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 Code
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.
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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 (aiohandle, gdshandle, asyncio and gds operators, dsnvmetune, dsreport) for fast transfers between NVMe storage and host or GPU tensors.…
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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.
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude Code needs its repo
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex needs its repo
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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 ESMAPIKEY. Use when generating or completing proteins with ESM3…
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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.
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude Code
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…
KalarisLabs/research-agent-skills
Skill Claude CodeCodex
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…
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