Research & Science · By aipoch

Prepares setup instructions and a named activation file for a user-managed software environment on an Open-Science SSH or Slurm compute host.

aipoch/open-science

Publication-grade correctness and legibility rules for final-deliverable scientific figures, not exploratory plots.

aipoch/open-science

Judge and reshape the story told by an entire paper figure deck.

aipoch/open-science

Teaches an agent to inspect Open-Science's JavaScript control REPL, check which host.* calls are allowed, and find project files, sessions and agent frames.

aipoch/open-science

Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.

aipoch/medical-research-skills

Compose one publication-grade multi-panel figure. An agent skill from aipoch/open-science.

aipoch/open-science

A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS.

aipoch/medical-research-skills

Evaluate and use SSH Remote Compute before choosing where to run GPU, high-memory, parallel, batch, model-inference, bioinformatics, or other long-running scientific work; supports short remote…

aipoch/open-science

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…

aipoch/medical-research-skills

Expert system for generating comprehensive biomedical phenotype introductions with structured academic content.

aipoch/medical-research-skills

Multi-database literature search and search-strategy design that outputs structured, reproducible result lists; use when you need reference retrieval, systematic searching, review topic selection…

aipoch/medical-research-skills

Generate clinical trial protocols for medical devices or drugs.

aipoch/medical-research-skills

Generate medical referral letters with patient summary, reason for referral, key findings, and requested next steps; use when transferring care or communicating with another clinician or department.

aipoch/medical-research-skills

Venue-specific LaTeX templates, formatting requirements, and submission guidelines for journals, conferences, posters, and grants—use when a target venue imposes strict layout, page limits…

aipoch/medical-research-skills

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results.

aipoch/medical-research-skills

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package.

aipoch/medical-research-skills

Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for…

aipoch/medical-research-skills

Generates submission-ready Elsevier/SCI Highlights from manuscript text or extracted PDF/DOCX/TXT content.

aipoch/medical-research-skills

Design and simulate adaptive clinical trials with interim analyses, decision rules, and operating-characteristic summaries; use when planning adaptive designs or comparing stopping, enrichment, or…

aipoch/medical-research-skills

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

aipoch/medical-research-skills

Infer gene regulatory networks (GRNs) from gene expression matrices using GRNBoost2 or GENIE3; use when analyzing bulk or single-cell RNA-seq to identify TF→target regulatory relationships.

aipoch/medical-research-skills

Search and retrieve scientific preprints from arXiv; use it when you need to find papers by keyword/author/category, fetch metadata (abstract, DOI, PDF URL), or download PDFs for offline reading.

aipoch/medical-research-skills

A skill your agent uses when determining author order on research manuscripts, assigning CRediT contributor roles for transparency, documenting individual contributions to collaborative projects, or…

aipoch/medical-research-skills

Generate structured SOAP notes from clinical narratives, transcripts, or existing notes; use when the user needs de-identified clinical documentation organized into Subjective, Objective…

aipoch/medical-research-skills

A skill your agent uses when correcting batch effects in merged bulk expression matrices with sample-level batch metadata while preserving biological group structure and generating before-and-after…

aipoch/medical-research-skills

Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping.

aipoch/medical-research-skills

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores).

aipoch/medical-research-skills

Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases.

aipoch/medical-research-skills

Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

aipoch/medical-research-skills

Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially…

aipoch/medical-research-skills

Programmatic access to the BRENDA enzyme database via the SOAP API; use when you need kinetic constants (Km, kcat, Vmax), reaction equations, enzyme properties (pH/temperature optima, stability), or…

aipoch/medical-research-skills

A skill your agent uses when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF…

aipoch/medical-research-skills

Query the ChEMBL database for bioactive molecules, targets, bioactivities, and approved drugs; use this when you need to filter by physicochemical properties (e.g., MW, LogP), chemical structure…

aipoch/medical-research-skills

A skill your agent uses when estimating relative immune cell infiltration from a bulk expression matrix with a CIBERSORT-style nu-SVR deconvolution workflow based on an LM22 signature matrix…

aipoch/medical-research-skills

Comprehensive citation management for academic research; use when you need to discover papers (Google Scholar/PubMed), extract/verify metadata (DOI/PMID/arXiv/URL), and produce validated, clean…

aipoch/medical-research-skills

Build and visualize a citation network from a source/target CSV to identify key papers, communities, and emerging hotspots; use when you have citation pairs and need fast literature review or trend…

aipoch/medical-research-skills

A skill your agent uses when cleaning clinical trial data, preparing data for FDA/EMA submission, standardizing SDTM datasets, handling missing values in clinical studies, detecting outliers in lab…

aipoch/medical-research-skills

Batch extracts and verifies structured information (PMID, title, abstract, methodology, results, etc.) from clinical research literature using PMIDs.

aipoch/medical-research-skills

Query the ClinicalTrials.gov API v2 to search for clinical trials, retrieve detailed study protocols, and analyze recruitment status; use when you need to find trials by condition/drug, export…

aipoch/medical-research-skills

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance…

aipoch/medical-research-skills

Adapt scientific abstracts to conference-specific word limits, section rules, and formatting constraints; use when reshaping an existing abstract for submission.

aipoch/medical-research-skills

A skill your agent uses when identifying stable sample subtypes from bulk expression matrices with ConsensusClusterPlus, including PAC-based model selection and consensus matrix/CDF visualization.

aipoch/medical-research-skills

Accesses Comparative Toxicogenomics Database (CTD) for chemical, gene, disease, and pathway interaction data.

aipoch/medical-research-skills

A skill your agent uses when evaluating the clinical utility of a binary prediction model from a single clinical CSV file by fitting a logistic decision-curve model, plotting decision and…

aipoch/medical-research-skills

A skill your agent uses when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap.

aipoch/medical-research-skills

Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.

aipoch/medical-research-skills

Diffusion-based molecular docking to predict 3D ligand–protein binding poses (blind docking) with confidence scoring; use when you need pose prediction for drug discovery or virtual screening.

aipoch/medical-research-skills

A skill your agent uses when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and…

aipoch/medical-research-skills