Turn any AI agent into a research co-scientist: 280+ open-source agent skills for literature reviews, hypotheses, experimental design, data analysis, paper writing, citation verification and peer review. Claude Code, Codex, Cursor, Gemini CLI and any Agent Skills harness. npx skills add KalarisLabs/research-agent-skills
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Provides the HuggingFace Tokenizers library (Rust core with Python and Node.js bindings) for training and using BPE, WordPiece, and Unigram tokenizers. Covers the pipeline of normalizers, pre-tokenizers, models, post-processors and decoders, padding and truncation, batch encoding, alignment tracking, and conversion to…
KalarisLabs/research-agent-skills
Skill Claude Code
Plans and audits use of ChicagoHAI HypoGeniC/HypoRefine for LLM-assisted hypothesis generation from labeled text datasets. Use for the hypogenic package, its task configs, hypothesis banks, or HypoBench datasets—not for manual hypothesis formulation or scientific validation.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready analysis plans. Use when turning observations or preliminary findings into transparent, testable research plans without treating…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Format and submit papers to IEEE journals (Transactions, Journals, Letters, IEEE Access) and IEEE conferences using the IEEEtran LaTeX class or Word templates, covering journal vs conference modes, abstracts and index terms, numbered IEEE reference style, figures and equations, author biographies, page limits and…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Query and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM data access, radiology (CT, MR, PET) or pathology AI training sets, metadata queries, visualization, or license checks — even when the user doesn't explicitly…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
Implements 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.
KalarisLabs/research-agent-skills
Skill Claude Code
Generates infographics from natural-language prompts using Nano Banana Pro image generation, with optional Perplexity Sonar research for facts and a Gemini 3.6 Flash quality review that regenerates only when the score is below a document-type threshold. Supports 10 types (statistical, timeline, process, comparison…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Extracts structured, validated data from LLM responses using the Instructor Python library with Pydantic response models, including nested models, enums, custom validators, automatic retries with validation error feedback, and streaming of partial objects or iterables. Works with Anthropic, OpenAI, and local Ollama…
KalarisLabs/research-agent-skills
Skill Claude Code
Prepares and structurally reviews readiness evidence for ISO management-system and laboratory-competence standards - ISO 13485 medical device QMS, ISO 14971 device risk management, ISO/IEC 17025 testing and calibration laboratories, and ISO 15189 medical laboratories. Use when organizing declared scope, controlled…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Compress 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…
KalarisLabs/research-agent-skills
Skill Claude Code
Design 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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Securely integrate with the official LabArchives ELN REST-like API and Inventory API v1. Use for regional endpoint selection, signed-request construction, user authorization and UID flows, local LA container validation, and verified LabArchives integration workflows.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Reserved and on-demand GPU cloud instances for ML training and inference. Use when you need dedicated GPU instances with simple SSH access, persistent filesystems, or high-performance multi-node clusters for large-scale training.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation with Bionty, collections, branches, storage, and workflow integrations.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Framework 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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
LLM observability platform for tracing, evaluation, and monitoring. Use when debugging LLM applications, evaluating model outputs against datasets, monitoring production systems, or building systematic testing pipelines for AI applications.
KalarisLabs/research-agent-skills
Skill Claude Code
Build, register, debug, and operate bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP. Use when authoring or deploying Latch workflows, configuring resources or interfaces, moving data, integrating Registry, or launching and…
KalarisLabs/research-agent-skills
Skill Claude Code
Creates research posters in LaTeX with beamerposter, tikzposter, or baposter, covering page sizes (A0, A1, 36x48 inch), multi-column layouts, color schemes, figure and QR code placement, and pdflatex/overfull-box checks before printing. Also guides generating poster graphics with AI schematic tools under strict…
KalarisLabs/research-agent-skills
Skill Claude Code
Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents. Distinguishing capabilities…
KalarisLabs/research-agent-skills
Skill Claude Code
Runs systematic literature reviews by searching PubMed, arXiv, bioRxiv, and Semantic Scholar (plus web search via parallel-cli), screening studies, extracting data, synthesizing themes, and verifying citations with verifycitations.py. Produces a markdown and PDF review with a PRISMA-style flow diagram and a…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Runs LLM inference on CPU, Apple Silicon, and consumer GPUs without NVIDIA hardware. Use for edge deployment, M1/M2/M3 Macs, AMD/Intel GPUs, or when CUDA is unavailable. Supports GGUF quantization (1.5-8 bit) for reduced memory and 4-10× speedup vs PyTorch on CPU.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Guides fine-tuning of large language models with LLaMA-Factory, covering the WebUI no-code interface, training across 100+ supported models, quantized QLoRA at 2/3/4/5/6/8-bit precision, and multimodal model support. Use when setting up or configuring a LLaMA-Factory fine-tuning run, choosing a quantization level for…
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