미생물학자

Cell

Cellular biology fundamentals

ffsshhttiikk2

건강 및 피트니스

Metabolic Tracker

Record and analyze the metabolic activity of Being Skill invocations. Use after any Skill execution to log energy consumption, output quality, and efficiency. Also generates aggregated statistics for fitness evaluation.

scilid2

PyOpenMS

Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.

영업 및 마케팅

Cell Bank Management

Design cell bank management systems. TRIGGERS - Use when user needs help with cell-bank-management related tasks.

Winbda2

Molecular Biology Expert

Expert-level molecular biology knowledge. Use when working with DNA replication, transcription, translation, gene regulation, cloning, PCR, sequencing, CRISPR, epigenetics, or molecular techniques. Also use when the user mentions 'DNA replication', 'transcription', 'translation', 'gene expression', 'PCR', 'cloning', 'restriction enzyme', 'gel electrophoresis', 'Western blot', 'CRISPR', 'epigenetics', 'promoter', 'enhancer', or 'RNA splicing'.

Microbiology

Study of microorganisms

ffsshhttiikk2

Hmdb Database

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

디버깅

Fungi Identification

Field identification of fungi using morphological features, spore prints, habitat analysis, and seasonal context with a safety-first approach. Covers cap, gill, stem, and spore characteristics, look-alike differentiation, toxicity risk assessment, and the critical rule of absolute certainty before consumption. Use when encountering an unknown fungus, foraging for edible mushrooms and needing to confirm species before consumption, assessing whether fungi in a garden or property are harmful, or differentiating an edible species from a dangerous look-alike.

merceralex397-collab2

건강 및 피트니스

Experiment

Design a new N=1 experiment — supplement, sleep intervention, dietary change, anything. Triggers on "I want to try", "experiment", "test", "what if I tried", or any request for formal intervention testing.

teoobarca2

웰니스 및 건강

Immunology Expert

Expert-level immunology covering innate and adaptive immunity, antibody structure and function, T cell biology, immune evasion, vaccines, autoimmunity, and immunotherapy.

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Bio Read Qc Contamination Screening

Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.

Cellcellcommunication

Infer ligand-receptor interactions and cell-cell communication networks from single-cell RNA-seq data using the LIANA+ framework. Identifies potential signaling events between cell types based on gene expression patterns and curated ligand-receptor interaction databases.

Bio Viromics

Detect, classify, and QC viral contigs.

Bio Epidemiological Genomics Amr Surveillance

Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.

디버깅

Correlation Methylation Epifeatures

This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks/TF signals.

Scikit Bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

ViggyV4

Chipseq Qc

Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics.

BIsnake20014

Metagenome Host Removal

Remove host-derived reads from metagenomic samples by aligning to a host reference genome and extracting unmapped pairs.

Metagenome Binning

Recover metagenome-assembled genomes (MAGs) from contigs using MetaBAT2, refine with DAS Tool, and assess quality with CheckM2.

Metagenome Assembly

De novo assembly of metagenomic contigs from short reads using MEGAHIT or metaSPAdes.

Metagenome Functional Profiling

Functional annotation of metagenomic data using HUMAnN 3 for pathway abundance, Prokka for gene prediction, and eggNOG-mapper for ortholog assignment.

LLM & AI

Arrive Guideline Architect

Generate ARRIVE 2.0 compliant animal research protocols with structured

dvcrn3

실험실 도구

Autoresearch

Infinite improvement loop for any research artifact in any phase — worker makes one focused change per iteration, evaluator compares to previous best, keeps or reverts. Loop never stops until the human interrupts it. Inspired by Andrej Karpathy's autoresearch (MIT).

stanislavjiricek3

문서

Paper Fetcher

Fetch academic papers from Sci-Hub given a DOI. Automatically downloads PDFs and saves them to research/papers/ with clean filenames. Use when the user provides a DOI or requests a paper from PubMed.

dvcrn3

Bio Basecalling

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.

zja20042

Microbiology

Study of microorganisms including bacteria, viruses, fungi, and parasites

ffsshhttiikk2

Gtex Database

Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, understanding tissue-specific expression, and interpreting non-coding variant effects.

Depmap

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.

Microbiology Expert

Expert-level microbiology covering bacterial and viral biology, microbial physiology, pathogenesis, antimicrobial resistance, microbiome science, and industrial microbiology.