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
Classifies LLM prompts and responses as safe or unsafe using Meta's LlamaGuard (7B v1, 8B v2 and v3) across six categories: violence and hate, sexual content, guns and illegal weapons, regulated substances, suicide and self-harm, and criminal planning. Covers HuggingFace Transformers and vLLM inference, a FastAPI…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Data 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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
Large 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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
Extend context windows of transformer models using RoPE, YaRN, ALiBi, and position interpolation techniques. Use when processing long documents (32k-128k+ tokens), extending pre-trained models beyond original context limits, or implementing efficient positional encodings. Covers rotary embeddings, attention biases…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
Explains how to use Mamba selective state-space models (state-spaces/mamba package, Mamba-1 with dstate=16 and Mamba-2 with multi-head structure and dstate=128) for linear-time sequence modeling. Covers installation, the Mamba block, building a language model with MambaLMHeadModel, loading pretrained state-spaces…
KalarisLabs/research-agent-skills
Skill Claude Code
Writes scientific documents and documentation as markdown with embedded Mermaid diagrams as the canonical, git-diffable source format. Covers a markdown style guide, a Mermaid style guide, 24 Mermaid diagram type references (flowchart, sequence, ER, Gantt, state, mindmap, radar, sankey, XY chart, and others), and 9…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Build evidence-traceable market research reports and assumption-driven market sizing or forecast scenarios. Use for market definition, industry and customer evidence, competitive landscapes, TAM/SAM/SOM reconciliation, forecast sensitivity, and auditable report scaffolds.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Converts documents to Markdown with Microsoft MarkItDown (Python API, markitdown CLI, markitdown-ocr plugin, markitdown-mcp server), covering PDF, Word, PowerPoint, Excel, HTML, CSV, EPUB, ZIP, and streams, plus Azure extraction. Use when preparing papers or reports for LLM/RAG ingestion; when batch-converting a…
KalarisLabs/research-agent-skills
Skill Claude Code
Process, clean, compare, and search tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral similarity, library matching, score matrices, and molecular-similarity networks. Use pyopenms instead for LC-MS feature detection or proteomics pipelines.
KalarisLabs/research-agent-skills
Skill Claude Code
Designs, reviews, and migrates MATLAB R2026a and GNU Octave numerical code, covering functions with arguments blocks, arrays and indexing, tables and timetables, matlab.unittest tests, MATLAB Projects, exportgraphics figures, MAT file inventory, and MATLAB-Python interoperability. Includes static helper scripts that…
KalarisLabs/research-agent-skills
Skill Claude Code
Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for…
KalarisLabs/research-agent-skills
Skill Claude Code
Filters and triages small-molecule libraries with the Python medchem library (datamol-io, v2.0.5) on top of RDKit and datamol. Covers drug-likeness rules (Lipinski, Veber, CNS, lead-like) via RuleFilters, structural alerts (ChEMBL-derived sets, NIBR, PAINS, Brenk), chemical group detection, ZINC-based complexity…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Provides guidance for enterprise-grade RL training using miles, a production-ready fork of slime. Use when training large MoE models with FP8/INT4, needing train-inference alignment, or requiring speculative RL for maximum throughput.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Write publication-ready ML/AI papers for NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Use when drafting papers from research repos, structuring arguments, verifying citations, or preparing camera-ready submissions. For systems venues (OSDI, NSDI, ASPLOS, SOSP), use systems-paper-writing instead.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Battle-tested PyTorch training recipes for all domains — LLMs, vision, diffusion, medical imaging, protein/drug discovery, spatial omics, genomics. Covers training loops, optimizer selection (AdamW, Muon), LR scheduling, mixed precision, debugging, and systematic experimentation. Use when training or fine-tuning…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Tracks machine learning experiments and manages model lifecycles with MLflow, covering mlflow.logparam, logmetric and logartifact, autologging for scikit-learn, PyTorch Lightning, XGBoost and HuggingFace Transformers, the Model Registry with versions and stage transitions, run searching, and local or cloud model…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Serverless GPU cloud platform for running ML workloads. Use when you need on-demand GPU access without infrastructure management, deploying ML models as APIs, or running batch jobs with automatic scaling.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Modal is a serverless cloud platform for running Python on demand, including on-demand GPUs. Use when deploying or serving AI/ML models, running GPU-accelerated workloads (training, fine-tuning, inference), serving web endpoints, scheduling batch jobs, or scaling Python code to cloud containers with the Modal SDK.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Merge multiple fine-tuned models using mergekit to combine capabilities without retraining. Use when creating specialized models by blending domain-specific expertise (math + coding + chat), improving performance beyond single models, or experimenting rapidly with model variants. Covers SLERP, TIES-Merging, DARE, Task…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Reduce LLM size and accelerate inference using pruning techniques like Wanda and SparseGPT. Use when compressing models without retraining, achieving 50% sparsity with minimal accuracy loss, or enabling faster inference on hardware accelerators. Covers unstructured pruning, structured pruning, N:M sparsity, magnitude…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Train Mixture of Experts (MoE) models using DeepSpeed or HuggingFace. Use when training large-scale models with limited compute (5× cost reduction vs dense models), implementing sparse architectures like Mixtral 8x7B or DeepSeek-V3, or scaling model capacity without proportional compute increase. Covers MoE…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Runs and analyzes molecular dynamics simulations using OpenMM and MDAnalysis. Covers system preparation with PDBFixer and OpenFF/GAFF2, force field choice (AMBER14, CHARMM36m, ff19SB), energy minimization, NVT/NPT equilibration, production MD, and trajectory analysis (RMSD, RMSF, protein-ligand contacts). Use when…
KalarisLabs/research-agent-skills
Skill Claude Code
Converts SMILES strings or RDKit/datamol molecules into numerical features using molfeat (0.11.0), which provides calculators, scikit-learn compatible transformers, and pretrained embedding models. Covers fingerprints (ECFP, MACCS, MAP4), RDKit and Mordred descriptors, pharmacophore descriptors, and pretrained models…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
Provides nanoGPT, Karpathy's minimal PyTorch GPT implementation (model.py and train.py), with workflows for training character-level Shakespeare on CPU, reproducing GPT-2 124M on OpenWebText with multi-GPU torchrun, fine-tuning pretrained GPT-2 checkpoints, and training on custom text. Use when learning how GPT and…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: