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SkillsMP has collected 305 skills from MarieLynneBlock/arcanum-artifex. Open a skill to review its source and details.
MarieLynneBlock/arcanum-artifexShowing 40 of 305 collected skills.
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for…
Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or…
Analyse 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…
Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function…
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…
Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, understanding tissue-specific expression, and interpreting…
Query NHGRI-EBI GWAS Catalogue 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.
Query the OFR (Office of Financial Research) Hedge Fund Monitor API for hedge fund data including SEC Form PF aggregated statistics, CFTC Traders in Financial Futures, FICC Sponsored Repo volumes, and FRB SCOOS dealer financing terms. Access time series data…
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalisation for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial…
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven…
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.…
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualise in…
Create professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Integrates research-lookup and web search for accurate data. Supports 10 infographic types, 8 industry styles, and colorblind-safe…
Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, and 11 other member databases. Use for protein function prediction, domain architecture analysis, evolutionary classification,…
Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating…
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…
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
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…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
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 markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualisation. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24…
Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with…
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral…
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualisation, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimisation,…
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritisation and library filtering.
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
Cloud computing platform for running Python on GPUs and serverless infrastructure. Use when deploying AI/ML models, running GPU-accelerated workloads, serving web endpoints, scheduling batch jobs, or scaling Python code to the cloud. Use this skill whenever…
Run and analyse molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimisation and production MD, analyse trajectories (RMSD, RMSF, contact maps, free energy surfaces). For…
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease…
Comprehensive biosignal processing toolkit for analysing 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…
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when…
Microscopy data management platform. Access images via Python, retrieve datasets, analyse pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organising research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating…
Query and analyse scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analysing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or…
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor…
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…
Search the web, extract URL content, and run deep research using the Parallel Chat API and Extract API. Use for ALL web searches, research queries, and general information gathering. Provides synthesised summaries with citations.