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
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Write and sharpen research paper titles, abstracts (structured and unstructured), keywords, highlights, significance statements, graphical-abstract text and lay summaries. Use when drafting or revising an abstract to a word limit, turning results into a one-sentence contribution, choosing between candidate titles…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Generates publication-quality figures for ML papers from research context. Given a paper section or description, extracts system components and relationships to generate architecture diagrams via Gemini. Given experiment results or data, auto-selects chart type and generates data-driven figures via matplotlib/seaborn.…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Format ACM conference papers and journal articles with the acmart LaTeX class (sigconf, sigplan, acmsmall, acmlarge, acmtog, manuscript/review/anonymous modes) or the ACM Word template, covering CCS concepts, keywords, ACM Reference Format, rights management and copyright blocks, anonymization for double-blind review…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for…
KalarisLabs/research-agent-skills
Skill Claude Code
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard…
KalarisLabs/research-agent-skills
Skill Claude Code
Look up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), score variants or scan windows…
KalarisLabs/research-agent-skills
Skill Claude Code
Plans and evaluates analytical method validation, verification, and transfer using Python scripts (planvalidation, checkresponse, checkaccuracyprecision, checkdetectionlimits, checkbioanalyticalrun, comparemethods) under ICH Q2(R2)/Q14, ICH M10, USP 1220/1225/1226, CLSI EP, or ISO/IEC 17025. Covers protocols…
KalarisLabs/research-agent-skills
Skill Claude Code
Data 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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Format papers, theses and references in APA Style 7th edition for psychology, education, social sciences, nursing and business, covering student vs professional papers, title page, abstract and keywords, heading levels, in-text citations, reference list entries (journal articles, books, chapters, datasets, software…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Compiles any research input — PDF papers, GitHub repositories, experiment logs, code directories, or raw notes — into a complete Agent-Native Research Artifact (ARA) with cognitive layer (claims, concepts, heuristics), physical layer (configs, code stubs), exploration graph, and grounded evidence. Use when ingesting a…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Records research provenance at the end of a coding or research session by scanning the conversation and writing decisions, experiments, dead ends, pivots, claims, and heuristics into the ara/ directory (explorationtree.yaml, claims.md, heuristics.md, observations.yaml, session records), each tagged user, ai-suggested…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Performs ARA Seal Level 2 semantic epistemic review of an Agent-Native Research Artifact directory, reading PAPER.md, logic/claims.md, logic/experiments.md, and trace/explorationtree.yaml. Scores six dimensions (evidence relevance, falsifiability, scope calibration, argument coherence, exploration integrity…
KalarisLabs/research-agent-skills
Skill Claude Code
Autonomously improve a real artifact (code, training recipe, agent harness, data pipeline, prompt) against an objective and an evaluator, using Hypothesis Tree Refinement (HTR) from the Arbor paper. Use this whenever someone wants to iteratively optimize something over many experiments without overfitting — e.g. "get…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Prepare and post preprints to arXiv without processing failures or leaks, covering TeX source packaging (.bbl, figures, case-sensitive paths), stripping private comments, choosing categories and license, endorsement, metadata (title, abstract, comments field), versioning and replacements, and linking the journal DOI…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Core Python library for astronomy and astrophysics workflows that need Astropy APIs, including units/quantities, coordinates, FITS I/O, tables, time systems, WCS, and cosmology. Use when implementing or debugging astronomical data analysis code with Astropy.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
PyTorch library for audio generation including text-to-music (MusicGen) and text-to-sound (AudioGen). Use when you need to generate music from text descriptions, create sound effects, or perform melody-conditioned music generation.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Autonomous AI agent platform for building and deploying continuous agents. Use when creating visual workflow agents, deploying persistent autonomous agents, or building complex multi-step AI automation systems.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Orchestrates end-to-end autonomous AI research projects using a two-loop architecture. The inner loop runs rapid experiment iterations with clear optimization targets. The outer loop synthesizes results, identifies patterns, and steers research direction. Routes to domain-specific skills for execution, supports…
KalarisLabs/research-agent-skills
Skill Claude Code needs its repo
Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing research-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
Activation-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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
Provides guidance for fine-tuning large language models with Axolotl, covering YAML training configs, LoRA and QLoRA, preference training with DPO, KTO, ORPO and GRPO, multimodal models, FSDP and multi-GPU setups, sequence (context) parallelism, NCCL bandwidth tests, dataset formats, compressed model saving for vLLM…
KalarisLabs/research-agent-skills
Skill Claude Code
Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.
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: