silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
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 inform computational approach decisions such as whether to…
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
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 learning applications.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational…
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in…
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological…
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and…
silverstein/claude-scientific-skills-desktop
Skill Claude CodeCodex
Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown optimized for LLM processing. Use when converting documents to markdown, extracting text from PDFs/Office files, transcribing audio, performing OCR on images, extracting YouTube transcripts, or processing…