Retrieves scientific papers from PubMed and creates plain-language research summaries. Use when users ask about medical research, scientific studies, clinical trials, disease…
Matches a user’s biomedical research direction, disease problem, study aim, data modality, and resource constraints to the most relevant recent algorithms and method papers.
Identifies real, evidence-audited, topic-specific research gaps in medical research by first retrieving and verifying literature from trusted sources, then mapping the current…
Résume prudemment des articles, recommandations ou contenus médicaux. À utiliser quand l'utilisateur demande une synthèse scientifique, une revue rapide, ou veut comprend — from…
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
Investigador médico senior. PubMed, evidencia clínica, systematic reviews, guidelines, farmacología.
Generate daily or on-demand medical research briefs for any medical specialty. Searches latest research from top-tier journals, delivers concise summaries with 1-sentence…
Vector database retrieval and evidence-based answering for medical research topics. Use when users need knowledge-base-backed answers about methodology, disease mechanisms, drug…
Use when you have a baseline GNN model for predicting a continuous molecular property (e.
Medical literature search strategy generator. Given a user's natural-language description (e.g., meta-analysis topic, PICOS elements, research question), automatically extract…
Use when you have a set of candidate metabolites for an unknown compound detected in a liquid chromatography–mass spectrometry (LC-MS) experiment, predicted RTs from a trained DNN…
Use when you have peak-abundance data (after molecular formula assignment, peak filtering by m/z, isotope, ppm error, and sample presence thresholds) and you need to quantify and…
Use when after running RAMClustR clustering on XCMS-detected LC-MS features in positive ionization mode, when you need to assign molecular weights to compound clusters and want to…
Use when after running do.findmain on a RAMClustR-clustered object to infer molecular weights and assign features to compound clusters, when you need to conduct structural…
Use when you have a measured m/z value from spatially-resolved metabolomics or mass spectrometry imaging and need to assign a molecular formula with high confidence.
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to identify probable metabolites or degradation products in a specific biological — from…
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to predict its metabolic fate across one or more biological systems.
Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or…
Use when you have two or more mass spectral libraries in different formats (NIST binary exports converted to MSP, MoNA downloads, RIKEN public databases, GNPS MGF, or batches of…
Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural…
Use when when you have raw or GNPS-processed MS2 spectral data from microbial strains and need to organize spectra into molecular families (grouped by spectral similarity) while…
Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads).
Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs.
Use when when analyzing DNA methylation data from bisulfite sequencing (RRBS, target-capture, or whole-genome) and the dataset is too large to fit comfortably in memory, or when…
Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL…
Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single…
Battle-tested PyTorch training recipes for all domains — LLMs, vision, diffusion, medical imaging, protein/drug discovery, spatial omics, genomics.
Prepare, validate, and submit UMA/fairchem machine-learning interatomic potential calculations on Genkai with the established PJM launcher and UMA virtual environment.
Use when when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you…
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation.
Use when you have a pre-trained GNN model for CCS prediction and need to verify that it generalizes to test data that was held out during training.
Use when a deep learning model for molecular structure prediction (e.g., NMR2Struct) has been trained and evaluated on a limited molecular size range (e.
Deterministic validity / synthesizability / drug-likeness gate over GENERATED molecules with karyon — reject invalid, unsynthesizable, or out-of-range candidates with named…
Use when targeting Molecular Biology and Evolution (MBE) or deciding whether a molecular evolution manuscript fits this venue.
分子生物学设计与验证范畴路由。用于 PCR/qPCR 引物探针、CRISPR sgRNA pegRNA donor、限制性酶切和克隆图谱、质粒注释、RNA 二级结构和结构探针等实验设计任务，选择具体 skill 并生成可执行交接物。
Use when after a trained CNN model has generated molecular embeddings for query spectra, and you need to retrieve the most likely candidate molecules from a reference database.
Use when you have a curated dataset of small molecules with SMILES, optional 3D coordinates, adduct information, and experimentally measured CCS values (in Ångströms or similar…
Use when targeting Molecular Cell (Mol Cell) or deciding whether a molecular-biology manuscript fits this Cell Press venue.
Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredic — from…
Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational…
Use when you have 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its…
Use when when setting up a ViMMS chemical sampling environment and you need to restrict the chemical search space to a specific m/z range (e.g., 100–1000) and MS level (e.g., MS1…
Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and…
Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
Use when when you have a query mass spectrum and a set of candidate molecular structures (as SMILES or 2D/3D coordinates), and you need to prepare them for cross-view similarity…
Use when when you have validated SMILES strings or canonical molecule objects from RDKit and need to convert them into the fixed-size numerical tensor format expected by a deep…
Use when you have a collection of chemical structures (SMILES, InChI, SDF, or mol formats) and need to train or apply a machine learning model for retention time prediction or…
OneScience 小分子生成与药物设计模型 skill。用于 MolSculptor 的 SMILES/分子图、autoencoder、latent diffusion、分子优化、reward、DSDP/docking 相关 case、训练和推理任务。
Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD,…
Use when targeting Molecular Ecology (Mol Ecol) or deciding whether a manuscript applying molecular approaches to ecological, evolutionary, or conservation questions fits this…
Use when you have downloaded and extracted a GNPS archive (from METABOLOMICS-SNETS,
Use when you have untargeted metabolomics peak intensity data and spectral groupings (Molecular Families or Mass2Motifs) but lack confident chemical annotations or want to avoid…
Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties…
Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a…
Use when you have annotated metabolite structures (with SMILES strings) from a reference library (e.
Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract…
Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES),…
Use when when evaluating how well mass spectral similarity scores correlate with actual chemical structure for annotated spectral pairs (e.g., spectra with InChIKey metadata).
Use when you have a calibrated FT-ICR transient (ESI_NEG or similar ionization mode) and need to annotate each detected m/z peak with its most likely elemental composition.