar-pro-search (academic paper searches). Automatically routes queries to the best backend. Use for finding…

Langue du texte source : anglais

resend-email-api

Sending programmatic, HTML transactional emails with custom domains using Resend.

Langue du texte source : anglais

scanpy

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning…

Langue du texte source : anglais

scholar-evaluation

Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.

Langue du texte source : anglais

scientific-brainstorming

Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific…

Langue du texte source : anglais

scientific-critical-thinking

Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding…

Langue du texte source : anglais

scientific-schematics

Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network…

Langue du texte source : anglais

scientific-slides

Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing…

Langue du texte source : anglais

scientific-visualization

Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates…

Langue du texte source : anglais

scientific-writing

Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure,…

Langue du texte source : anglais

scikit-bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Langue du texte source : anglais

scikit-learn

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML…

Langue du texte source : anglais