Use when you have tandem MS spectra from structurally related or known compounds and need to decide which similarity metric will maximize correct ranking of related molecules in a…
Use when when you have a USI (Universal Spectrum Identifier) string referencing a spectrum in a public metabolomics repository (GNPS Molecular Networking, GNPS Spectral Libraries,…
Use when when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a…
Use when you have raw MS/MS spectra in MGF or other standard formats that need to be ingested into a machine learning pipeline for cross-modal matching against molecular…
Use when you have parsed LC-MS/MS spectral data (precursor m/z, ionization mode, collision energy, and a list of fragment m/z and intensity pairs) and need to submit it to the…
Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions.
Set up your bio-research environment and explore available tools. Use when first getting oriented with the plugin, checking which literature, drug-discovery, or visualization MCP…
Recommend appropriate statistical tests (T-test, ANOVA, Mann-Whitney, etc.) based on data type, distribution, sample size, and research design.
Use when you have a metabolite abundance table (rows=metabolites, columns=samples)
Use when you have RNA-seq count matrices (from alignment, transcript quantification, or HTSeq-count files) and need to test for differential expression between two or more…
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for system — from…
Use when after executing a molecular structure prediction model on spectroscopic
Use when when you have tandem mass spectra (MSMS) from related or candidate molecules and need to determine which similarity metric—cosine, modified cosine, or neutral loss— ranks…
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RER — from…
Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.
Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to…
Use when you have created a GNPS molecular network (either classical or feature-based) and have computed MS2LDA motif assignments (probability and overlap scores) for the same…
Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anch — from…
Use when you are preparing to run a complex multi-tool bioinformatics pipeline (such as HiC-Pro) on a new system or cluster, and need to confirm that all required binaries exist…
Use when wiring LLM APIs to bioinformatics analysis result tables in this repository, especially when users ask to interpret DEG, enrichment, ssGSEA, pathway-map, or…
Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required.
Use when you have a collection of molecular fingerprint vectors (such as biosynfoni count fingerprints) and need to measure structural similarity between all pairs of molecules.
Use when the user asks about TBtools, TBtools-II, TBtools RPC API, TBtools CLI, or bioinformatics operations available through TBtools such as sequence manipulation, BLAST,…
生物作业生成 Skill是面向班级作业的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: teacher_biology_homework_generation.run.
生物单元复习 Skill是面向单元复习的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: teacher_biology_unit_review.run.
Use when when you have validated SMILES strings or RDKit molecule objects representing chemical structures and need to feed them into a pre-trained deep learning model (such as…
Use when targeting The EMBO Journal (EMBO J) or deciding whether a mechanistic molecular biology manuscript fits this venue.
Use when targeting The Plant Cell or deciding whether a plant biology manuscript fits this venue. Encodes the journal's fit, framing, method-and-evidence bar, house style,…
Use when targeting The Plant Journal or deciding whether a plant-science manuscript fits this venue. Encodes the journal's fit, the mechanistic gene-to-function and…
Use when when you have peak-abundance .csv files with assigned molecular formulas (elemental composition: C, H, O, N, P, S) from FT-ICR MS or high-resolution MS and need to…
Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both…
Exhaustive problem space exploration using the MIT Synthetic Neurobiology "tiling tree" method. Partitions a problem into MECE (Mutually Exclusive, Collectively Exhaustive)…
Use when converting medical text between academic and patient-friendly tones, translating medical jargon for patients, adapting research papers for public audiences, or rewriting…
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches.
Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs…
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks…
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections.
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG…
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3…
Neuroscience research workflows: neuroanatomy, neural circuits, neurotransmitter biology, neurological/psychiatric disease genetics, neural-protein function.
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance…
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.
Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering.
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.
Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering,…
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels).
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug…
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions.
Research any topic end to end and get back a fact-checked, branded HTML report plus an agent-readable markdown brief.
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reaso — from…
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reaso — from…
Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, G — from…