Agent skills by jimmc414

Systematic framework for evaluating scholarly and research work based on the ScholarEval methodology. This skill should be used when assessing research papers, evaluating literature reviews, scoring research…

Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.

Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.

Create publication-quality scientific diagrams, flowcharts, and schematics using Python (graphviz, matplotlib, schemdraw, networkx). Specialized in neural network architectures, system diagrams, and flowcharts.…

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…

Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions.

Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models,…

This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for…

Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service…

Use this skill for reinforcement learning tasks including training RL agents (PPO, SAC, DQN, TD3, DDPG, A2C, etc.), creating custom Gym environments, implementing callbacks for monitoring and control, using vectorized…

Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives,…

Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+…

Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management,…

UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for…

Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.

Kosmos: An AI Scientist for Autonomous Discovery - An implementation and adaptation to be driven by Claude Code or API - Based on the Kosmos AI Paper - https://arxiv.org/abs/2511.02824

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…

Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI),…