jimmc414/kosmos

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markitdown Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown optimiz…

jimmc414/kosmos

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scientific-schematics Create publication-quality scientific diagrams, flowcharts, and schematics using Python (graphviz, matplotlib, schemd…

jimmc414/kosmos

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ensembl-database Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparat…

jimmc414/kosmos

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pptx Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic present…

jimmc414/kosmos

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docx Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction,…

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scientific-slides Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentatio…

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research-grants Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budge…

jimmc414/kosmos

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scientific-visualization Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, col…

jimmc414/kosmos

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clinical-decision-support Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, in…

jimmc414/kosmos

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latex-posters Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference pre…

jimmc414/kosmos

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reportlab PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Pla…

jimmc414/kosmos

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bioservices Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, P…

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citation-management Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurat…

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literature-review Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Seman…

jimmc414/kosmos

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paper-2-web This skill should be used when converting academic papers into promotional and presentation formats including interac…

jimmc414/kosmos

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treatment-plans Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Suppor…

jimmc414/kosmos

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aeon This skill should be used for time series machine learning tasks including classification, regression, clustering, fo…

jimmc414/kosmos

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clinical-reports Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/patholog…

jimmc414/kosmos

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exploratory-data-analysis Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should …

jimmc414/kosmos

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neurokit2 Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, a…

jimmc414/kosmos

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opentrons-integration Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (hea…

jimmc414/kosmos

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pylabrobot Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, cent…

jimmc414/kosmos

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research-lookup Look up current research information using Perplexity's Sonar Pro or Sonar Reasoning Pro models through OpenRouter. A…

jimmc414/kosmos

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scientific-writing Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (C…

jimmc414/kosmos

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stable-baselines3 Use this skill for reinforcement learning tasks including training RL agents (PPO, SAC, DQN, TD3, DDPG, A2C, etc.), c…

jimmc414/kosmos

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statistical-analysis Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, …

jimmc414/kosmos

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venue-templates Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publica…

jimmc414/kosmos

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xlsx Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate form…

jimmc414/kosmos

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cellxgene-census Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with …

jimmc414/kosmos

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esm Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequenc…

jimmc414/kosmos

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histolab Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathol…

jimmc414/kosmos

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hypothesis-generation Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develo…

jimmc414/kosmos

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kegg-database Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug …

jimmc414/kosmos

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matchms Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonizati…

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matplotlib Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SV…

jimmc414/kosmos

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modal Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running…

jimmc414/kosmos

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omero-integration Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotat…

jimmc414/kosmos

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peer-review Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, …

jimmc414/kosmos

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perplexity-search Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This s…

jimmc414/kosmos

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pymoo Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZD…

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pytdc Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molec…

jimmc414/kosmos

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pytorch-lightning Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for mult…

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reactome-database Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interacti…

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scikit-bio Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), …

jimmc414/kosmos

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scikit-learn Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression),…

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seaborn Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted…

jimmc414/kosmos

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statsmodels Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rig…

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sympy Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation t…

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tooluniverse Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, geno…

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transformers This skill should be used when working with pre-trained transformer models for natural language processing, computer …

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