medical-research-skills

A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS. Use when you need to perform a documentation gap analysis, draft or update a Quality Manual, create required procedures/work instructions, build Medical Device Files (MDF), interpret ISO 13485 clauses, or identify missing documents for certification (often triggered by ISO 13485, QMS certification, FDA QMSR, EU MDR, or quality system documentation requests).

Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Use when user wants to search for transcription factors, retrieve matrix details (PFM/PWM), infer profiles from protein sequences, or explore JASPAR collections.

Generate journal club slides with background, critique, and discussion.

Use when creating journal cover images, generating scientific artwork prompts, or designing graphical abstracts. Creates detailed prompts for AI image generators to produce publication-quality scientific visuals.

Show journal impact factor and quartile trends over 5 years.

Retrieve the latest journal issue's table of contents and abstracts from URL/DOI/PMID/RSS/TOC sources, then generate Chinese key points locally (no external translation APIs) when a new issue needs quick review and archiving.

Analyzes academic paper abstracts to recommend optimal journals for submission, considering impact factors, scope alignment, and domain expertise.

Recommend academic journals based on manuscript topic, abstract, and impact factor expectations. Use when the user wants to find suitable journals for their research manuscript, especially when they provide a topic, abstract, and target Impact Factor.

Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal recommendation/matching, submission strategy, PubMed search, or similar-literature statistics.

Access the KEGG database API to retrieve biological data (genes, pathways, compounds, drugs). Invoke when the user asks to search, list, or get details from KEGG.

Direct access to KEGG via the REST API for academic-only pathway/gene/compound/drug queries; use when you need precise HTTP-level control or targeted KEGG ID mapping.

Extracts and summarizes key takeaways from documents, meeting notes, articles, and other text content. Use when the user asks for summaries, bullet points, main points, highlights, or a TL;DR of any document or body of text. Produces structured outputs such as numbered lists, executive summaries, and action items. Supports configurable output formats including JSON export for downstream use.

Calculate literature growth velocity and acceleration to assess research.

Use when generating Kaplan-Meier survival curves from tabular survival data containing time, event status, and a precomputed risk group. Supports command-line parameter input, parameter validation, automatic time-unit handling, single-file PDF figure export, and session metadata capture.

Use when filtering genes with high missingness and then imputing missing values in a bulk expression matrix with group-aware KNN through DMwR2, where donor samples are restricted by one annotation column before imputation. For strata with 10 or fewer samples, the script falls back to row-wise direct filling with mean or median. NOT for: single-cell data, multi-column stratification, non-tabular inputs, network access, or interactive workflows.

Search and locate relevant content within a local knowledge base (files, indices, or PageIndex). Use when you need verifiable citations (file + page/paragraph) to support answers from local sources.

Generate professional Key Visual (KV) design proposals and images; use when you have a slogan/copy and a marketing scenario but need a clear visual direction and a ready-to-generate image prompt.

Converts LabArchives notebook data, entry metadata, and authorized ELN exports into manuscript-ready academic writing outputs such as Methods sections, data-availability statements, reproducibility appendices, experiment timelines, and submission support notes. Optional bundled scripts can be used to collect or validate source notebook data before writing.

Use lab budget forecaster for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

Predict depletion time of critical lab reagents based on historical usage frequency, and automatically generate purchase alerts when stock falls below safety thresholds.

Perform pre-experiment calculations and generate step-by-step preparation protocols for dilutions, solution preparation, dissolution, and % concentrations when planning formulations and lab prep workflows.

Transforms biochemical lab test results into clear, patient-friendly explanations. Covers blood routine, lipid panel, liver/kidney function, thyroid, electrolytes, and inflammation markers. Flags critical values, classifies severity, and generates structured interpretation rep...

This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakes, or ensuring data lineage and reproducibility in biological research. It covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integration with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

Use when building a binary classification model from an expression matrix or other omics feature matrix with LASSO logistic regression, cross-validation, and coefficient path visualization. NOT for: multiclass classification, survival/Cox models, or ordinary linear regression.

Converts existing manuscript content into LaTeX format aligned with a target journal, conference, or template while preserving manuscript meaning and structural integrity.