synthetic-sciences
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- ▌ Drug Design · synthetic-sciences bundleEnd-to-end drug discovery pipeline orchestration. Deterministic Python script that auto-chains structure prediction, pocket detection, de novo design, docking, scoring, and ADMET filtering into reproducible workflows.
- ▌ Vast AI Gpu Cloud · synthetic-sciencesSafely inspect and operate Vast.ai marketplace instances with the vastai CLI, live offer data, and explicit approval before paid or destructive actions.
- ▌ Ml Paper Writing · synthetic-sciences bundleWrites and revises machine-learning papers for NeurIPS, ICML, ICLR, ACL, COLM and AAAI, from a research repository or a set of tracked runs to a compiling LaTeX draft in the venue's template, with the contribution stated as claims backed by experiments, ablations and honest baselines. Use for ML or AI conference papers, workshop papers, camera-ready preparation, and rebuttals. For journal articles and other fields use paper-writing; for references use citations; for figures use figures.
- ▌ DOCX · synthetic-sciences bundleUse this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document generation.
- ▌ PPTX · synthetic-sciences bundleUse this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates (.potx), layouts, speaker notes, or comments. Trigger whenever the user mentions "deck," "slides," "presentation," or references a .pptx or .potx filename, regardless of what they plan to do with the content afterward. If a .pptx or .potx file needs to be opened, created, or touched, use this skill.
- ▌ XLSX · synthetic-sciences bundleCreate, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for Word documents, HTML reports, standalone Python scripts, database pipelines, or Google Sheets API work.
- ▌ Ray Train · synthetic-sciences bundleDistributed training orchestration across clusters. Scales PyTorch/TensorFlow/HuggingFace from laptop to 1000s of nodes. Built-in hyperparameter tuning with Ray Tune, fault tolerance, elastic scaling. Use when training massive models across multiple machines or running distributed hyperparameter sweeps.
- ▌ Skill Installer · synthetic-sciencesInstall or remove third-party openscience skills from a public git repository. Use when the user says "add this skill <url>", "install skill <url>", or "remove skill <namespace>". The skill runs locally via `openscience skill add|list|remove`, fetches the repo, runs a 6-layer safety gate (regex + server-side Haiku classifier), prompts the user to confirm, then writes the skills to ~/.openscience/installed-skills/ and uploads to the dashboard for cross-machine sync.
- ▌ Pinn Training · synthetic-sciencesTrain Physics-Informed Neural Networks (PINNs) using DeepXDE. Solve forward and inverse PDE problems by embedding physics equations into the neural network loss function. Supports 1D/2D/3D, time-dependent, and parametric PDEs.
- ▌ Paper Lookup · synthetic-sciences bundleSearch 18 scholarly APIs for papers, preprints, citations, open-access full text, repository records, and journal OA status, and return results with reproducible provenance. Covers PubMed, PMC, Europe PMC, bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall, OpenCitations, PubTator3, Zenodo, Figshare, ROR, BioStudies, and DOAJ. Use when searching for papers, citations, DOI/PMID/arXiv lookups, abstracts, full text, open-access PDFs, preprints, citation graphs, author publications, biomedical entity annotations, deposited records (Zenodo, Figshare, BioStudies), institution ROR IDs, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X", "look up this DOI", "who cites this paper", or "get me the PDF".
- ▌ Latex Posters · synthetic-sciences bundleCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
- ▌ Skypilot Multi Cloud Orchestration · synthetic-sciences bundleMulti-cloud orchestration for ML workloads with automatic cost optimization. Use when you need to run training or batch jobs across multiple clouds, leverage spot instances with auto-recovery, or optimize GPU costs across providers.
- ▌ Torch Geometric · synthetic-sciences bundleGraph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.
- ▌ Execution Hygiene · synthetic-sciencesRuns computations so they finish, reproduce and fit the machine that will re-execute them, detaching long jobs through compute_job instead of blocking or sleeping shells, checkpointing so reruns resume, fixing seeds and capping BLAS and OpenMP threads, streaming large tables with explicit dtypes, writing outputs atomically, logging every command with its exit code and rerunning the final pipeline from scratch under the target limits before finishing. Use for any analysis or pipeline that runs longer than a minute, reads files larger than memory, or will be re-executed on a machine with tighter CPU, memory, wall-clock or network limits than this one; a one-off shell command whose output is read immediately does not need it.
- ▌ Literature Review · synthetic-sciences bundleFinds, ranks and reads the literature on a question, the retrieval loop the lead runs itself over OpenAlex, arXiv, Crossref, PubMed and bioRxiv with a fixed budget, deduplication, ranking by topical fit, reading of the load-bearing papers and claim-level links, for related-work sections, prior-art checks, surveys and systematic reviews. Use for "find papers", "what is known about", related work, or a review; escalate to PRISMA screening only when a systematic review is requested. For one quick fact or definition use research-lookup.
- ▌ Ena Database · synthetic-sciences bundleAccess European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
- ▌ Fda Database · synthetic-sciences bundleQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
- ▌ Geo Database · synthetic-sciences bundleAccess NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
- ▌ Pdb Database · synthetic-sciences bundleAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
- ▌ Usfiscaldata · synthetic-sciences bundleQuery the U.S. Treasury Fiscal Data REST API for federal financial data. No API key required. Use for national debt (Debt to the Penny), Daily Treasury Statements, Monthly Treasury Statements, Treasury securities auctions, interest rates, foreign exchange rates, savings bonds, or U.S. government revenue and spending statistics.
- ▌ Transformers · synthetic-sciences bundleThis skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
- ▌ Lab Hardware Cad · synthetic-sciences bundleDesign custom laboratory hardware as parametric build123d models and export fabrication-ready STEP, STL, and DXF files - microfluidic chips and molds, optomechanical mounts and breadboard adapters, cuvette and microplate holders, tube racks, animal-behavior rigs, and 3D-printed instrument fixtures. Use when a research task needs a physical part that must mate with standardized labware, an optical table, a cage system, or a printer, CNC, or laser process.
- ▌ Energy Systems · synthetic-sciencesApplies energy-systems modelling conventions so that capacity, energy, cost and emissions numbers are consistent and comparable, covering kW versus kWh and MW versus MWh, capacity versus energy, capacity factors, load duration curves, the LCOE formula with discounting and capital recovery factors, dispatch and capacity-expansion modelling with PyPSA and pyomo, time-series alignment across time zones and interval conventions, emissions factors by scope, and the assumptions table every result needs. Use for power-system, generation cost, storage, grid-mix or decarbonization analyses; use statistical-conventions for the statistics and geoscience-data for weather and resource rasters.
- ▌ Fluid Dynamics · synthetic-sciencesComputational fluid dynamics — Navier-Stokes solvers, lid-driven cavity, channel flow, vortex methods, turbulence statistics, drag/lift computation. Spectral and finite-difference methods for incompressible and compressible flows.
- ▌ Patent Mining · synthetic-sciencesRetrieves and interprets patent data with the conventions that make counts and claims defensible, covering Google Patents, Lens, EPO Open Patent Services, USPTO data through PatentsView and the Open Data Portal, and WIPO PATENTSCOPE, together with kind codes, DOCDB and INPADOC families, priority versus filing versus publication dates, CPC and IPC classification, claim structure, assignee normalization and the limits of chemistry in patents, and records every query with the date it was run. Use for prior-art checks, freedom-to-operate scoping, technology landscapes, assignee or inventor analyses and patent-derived chemistry; use literature-review for scholarly sources and research-lookup for one quick fact.
- ▌ Treatment Plans · synthetic-sciences bundleGenerate 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, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
- ▌ Denovo Design · synthetic-sciences bundleDe novo molecule generation for drug discovery. Scaffold-based analog enumeration, fragment growing/linking, structure-based design, multi-objective optimization, and drug-likeness filtering.
- ▌ Molecular RAG · synthetic-sciences bundleRetrieve structurally similar compounds with known properties from ChEMBL/ZINC to ground predictions and inform optimization. Based on MolRAG (Xian 2025, ACL).
- ▌ Pkpd Modeling · synthetic-sciences bundlePharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when analysing concentration-time data, deriving exposure metrics, fitting PK or PD models, or evaluating dosing regimens. Triggers include "pharmacokinetics", "pharmacodynamics", "PK/PD", "NCA", "non-compartmental", "AUC", "Cmax", "lambda z", "half-life", "clearance", "volume of distribution", "compartmental model", "population PK", "popPK", "NONMEM", "nlmixr2", "Pharmpy", "Monolix", "exposure-response", "Emax", "EC50", "indirect response", "effect compartment", "TMDD", "PBPK", "bioequivalence", "RSABE", "ABEL", "allometric scaling", "first-in-human", "MABEL", "drug-drug interaction", "DDI", "ICH M12", "concentration-QTc", "therapeutic drug monitoring", "MIPD", and "dosing regimen".
- ▌ Optimize For Gpu · synthetic-sciences bundleGPU-accelerates scientific Python on NVIDIA hardware and verifies that the result is correct and faster. Use for CUDA/GPU optimization; CPU-bound NumPy, SciPy, pandas, scikit-learn, NetworkX, scikit-image, vector-search, image-processing, graph, simulation, or file-I/O workloads; CuPy, cuDF, cuML, cuGraph, cuVS, cuCIM, KvikIO, Warp, Newton, Numba-CUDA, or RAFT questions; and profiling, memory-transfer, kernel, or multi-GPU bottlenecks. Also use when large data-parallel Python code is slow and GPU acceleration is a plausible option, even if the user does not name CUDA.
- ▌ Gene Database · synthetic-sciences bundleQuery NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
- ▌ Gwas Database · synthetic-sciences bundleQuery 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.
- ▌ Hmdb Database · synthetic-sciences bundleAccess Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
- ▌ Kegg Database · synthetic-sciences bundleDirect 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.
- ▌ Zinc Database · synthetic-sciences bundleAccess ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.
- ▌ Hugging Face Jobs · synthetic-sciences bundleThis skill should be used when users want to run any workload on Hugging Face Jobs infrastructure. Covers UV scripts, Docker-based jobs, hardware selection, cost estimation, authentication with tokens, secrets management, timeout configuration, and result persistence. Designed for general-purpose compute workloads including data processing, inference, experiments, batch jobs, and any Python-based tasks. Should be invoked for tasks involving cloud compute, GPU workloads, or when users mention running jobs on Hugging Face infrastructure without local setup.
- ▌ Geoscience Data · synthetic-sciencesReads, transforms and summarizes gridded and geospatial data without losing the metadata that gives it meaning, covering NetCDF and HDF5 through xarray and netCDF4 with CF conventions, dimensions versus coordinates, time encodings and calendars and fill values, GeoTIFF and other rasters through rasterio and GDAL with nodata and resampling choices, coordinate reference systems and reprojection with pyproj and EPSG codes, geodesic versus planar distances and areas, vector data through geopandas, and unit handling with area weighting on latitude-longitude grids. Use for climate, weather, hydrology, remote sensing, land use and any map-based analysis; use the physics-fitting or spectral-analysis skills once the data is a clean array.
- ▌ Neural Operator · synthetic-sciencesTrain neural operators (FNO, DeepONet) to learn solution maps for parametric PDE families. Once trained, solve new PDE instances in milliseconds. Use when you need to solve many instances of the same PDE with different parameters/ICs/BCs.
- ▌ Physics Fitting · synthetic-sciencesNonlinear curve fitting for physics data with proper error propagation, chi-squared analysis, residual diagnostics, confidence intervals, and model comparison (AIC/BIC). Use for any parameter extraction from experimental or simulation data.
- ▌ Analysis Report · synthetic-sciencesWrites the trace and report for an analysis whose output a reader will judge, restating the question with its binding clauses, recording data provenance, the method with every parameter that matters, results with raw and adjusted numbers and uncertainty, the checks performed, limitations, a decision log of alternatives considered and why they were rejected, and the exact commands that reproduce every number, using the Markdown skeleton included here. Use when delivering any quantitative analysis, model comparison, data audit or computational experiment to a person who did not watch the work; use paper-writing for manuscripts and ml-paper-writing for machine-learning papers.
- ▌ Clinical Imaging · synthetic-sciences bundleClinical and physiological imaging analysis. Diffusion MRI ADC maps, micro-CT bone morphometry, hemodynamic parameter analysis, circadian rhythm cosinor analysis, ciliary beat frequency (FFT), and tissue deformation optical flow. For DICOM file handling use pydicom; for biosignals use neurokit2.
- ▌ Clinical Reports · synthetic-sciences bundleWrite 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 tools.
- ▌ Ginkgo Cloud Lab · synthetic-sciences bundleSubmit 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 protein expression and purification (cell-free, E. coli, or Pichia), HiBiT or A280 or LabChip quantification, IVT mRNA/circRNA synthesis, thermal shift / developability assays, Echo-MS enzyme or analyte methods, SPR target onboarding, fluorescent pixel art, or otherwise interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.
- ▌ Glycoengineering · synthetic-sciences bundleAnalyze 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 antibody optimization, and vaccine design.
- ▌ Tensorpool Gpu Cloud · synthetic-sciencesSafely inspect and operate TensorPool GPU clusters and jobs using the current tp CLI, with explicit approval before any billable or destructive action.
- ▌ Datalad · synthetic-sciences bundleRetrieve, version, and publish scientific datasets with DataLad and git-annex, and capture computational provenance with datalad run, rerun, and containers-run. Use when cloning or fetching data from OpenNeuro, DANDI, datasets.datalad.org, or any DataLad dataset; when a file in a dataset reads as a broken symlink or a small pointer instead of real data; when an analysis needs a machine-readable record of how each output was produced so it can be re-executed; or when publishing a dataset to siblings such as a GitHub repository plus a storage remote. Also use to decide between DataLad and plain Git for a data-carrying repository.
- ▌ Uspto Database · synthetic-sciences bundleAccess USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
- ▌ Generate Image · synthetic-sciences bundleGenerate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that isn't a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead.
- ▌ Quantizing Models Bitsandbytes · synthetic-sciences bundleQuantizes LLMs to 8-bit or 4-bit for 50-75% memory reduction with minimal accuracy loss. Use when GPU memory is limited, need to fit larger models, or want faster inference. Supports INT8, NF4, FP4 formats, QLoRA training, and 8-bit optimizers. Works with HuggingFace Transformers.
- ▌ Wave Propagation · synthetic-sciencesSimulate wave propagation — acoustic, electromagnetic, elastic, and quantum waves. FDTD, spectral methods, and absorbing boundary conditions for 1D/2D/3D wave equations with sources, scattering, and dispersion.
- ▌ Research Grants · synthetic-sciences bundleWrite competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
- ▌ Bioimage Analysis · synthetic-sciences bundleMicroscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. For pathology WSI use pathml; for flow cytometry use flow-cytometry-analysis.
- ▌ Immunology Assays · synthetic-sciences bundleComputational analysis of immunology experimental data. ATAC-seq differential accessibility, immune cell tracking from microscopy, ELISA data processing with 4-parameter logistic fitting, immunohistochemistry quantification, antibody titer analysis, and cell cycle phase duration estimation. For flow cytometry use flow-cytometry-analysis; for scRNA-seq use scanpy.
- ▌ Molecular Cloning · synthetic-sciences bundleMolecular cloning simulation and design. PCR amplicon prediction, restriction enzyme digestion, Golden Gate and Gibson assembly simulation, primer design, CRISPR sgRNA design, and plasmid annotation. For protein-level sequence analysis use biopython or esm; for database lookups use gene-database or ensembl-database.
- ▌ Synthetic Biology · synthetic-sciences bundleSynthetic biology design and simulation tools. Codon optimization, gene circuit ODE modeling with growth feedback, SBML model creation, bifurcation analysis, barcode sequencing fitness analysis, and therapeutic genome engineering. For metabolic modeling use cobrapy; for sequence tools use biopython.
- ▌ Admet Reasoning · synthetic-sciences bundleInterpretable ADMET analysis with mechanistic reasoning. Maps liabilities to structural causes and biological pathways. Based on CoTox (Park 2025) and DrugR (Liu 2026).
- ▌ Givemeanode Agent Compute · synthetic-sciencesOperate GiveMeANode GPU nodes, batch jobs, storage, and rollout sandboxes through its connected MCP server with bounded spend, durable recovery, and explicit approval for paid or destructive actions.
- ▌ Lambda Gpu Cloud · synthetic-sciencesSafely inspect and operate Lambda Cloud GPU instances through the documented Cloud API and SSH, with explicit approval before billable or destructive actions.
- ▌ Together AI Inference · synthetic-sciencesServerless inference, fine-tuning, embeddings, image generation, and batch processing on 200+ open-source models via an OpenAI-compatible API. Use when you need fast, cost-effective access to open-source LLMs without managing infrastructure.
- ▌ Ray Data · synthetic-sciences bundleScalable data processing for ML workloads. Streaming execution across CPU/GPU, supports Parquet/CSV/JSON/images. Integrates with Ray Train, PyTorch, TensorFlow. Scales from single machine to 100s of nodes. Use for batch inference, data preprocessing, multi-modal data loading, or distributed ETL pipelines.
- ▌ Brenda Database · synthetic-sciences bundleAccess 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.
- ▌ Cosmic Database · synthetic-sciences bundleAccess COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
- ▌ Database Lookup · synthetic-sciences bundleQuery documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a scientific, regulatory, financial, or other database-backed fact must be retrieved reproducibly from a named source rather than inferred from general knowledge.
- ▌ Pubmed Database · synthetic-sciences bundleDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
- ▌ String Database · synthetic-sciences bundleQuery STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
- ▌ Nemo Guardrails · synthetic-sciencesNVIDIA's runtime safety framework for LLM applications. Features jailbreak detection, input/output validation, fact-checking, hallucination detection, PII filtering, toxicity detection. Uses Colang 2.0 DSL for programmable rails. Production-ready, runs on T4 GPU.
- ▌ Training Llms Megatron · synthetic-sciences bundleTrains large language models (2B-462B parameters) using NVIDIA Megatron-Core with advanced parallelism strategies. Use when training models >1B parameters, need maximum GPU efficiency (47% MFU on H100), or require tensor/pipeline/sequence/context/expert parallelism. Production-ready framework used for Nemotron, LLaMA, DeepSeek.
- ▌ Dynamical Systems · synthetic-sciencesAnalyze nonlinear dynamical systems — phase portraits, fixed points, stability analysis, bifurcation diagrams, Poincare sections, Lyapunov exponents, and chaos detection. Use for any autonomous or non-autonomous ODE system where qualitative behavior matters.
- ▌ Physics Databases · synthetic-sciencesQuery physics databases — NIST CODATA constants, NIST Chemistry WebBook, Materials Project, Particle Data Group (PDG), OEIS sequences. Always use these instead of hardcoding physical constants.
- ▌ Spectral Analysis · synthetic-sciencesFrequency-domain analysis — FFT, power spectral density (Welch/periodogram), spectrograms, wavelet transforms, and coherence. Use for any signal with periodic, quasi-periodic, or transient frequency content in physics data.
- ▌ Scientific Slides · synthetic-sciences bundle[EXPERIMENTAL] Build slide decks and presentations for research talks using Nano Banana Pro AI. Generates stunning PDF presentations with AI-generated slides. Use for conference presentations, seminar talks, thesis defense slides, or any scientific talk. Provides slide structure, design guidance, timing recommendations, and visual validation.
- ▌ Microbial Dynamics · synthetic-sciences bundleMicrobial population dynamics modeling and analysis. Bacterial growth curve fitting (logistic, Gompertz, Baranyi), Lotka-Volterra community dynamics, Gillespie stochastic simulation, biofilm quantification, CFU enumeration, and genome annotation. For metabolic modeling use cobrapy; for sequence analysis use biopython.
- ▌ Pathway Enrichment · synthetic-sciences bundleRun pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".
- ▌ Structure Analysis · synthetic-sciencesHandles protein structure files and geometric criteria so that residue counts, contacts, hydrogen bonds and interfaces are reproducible, covering PDB versus mmCIF, author versus label chains and numbering, HETATM, water and ligand policy, alternate locations, insertion codes, biological assemblies versus the asymmetric unit, hydrogen-bond distance and angle cutoffs, interface definitions by distance or buried surface area, and the Biopython, MDAnalysis, gemmi, PyMOL and ChimeraX calls that implement them. Use whenever a task reads a structure file and reports anything derived from atom coordinates; use biopython for sequence work and molecular-docking or structure-prediction skills for generating structures.
- ▌ Admet Prediction · synthetic-sciences bundleADMET property prediction for drug candidates. Full pharmacokinetic panel (Caco-2, PPB, clearance, CYP), toxicity (hERG, AMES, DILI), drug-likeness (Lipinski, QED), using RDKit descriptors and TDC models.
- ▌ Binding Affinity · synthetic-sciences bundleEmpirical affinity estimates, ligand energy inspection, docking-score consensus, and batch virtual screening. Full MM/GBSA requires a validated external workflow.
- ▌ Pocket Detection · synthetic-sciences bundleMulti-method binding pocket detection and druggability assessment. Grid-based, fpocket, and P2Rank detection with druggability scoring, visualization, and cross-structure comparison.
- ▌ Fireworks AI Inference · synthetic-sciencesFast inference and fine-tuning platform with serverless and on-demand GPU deployments. OpenAI-compatible API for chat completions, embeddings, function calling, vision, and structured output. Supports SFT, DPO, and RL fine-tuning. SOC2 + HIPAA compliant.
- ▌ Timesfm Forecasting · synthetic-sciences bundleZero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.
- ▌ Geomaster · synthetic-sciences bundleComprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modeling, marine spatial analysis, atmospheric science, and any geospatial computation task.
- ▌ Biorxiv Database · synthetic-sciences bundleEfficient 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.
- ▌ Clinpgx Database · synthetic-sciences bundleAccess ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
- ▌ Clinvar Database · synthetic-sciences bundleQuery 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.
- ▌ Ensembl Database · synthetic-sciences bundleQuery Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
- ▌ Pubchem Database · synthetic-sciences bundleQuery PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
- ▌ Uniprot Database · synthetic-sciences bundleDirect 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 direct HTTP/REST work or UniProt-specific control.
- ▌ Hugging Face CLI · synthetic-sciences bundleExecute Hugging Face Hub operations using the `hf` CLI. Use when the user needs to download models/datasets/spaces, upload files to Hub repositories, create repos, manage local cache, or run compute jobs on HF infrastructure. Covers authentication, file transfers, repository creation, cache operations, and cloud compute.
- ▌ Hugging Face Trackio · synthetic-sciences bundleTrack and visualize ML training experiments with Trackio. Use when logging metrics during training (Python API) or retrieving/analyzing logged metrics (CLI). Supports real-time dashboard visualization, HF Space syncing, and JSON output for automation.
- ▌ Bayesian Inference · synthetic-sciencesBayesian parameter estimation with MCMC (emcee) and probabilistic programming (PyMC). Posterior distributions, corner plots, model evidence, convergence diagnostics. Use when you need full posterior distributions, not just point estimates.
- ▌ Statistical Power · synthetic-sciences bundleSample-size and statistical power calculations for planning studies. Use whenever someone asks "how many subjects/samples/replicates do I need", wants an a priori power analysis, a minimum detectable effect (MDE), a power curve, or needs to justify a sample size for a grant, IRB protocol, or pre-registration. Covers closed-form power for t-tests, ANOVA, proportions, correlations, chi-square, and regression, plus simulation-based (Monte Carlo) power for designs with no formula — logistic/Poisson regression, mixed models, cluster-randomized trials, survival, and interactions. Use this skill even when the request only mentions an effect size, alpha, or "80% power" without saying "power analysis" explicitly. For laying out the study (randomization, blocking, factorial/DOE, crossover, sequential designs) use experimental-design; for analyzing data already collected and reporting it use statistical-analysis.
- ▌ Infographics · synthetic-sciences bundle[EXPERIMENTAL] 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 palettes.
- ▌ Genomic Coordinates · synthetic-sciences bundleConvert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".
- ▌ Pharmacology Wetlab · synthetic-sciences bundleComputational analysis of pharmacology wet-lab experiments. Western blot densitometry, xenograft tumor growth inhibition, pharmaceutical stability modeling (Arrhenius), radiolabeled antibody biodistribution, MIRD dosimetry, and adverse event grading. For drug databases use chembl-database or fda-database; for molecular docking use diffdock.
- ▌ Molecular Docking · synthetic-sciences bundleEnd-to-end molecular docking pipeline. Target preparation, pocket detection, protein-ligand docking (DiffDock/Vina), scoring, interaction analysis, and pose ranking.
- ▌ Smiles Validation · synthetic-sciences bundleStrict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.
- ▌ Markitdown · synthetic-sciences bundleConvert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
- ▌ Drugbank Database · synthetic-sciences bundleAccess and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
- ▌ Openalex Database · synthetic-sciences bundleQuery and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open access publications, or conducting bibliometric analysis across 240M+ scholarly works. Use for literature searches, research output analysis, citation analysis, and academic database queries.
- ▌ Reactome Database · synthetic-sciences bundleQuery Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
- ▌ Constitutional AI · synthetic-sciencesAnthropic's method for training harmless AI through self-improvement. Two-phase approach - supervised learning with self-critique/revision, then RLAIF (RL from AI Feedback). Use for safety alignment, reducing harmful outputs without human labels. Powers Claude's safety system.