KalarisLabs

Searches OpenAlex, PubMed, and Google Scholar, extracts metadata from DOIs, PMIDs, PMCIDs, arXiv IDs, and URLs via CrossRef, PubMed, and arXiv, then formats, deduplicates, and validates BibTeX files using bundled Python scripts (search_openalex.py,…

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…

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,…

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…

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,…

Plans and evaluates analytical method validation, verification, and transfer using Python scripts (plan_validation, check_response, check_accuracy_precision, check_detection_limits, check_bioanalytical_run, compare_methods) under ICH Q2(R2)/Q14, ICH M10, USP…

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…

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…

Guides writing academic papers section by section using an 11-step workflow with LaTeX templates and counterintuitive writing tactics. Covers Abstract, Introduction, Method, Experiments, Related Work, Conclusion, and Supplementary. Use when: user asks to…

Pre-publish and publish path for crates.io, npm installer, GitHub Releases, SBOM. Use when cutting versions, editing release.yml, or adding publish steps. Never publish from a feature branch.

A simple greeting skill that says hello to the user.

You MUST use this before any creative work - creating features, building components, adding functionality, or modifying behavior. Explores user intent, requirements and design before implementation.

Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies

Use when you have a written implementation plan to execute in a separate session with review checkpoints

Use when implementation is complete, all tests pass, and you need to decide how to integrate the work

Skill Doctor product and architecture context. Use at the start of a session, when deciding where code lives, when the user asks how the scanner works, or before any non-trivial change.

Activate when an agent must parse high-throughput screening plate-reader data, reconcile plate maps, detect row/column/edge artifacts, normalize inhibition or activation assays, calculate Z-prime or robust Z-prime, compute robust z-scores or B-scores, assess…

Activate when an agent must generate, compare, quality-control, or select a diploid PacBio HiFi de novo genome assembly using hifiasm; when requests mention HiFi read assembly, haplotype-resolved assembly, hifiasm parameter optimization, primary and alternate…

Activate when an agent must enumerate, annotate, compare, or rank potential CRISPR nuclease off-target sites while accounting for germline variants or sample-specific haplotypes; when requests mention Cas-OFFinder, CRISPRitz, SpCas9 NGG, PAM-aware search, CFD…

Set up, write, and publish documentation sites with Mintlify. Use when the user wants to create a docs site for a repo or product, publish docs to a shareable URL, migrate docs from another platform, create docs pages, configure navigation, add components, or…

Choose, install and use Kalaris Labs Research Agent Skills for academic writing, literature reviews, citation verification, journal formatting and scientific data analysis. Use when the user is writing a paper, thesis or grant, running a systematic review,…

Scan AI agent skills, tool definitions and MCP servers for security issues with Skill Doctor before loading, installing or editing them. Use when the user asks whether a skill is safe, wants to audit a skills directory, or wants a CI gate for skills.

Detect and reduce AI-generated writing-risk patterns in English and Chinese thesis text. Scores paragraphs using external-detector-informed risk models (Turnitin, CNKI) and revises high-risk passages via conservative, minimal-edit rewrites that preserve…

Detect and reduce AI-generated writing-risk patterns in English and Chinese thesis text. Scores paragraphs using external-detector-informed risk models (Turnitin, CNKI) and revises high-risk passages via conservative, minimal-edit rewrites that preserve…