Claude Skills by KalarisLabs

Query 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.

Retrieve, 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 si...

Wraps RDKit through the datamol Python library (import datamol as dm) for molecular cheminformatics, returning native rdkit.Chem.Mol objects. Covers SMILES/SELFIES/InChI conversion, sanitization and standardization, descriptors, fingerprints and similarity, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds, BRICS/RECAP fragmentation, 3D conformers, reactions, SDF/CSV/Excel I/O including cloud paths, and parallel batch processing. Use when parsing or standardizing SMILES fro...

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 PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

Covers DeepSpeed for distributed deep learning training and I/O: ZeRO optimization stages, pipeline parallelism, FP16/BF16/FP8 training, 1-bit Adam, sparse attention, and DeepNVMe (aio_handle, gds_handle, async_io and gds operators, ds_nvme_tune, ds_report) for fast transfers between NVMe storage and host or GPU tensors. Use when configuring ZeRO stages for large-model training, enabling mixed precision or 1-bit Adam, offloading parameters or optimizer state to NVMe with ZeRO-Infinity, writin...

Runs deepTools command-line programs on NGS alignment data: bamCoverage and bamCompare for BAM to bigWig/bedGraph with RPGC, CPM, RPKM or BPM normalization, multiBamSummary with plotCorrelation and plotPCA, plotFingerprint, computeMatrix with plotHeatmap and plotProfile, and alignmentSieve with --ATACshift. Use when converting BAM files to normalized coverage tracks. Use when checking ChIP-seq quality or comparing replicates. Use when plotting signal around TSS or peak regions. Use when compa...

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.

Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyze how this person reasons", "cognitive profile", "thinking pattern", "DHDNA", "digital DNA", or wants to understand the mind behind any text. Also trigger when the user provides text and wants deeper insight into the au...

DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.

Provides PyTorch-native distributed LLM pretraining using torchtitan with 4D parallelism (FSDP2, TP, PP, CP). Use when pretraining Llama 3.1, DeepSeek V3, or custom models at scale from 8 to 512+ GPUs with Float8, torch.compile, and distributed checkpointing.

Build and operate reproducible genomics workloads on DNAnexus with the dx CLI, dxpy, apps/applets, native workflows, dxCompiler, and Nextflow. Use for DNAnexus data transfers, dxapp.json development, execution monitoring, workflow import, and project automation.

Builds and optimizes language model programs with DSPy (Stanford NLP), using Signatures, modules (Predict, ChainOfThought, ReAct, ProgramOfThought) and optimizers (BootstrapFewShot, MIPRO, BootstrapFinetune). Use when replacing hand-written prompts with declarative signatures, when automatically tuning prompts against training data and a metric, when building multi-stage RAG pipelines or ReAct agents, when building classifiers or structured-output programs, or when saving and evaluating optim...

Prepare submissions to Elsevier journals (including The Lancet family style notes, Cell-independent Elsevier titles, and thousands of society journals) using the elsarticle LaTeX class, the CAS single/double-column templates or Word, covering highlights, graphical abstracts, keywords, CRediT author statements, declarations of interest, generative-AI disclosure, data availability, reference styles per journal, Editorial Manager submission and "Your Paper Your Way" format-free first submission....

Covers the EvolutionaryScale/Biohub `esm` Python SDK: ESM3 generative protein design (sequence, structure and function tracks, chain-of-thought), ESMC embeddings, inverse folding, ESMFold2 structure prediction, and hosted Forge/Biohub inference with ESM_API_KEY. Use when generating or completing proteins with ESM3, extracting ESMC embeddings for classification or similarity, folding a sequence or designing sequences from a structure, or choosing between esm3-open, esmc_300m and Forge-hosted m...

Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.

Evaluates 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.

Evaluates NVIDIA Cosmos Policy on LIBERO and RoboCasa simulation environments. Use when setting up cosmos-policy for robot manipulation evaluation, running headless GPU evaluations with EGL rendering, or profiling inference latency on cluster or local GPU machines.

Evaluates 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.

Provides guidance for automatically evolving and optimizing AI agents across any domain using LLM-driven evolution algorithms. Use when building self-improving agents, optimizing agent prompts and skills against benchmarks, or implementing automated agent evaluation loops.

Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and academic domain filtering) and URL extraction (fetching pages, articles, academic PDFs in batch). Use this skill for web-related tasks when the user wants high-quality search or scholarly filtering via category=research paper. Triggers o...

Tracks ML experiments with SwanLab, an open-source tool covering swanlab.init, config and metric logging, scalar charts, and media logging (images, audio, text, GIFs, point clouds, molecules), in cloud, local (mode="local" with swanlab[dashboard]), or self-hosted setups. Includes integrations for PyTorch, Transformers, PyTorch Lightning, and Fastai. Use when logging metrics and hyperparameters for training runs, comparing runs across seeds, checkpoints, or hyperparameters, running an offline ...

Design experiments and studies BEFORE data is collected — choosing a design, randomizing, blocking, and laying out treatment combinations so results are interpretable. Use whenever someone is planning a study, asks how to assign subjects/samples to groups, mentions randomization, blocking, stratification, controls, factorial or fractional-factorial designs, design of experiments (DOE), screening many factors, response-surface optimization, crossover or repeated-measures or split-plot designs,...

Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain formats are reference-only and unknown formats fail closed.

Facebook'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.

Drives the Fictiv on-demand manufacturing web app (app.fictiv.com) in the user's browser, since there is no public API. Covers uploading CAD files (STEP, SLDPRT, STL), configuring process, material, finish, threads and tolerances, reading DFM feedback, instant or manual quotes, lead-time tiers, checkout by card or PO, order tracking and reorders. Use when the user mentions Fictiv. Use when they want a part CNC machined, 3D printed, sheet-metal fabricated, cast, or molded online. Use when they...

Fine-tunes and evaluates OpenVLA-OFT and OpenVLA-OFT+ policies for robot action generation with continuous action heads, LoRA adaptation, and FiLM conditioning on LIBERO simulation and ALOHA real-world setups. Use when reproducing OpenVLA-OFT paper results, training custom VLA action heads (L1 or diffusion), deploying server-client inference for ALOHA, or debugging normalization, LoRA merge, and cross-GPU issues.

Fine-tune and serve Physical Intelligence OpenPI models (pi0, pi0-fast, pi0.5) using JAX or PyTorch backends for robot policy inference across ALOHA, DROID, and LIBERO environments. Use when adapting pi0 models to custom datasets, converting JAX checkpoints to PyTorch, running policy inference servers, or debugging norm stats and GPU memory issues.

Fine-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.

Query Firecrawl Research Index paper endpoints for topic discovery, source metadata, question-matched passages, and citation-neighbor expansion. Use when a researcher explicitly asks for Firecrawl Research or its hosted arXiv and biomedical paper records.

Read, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table export, and FCS 3.1 creation; use FlowKit for compensation, cytometry transforms, gating, or FlowJo workspaces.

Plan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for FluidSim solver selection, parameter review, FFT/MPI setup, output diagnostics, or restart compatibility.

Retrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP. Use when a scientific agent must branch deterministically on resolved, ambiguous, not-found, invalid, unsupported, or unavailable variant outcomes; chain a resolved public variant into related literature or publication details; or preserve evide...

Generate or edit images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams, use the scientific-schematics skill instead.

Plans and audits local genomic-interval machine learning workflows with Geniml (0.8.4) and Gtars: validates BED files against chromosome sizes and assembly contracts, plans Region2Vec, scEmbed, and BEDspace runs, checks model, tokenizer, and universe.bed compatibility, and assesses consensus universes (CC, CCF, ML, HMM, assess-universe). Bundled scripts only validate or plan; they do not train. Use when checking BED coordinates, contigs, or assembly before analysis. Use when planning Region2V...

Convert 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...

Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence''s hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer activity, chromatin state, sequence-to-expression (log TPM), and de-novo gene annotation, plus a composite find-genes-then-predict-expression workflow. Use when the user has a gen...

Provides geospatial and Earth observation workflows using GeoPandas, Rasterio, GDAL, Xarray, Shapely, Laspy, PDAL, Google Earth Engine, and STAC/Planetary Computer, covering Sentinel, Landsat, MODIS, SAR and hyperspectral imagery, spectral indices, terrain and network analysis, point clouds, COGs, CRS handling, and spatial ML, with code in Python, R, Julia, JavaScript, C++, Java, Go, and Rust. Use when computing NDVI or other indices from satellite imagery, when running vector overlays, repro...

Guidance and local audit CLIs for Python workflows using GeoPandas 1.1.4 GeoSeries and GeoDataFrame for planar vector data: CRS handling, geometry validity and repair, sjoin, overlay, clip, dissolve, union, GeoPackage, GeoParquet and PostGIS I/O, and plotting. Use when reprojecting or assigning a CRS, auditing invalid or empty geometries, running spatial joins and checking cardinality, exporting vector data with a reproducible contract, or migrating code from GeoPandas 0.14 to 1.x. Use when c...

Detect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload. Produces a redacted JSON snapshot and conservative planning helpers without stress tests or assuming visible host hardware is usable.

Queries 20+ bioinformatics databases and analysis services through the gget CLI and Python package, covering Ensembl gene search, info and sequences (ref, search, info, seq), BLAST, BLAT, MUSCLE, DIAMOND, PDB, AlphaFold, ELM, ARCHS4, CELLxGENE, Enrichr, Bgee, OpenTargets, cBioPortal, COSMIC, viral sequence downloads (virus), and 8cube mouse specificity and expression data. Use when looking up gene or transcript details, running a quick BLAST/BLAT search, fetching AlphaFold or PDB structures, ...

GGUF 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.

Submit 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 Clo...

Quantizes LLMs to 4-bit (also 3-bit) with GPTQ using group-wise quantization (group size 128 by default), via AutoGPTQ and transformers. Covers loading pre-quantized GPTQ models, quantizing your own model, choosing group size, selecting ExLlamaV2, Marlin, or Triton kernels, and QLoRA fine-tuning with PEFT. Use when fitting 70B-class models onto limited or consumer GPUs, cutting memory about 4x versus FP16, speeding up inference, finding pre-quantized checkpoints on HuggingFace, or fine-tuning...

Guides GRPO (Group Relative Policy Optimization) fine-tuning of language models with the TRL library, including GRPOTrainer configuration, composing multiple reward functions (correctness, format, length, style), dataset prep in chat format, Unsloth setup, LoRA merging, and monitoring reward, reward_std and KL. Use when training a model to follow a strict output format such as XML or JSON. Use when teaching verifiable tasks like math or code with objective correctness rewards. Use when improv...

Inspects and plans work with Gtars, the Rust/Python/CLI toolkit for genomic intervals: BED RegionSet set algebra (reduce, setdiff, intersect, closest, cluster, gaps), overlap counts, consensus peak sets, coverage, tokenizers, fragment processing, and refget/BEDbase stores. Use when merging or comparing BED interval sets, building a consensus or universe from peaks, tokenizing regions for ML models, working with fragment files, or planning refget sequence-collection and BEDbase cache use. Use ...

Constrains LLM output during generation with Guidance (Microsoft Research), using regex, select() choices, context-free grammars, token healing, and @guidance functions, with Anthropic, OpenAI, Transformers, and llama.cpp backends. Use when you need generated text to match a regex or fixed format such as dates, emails, or IDs. Use when you need guaranteed valid JSON, XML, or code from a model. Use when building multi-step generation workflows or ReAct-style agents with Python control flow. Us...

Extracts tiles and preprocesses H&E whole slide images with the histolab Python library (OpenSlide), covering slide inspection, tissue masks (TissueMask, BiggestTissueBoxMask), RandomTiler, GridTiler and ScoreTiler extraction, image and morphological filters, and Macenko or Reinhard stain normalization. Use when building a tile dataset from WSI files for deep learning. Use when detecting tissue and excluding background or pen annotations. Use when previewing tile locations and exporting tile ...

Half-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.

Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, theorem proving, single-cell, or PDE solving. Hugging Science is a curated catalog of scientific datasets, models, blog posts, and interactive Spaces. This skill helps discover and use resources via `datasets`, `transformers`, the HF Inference API, `gradio_clien...

Wraps existing PyTorch training scripts with HuggingFace Accelerate (Accelerator class, accelerate config, accelerate launch) so the same code runs on CPU, single GPU, multi-GPU, multi-node, TPU, or Apple MPS. Covers device placement, FP16/BF16/FP8 mixed precision, gradient accumulation, distributed checkpointing, and switching between DDP, DeepSpeed ZeRO, FSDP, and Megatron backends. Use when converting a single-GPU script to multi-GPU, enabling mixed precision, configuring DeepSpeed ZeRO or...