Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the…
Use when you have SMILES strings for candidate novel psychoactive substance structures and need to convert them into a machine-readable molecular representation before computing…
Use when when you have a dataset of molecular structures encoded as SMILES strings that will be processed downstream (e.
Use when you have raw molecular structures in SMILES or SDF format that will feed into BitterPredict.m or other structure-based classifiers.
Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score…
Workflow management system for bioinformatics. Use for creating reproducible and scalable computational biology pipelines.
Run SnpEff, a variant annotation and effect prediction tool for genomic variants. Use when the user wants to annotate VCF files, build genome databases, or use SnpEff utilities.
Use when you have a bioinformatics pipeline (like HiC-Pro) with mixed Python, R, and compiled tool dependencies, and you need to ensure consistent reproducibility across machines…
Use when you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.
Use when when you need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the…
Use when when you have loaded a dataset of molecular fingerprint vectors (such as biosynfoni fingerprints from a Zenodo deposit) and need to quantify how sparse the…
Use when when you have spatial molecular data (e.g., Visium, imaging-based cytometry) stored in an AnnData object with coordinate information in .
Use when you have paired MS/MS spectra (known compound and its structural analog) with assigned precursor m/z, charge, and SMILES; you want to quantify which parts of the…
Use when after running GNPS molecular networking, SIRIUS compound identification,
Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and…
Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular…
Use when you have completed a GNPS1 (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING) or GNPS2 (classical_networking_workflow,…
Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than…
Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural…
Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score…
Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their…
Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, m — from…
Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures…
Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment…
Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name,…
Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown organic compound with ≤19 heavy atoms, and you need to recover its molecular structure (both formula…
Use when when you need to prepare mass spectra and molecular structures for joint modeling in a BART or transformer-based sequence model, and you lack a unified representation…
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…
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…
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 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)…