Prompts, skills, and agents that survive contact with real workflows. No vendor loyalty. Occasionally heretical. 🧙🏻♀️
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MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
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 lookups use gget; for sequence/file manipulation use…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analysing your own data use scanpy or scvi-tools.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterisation experiments. Best for Google hardware, noise modelling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for…
MarieLynneBlock/arcanum-artifex
Skill Claude Code
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure…
MarieLynneBlock/arcanum-artifex
Skill Claude Code
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading…
MarieLynneBlock/arcanum-artifex
Skill Claude Code
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Constraint-based metabolic modelling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
MarieLynneBlock/arcanum-artifex
Skill Claude Code
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 problem from multiple angles, requests devil's advocate…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardisation, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualisation.
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
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 drug targets.
MarieLynneBlock/arcanum-artifex
Skill Claude Code
Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyse how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyse how this person reasons", "cognitive…
MarieLynneBlock/arcanum-artifex
Skill Claude CodeCodex
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
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