synthetic-sciences
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- ▌ Liteparse · synthetic-sciencesUse this skill when the user asks to parse, perform multi-format document conversion or spatially extract text from an unstructured file (PDF, DOCX, PPTX, XLSX, images, etc.) locally without cloud dependencies.
- ▌ Cellxgene Census · synthetic-sciences bundleQuery 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 analyzing your own data use scanpy or scvi-tools.
- ▌ Segment Anything Model · synthetic-sciences bundleFoundation model for image segmentation with zero-shot transfer. Use when you need to segment any object in images using points, boxes, or masks as prompts, or automatically generate all object masks in an image.
- ▌ Stable Diffusion Image Generation · synthetic-sciences bundleState-of-the-art text-to-image generation with Stable Diffusion models via HuggingFace Diffusers. Use when generating images from text prompts, performing image-to-image translation, inpainting, or building custom diffusion pipelines.
- ▌ Nemo Evaluator Sdk · synthetic-sciences bundleEvaluates LLMs across 100+ benchmarks from 18+ harnesses (MMLU, HumanEval, GSM8K, safety, VLM) with multi-backend execution. Use when needing scalable evaluation on local Docker, Slurm HPC, or cloud platforms. NVIDIA's enterprise-grade platform with container-first architecture for reproducible benchmarking.
- ▌ Statistical Analysis · synthetic-sciences bundleGuided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.
- ▌ Fine Tuning With Trl · synthetic-sciences bundleFine-tune LLMs using reinforcement learning with TRL - SFT for instruction tuning, DPO for preference alignment, PPO/GRPO for reward optimization, and reward model training. Use when need RLHF, align model with preferences, or train from human feedback. Works with HuggingFace Transformers.
- ▌ Dnanexus Integration · synthetic-sciences bundleDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
- ▌ Latchbio Integration · synthetic-sciences bundleLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
- ▌ Zarr Python · synthetic-sciences bundleChunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
- ▌ Grpo Rl Training · synthetic-sciences bundleExpert guidance for GRPO/RL fine-tuning with TRL for reasoning and task-specific model training
- ▌ Transformer Lens Interpretability · synthetic-sciences bundleProvides guidance for mechanistic interpretability research using TransformerLens to inspect and manipulate transformer internals via HookPoints and activation caching. Use when reverse-engineering model algorithms, studying attention patterns, or performing activation patching experiments.
- ▌ Labarchive Integration · synthetic-sciences bundleElectronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
- ▌ Benchling Integration · synthetic-sciences bundleBenchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
- ▌ Opentrons Integration · synthetic-sciences bundleOfficial 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 automation or broader equipment control use pylabrobot.
- ▌ Pytorch Lightning · synthetic-sciences bundleHigh-level PyTorch framework with Trainer class, automatic distributed training (DDP/FSDP/DeepSpeed), callbacks system, and minimal boilerplate. Scales from laptop to supercomputer with same code. Use when you want clean training loops with built-in best practices.
- ▌ Stable Baselines3 · synthetic-sciences bundleProduction-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.
- ▌ Get Available Resources · synthetic-sciences bundleThis skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
- ▌ Iso 13485 Certification · synthetic-sciences bundleComprehensive 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 Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
- ▌ Protocolsio Integration · synthetic-sciences bundleIntegration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
- ▌ Huggingface Tokenizers · synthetic-sciences bundleFast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.
- ▌ Evaluating Llms Harness · synthetic-sciences bundleEvaluates LLMs across 60+ academic benchmarks (MMLU, HumanEval, GSM8K, TruthfulQA, HellaSwag). Use when benchmarking model quality, comparing models, reporting academic results, or tracking training progress. Industry standard used by EleutherAI, HuggingFace, and major labs. Supports HuggingFace, vLLM, APIs.
- ▌ Knowledge Distillation · synthetic-sciences bundleCompress large language models using knowledge distillation from teacher to student models. Use when deploying smaller models with retained performance, transferring GPT-4 capabilities to open-source models, or reducing inference costs. Covers temperature scaling, soft targets, reverse KLD, logit distillation, and MiniLLM training strategies.
- ▌ Evaluating Code Models · synthetic-sciences bundleEvaluates code generation models across HumanEval, MBPP, MultiPL-E, and 15+ benchmarks with pass@k metrics. Use when benchmarking code models, comparing coding abilities, testing multi-language support, or measuring code generation quality. Industry standard from BigCode Project used by HuggingFace leaderboards.
- ▌ Scientific Visualization · synthetic-sciences bundleMeta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
- ▌ Pymc Bayesian Modeling · synthetic-sciences bundleBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
- ▌ Shap · synthetic-sciences bundleModel interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
- ▌ Bids · synthetic-sciences bundleUse this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
- ▌ Gget · synthetic-sciences bundleFast 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 multi-database Python workflows use bioservices.
- ▌ Gtars · synthetic-sciences bundleHigh-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 learning applications.
- ▌ Pymoo · synthetic-sciences bundleMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
- ▌ Simpy · synthetic-sciences bundleProcess-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 operations, network traffic, logistics, or any system where entities interact with shared resources over time.
- ▌ Sympy · synthetic-sciences bundleUse 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, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.
- ▌ Cirq · synthetic-sciences bundleGoogle quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
- ▌ Pysam · synthetic-sciences bundleGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
- ▌ Qutip · synthetic-sciences bundleQuantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
- ▌ Flowio · synthetic-sciences bundleParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
- ▌ Pathml · synthetic-sciences bundleFull-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
- ▌ Scanpy · synthetic-sciences bundleStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
- ▌ Denario · synthetic-sciences bundleMultiagent 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 publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
- ▌ Clip · synthetic-sciences bundleOpenAI's model connecting vision and language. Enables zero-shot image classification, image-text matching, and cross-modal retrieval. Trained on 400M image-text pairs. Use for image search, content moderation, or vision-language tasks without fine-tuning. Best for general-purpose image understanding.
- ▌ Qiskit · synthetic-sciences bundleIBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
- ▌ Anndata · synthetic-sciences bundleData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
- ▌ Cobrapy · synthetic-sciences bundleConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
- ▌ Lamindb · synthetic-sciences bundleThis 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 computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
- ▌ Pydicom · synthetic-sciences bundlePython library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
- ▌ Pytdc · synthetic-sciences bundleTherapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
- ▌ Rdkit · synthetic-sciences bundleCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
- ▌ Networkx · synthetic-sciences bundleComprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
- ▌ Faiss · synthetic-sciences bundleFacebook's library for efficient similarity search and clustering of dense vectors. Supports billions of vectors, GPU acceleration, and various index types (Flat, IVF, HNSW). Use for fast k-NN search, large-scale vector retrieval, or when you need pure similarity search without metadata. Best for high-performance applications.
- ▌ Llava · synthetic-sciences bundleLarge Language and Vision Assistant. Enables visual instruction tuning and image-based conversations. Combines CLIP vision encoder with Vicuna/LLaMA language models. Supports multi-turn image chat, visual question answering, and instruction following. Use for vision-language chatbots or image understanding tasks. Best for conversational image analysis.
- ▌ Awq Quantization · synthetic-sciences bundleActivation-aware weight quantization for 4-bit LLM compression with 3x speedup and minimal accuracy loss. Use when deploying large models (7B-70B) on limited GPU memory, when you need faster inference than GPTQ with better accuracy preservation, or for instruction-tuned and multimodal models. MLSys 2024 Best Paper Award winner.
- ▌ Hqq Quantization · synthetic-sciences bundleHalf-Quadratic Quantization for LLMs without calibration data. Use when quantizing models to 4/3/2-bit precision without needing calibration datasets, for fast quantization workflows, or when deploying with vLLM or HuggingFace Transformers.
- ▌ Astropy · synthetic-sciences bundleComprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
- ▌ Histolab · synthetic-sciences bundleLightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
- ▌ Pydeseq2 · synthetic-sciences bundleDifferential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
- ▌ Pyhealth · synthetic-sciences bundleComprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).
- ▌ Depmap · synthetic-sciences bundleQuery 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.
- ▌ Blip 2 Vision Language · synthetic-sciences bundleVision-language pre-training framework bridging frozen image encoders and LLMs. Use when you need image captioning, visual question answering, image-text retrieval, or multimodal chat with state-of-the-art zero-shot performance.
- ▌ Chroma · synthetic-sciences bundleOpen-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.
- ▌ Qdrant Vector Search · synthetic-sciences bundleHigh-performance vector similarity search engine for RAG and semantic search. Use when building production RAG systems requiring fast nearest neighbor search, hybrid search with filtering, or scalable vector storage with Rust-powered performance.
- ▌ Peft Fine Tuning · synthetic-sciences bundleParameter-efficient fine-tuning for LLMs using LoRA, QLoRA, and 25+ methods. Use when fine-tuning large models (7B-70B) with limited GPU memory, when you need to train <1% of parameters with minimal accuracy loss, or for multi-adapter serving. HuggingFace's official library integrated with transformers ecosystem.
- ▌ Rwkv Architecture · synthetic-sciences bundleRNN+Transformer hybrid with O(n) inference. Linear time, infinite context, no KV cache. Train like GPT (parallel), infer like RNN (sequential). Linux Foundation AI project. Production at Windows, Office, NeMo. RWKV-7 (March 2025). Models up to 14B parameters.
- ▌ Fluidsim · synthetic-sciences bundleFramework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
- ▌ Biopython · synthetic-sciences bundleComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
- ▌ Neurokit2 · synthetic-sciences bundleComprehensive biosignal processing toolkit for analyzing 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 activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
- ▌ Datamol · synthetic-sciences bundlePythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
- ▌ Matchms · synthetic-sciences bundleSpectral 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 matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
- ▌ Medchem · synthetic-sciences bundleMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
- ▌ Molfeat · synthetic-sciences bundleMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
- ▌ Umap Learn · synthetic-sciences bundleUMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
- ▌ Onekgpd · synthetic-sciences bundleQuery the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.
- ▌ Whisper · synthetic-sciences bundleOpenAI's general-purpose speech recognition model. Supports 99 languages, transcription, translation to English, and language identification. Six model sizes from tiny (39M params) to large (1550M params). Use for speech-to-text, podcast transcription, or multilingual audio processing. Best for robust, multilingual ASR.
- ▌ Gguf Quantization · synthetic-sciences bundleGGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.
- ▌ Simpo Training · synthetic-sciences bundleSimple Preference Optimization for LLM alignment. Reference-free alternative to DPO with better performance (+6.4 points on AlpacaEval 2.0). No reference model needed, more efficient than DPO. Use for preference alignment when want simpler, faster training than DPO/PPO.
- ▌ Pennylane · synthetic-sciences bundleHardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
- ▌ Etetoolkit · synthetic-sciences bundlePhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
- ▌ Pylabrobot · synthetic-sciences bundleVendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.
- ▌ Scikit Bio · synthetic-sciences bundleBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
- ▌ Scvi Tools · synthetic-sciences bundleDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
- ▌ Pyopenms · synthetic-sciences bundleComplete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
- ▌ Statsmodels · synthetic-sciences bundleStatistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.
- ▌ Guidance · synthetic-sciences bundleControl LLM output with regex and grammars, guarantee valid JSON/XML/code generation, enforce structured formats, and build multi-step workflows with Guidance - Microsoft Research's constrained generation framework
- ▌ Outlines · synthetic-sciences bundleGuarantee valid JSON/XML/code structure during generation, use Pydantic models for type-safe outputs, support local models (Transformers, vLLM), and maximize inference speed with Outlines - dottxt.ai's structured generation library
- ▌ Geniml · synthetic-sciences bundleThis skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
- ▌ Implementing Llms Litgpt · synthetic-sciences bundleImplements and trains LLMs using Lightning AI's LitGPT with 20+ pretrained architectures (Llama, Gemma, Phi, Qwen, Mistral). Use when need clean model implementations, educational understanding of architectures, or production fine-tuning with LoRA/QLoRA. Single-file implementations, no abstraction layers.
- ▌ Mlflow · synthetic-sciences bundleTrack ML experiments, manage model registry with versioning, deploy models to production, and reproduce experiments with MLflow - framework-agnostic ML lifecycle platform
- ▌ Pyvene Interventions · synthetic-sciences bundleProvides guidance for performing causal interventions on PyTorch models using pyvene's declarative intervention framework. Use when conducting causal tracing, activation patching, interchange intervention training, or testing causal hypotheses about model behavior.
- ▌ Bioservices · synthetic-sciences bundleUnified 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 biopython.
- ▌ Hypogenic · synthetic-sciences bundleAutomated 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 hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.
- ▌ Torchdrug · synthetic-sciences bundlePyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
- ▌ Scikit Learn · synthetic-sciences bundleMachine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
- ▌ Langchain · synthetic-sciences bundleFramework for building LLM-powered applications with agents, chains, and RAG. Supports multiple providers (OpenAI, Anthropic, Google), 500+ integrations, ReAct agents, tool calling, memory management, and vector store retrieval. Use for building chatbots, question-answering systems, autonomous agents, or RAG applications. Best for rapid prototyping and production deployments.
- ▌ Adaptyv · synthetic-sciences bundleCloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
- ▌ Axolotl · synthetic-sciences bundleExpert guidance for fine-tuning LLMs with Axolotl - YAML configs, 100+ models, LoRA/QLoRA, DPO/KTO/ORPO/GRPO, multimodal support
- ▌ Nanogpt · synthetic-sciences bundleEducational GPT implementation in ~300 lines. Reproduces GPT-2 (124M) on OpenWebText. Clean, hackable code for learning transformers. By Andrej Karpathy. Perfect for understanding GPT architecture from scratch. Train on Shakespeare (CPU) or OpenWebText (multi-GPU).
- ▌ Nnsight Remote Interpretability · synthetic-sciences bundleProvides guidance for interpreting and manipulating neural network internals using nnsight with optional NDIF remote execution. Use when needing to run interpretability experiments on massive models (70B+) without local GPU resources, or when working with any PyTorch architecture.
- ▌ Sparse Autoencoder Training · synthetic-sciences bundleProvides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.
- ▌ Instructor · synthetic-sciences bundleExtract structured data from LLM responses with Pydantic validation, retry failed extractions automatically, parse complex JSON with type safety, and stream partial results with Instructor - battle-tested structured output library
- ▌ Llamaindex · synthetic-sciences bundleData framework for building LLM applications with RAG. Specializes in document ingestion (300+ connectors), indexing, and querying. Features vector indices, query engines, agents, and multi-modal support. Use for document Q&A, chatbots, knowledge retrieval, or building RAG pipelines. Best for data-centric LLM applications.