Use when you have output from a biotransformation rules module (candidate transformed structures linked to anchor molecules) and untargeted MS/MS spectral data, and you want to…
Use when you have one or more small-molecule chemical structures (as SMILES, MOL, or SDF) and need to systematically explore their fate across mammalian biotransformation, human…
Use when you have untargeted metabolomics data with unknown or ambiguous molecular identities, anchor metabolites (known structures in SMILES or MOL format), and a curated…
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information.
Use when you need to represent natural product molecules as fixed-length bit vectors for downstream machine learning (e.
Provide specialist medical checkup and lab-tracking evidence from local documents when `body-data-qa` or `body-cadence-review` needs medical-domain depth, or when the user…
Design new protein binders with Boltz. Use when generating protein, peptide, antibody, nanobody, or custom binder candidates for a target.
Screen existing protein binders with Boltz. Use when ranking a supplied protein, peptide, antibody, nanobody, or binder library against a target.
Predict Tier-1 ADME/ADMET for small molecules with Boltz from bare SMILES — no target, no docking. Use when the user wants solubility, permeability, or lipophilicity/logD for a…
Design new small-molecule binders with Boltz. Use when generating novel ligands or hits for a target without a fixed compound library.
Screen existing small-molecule libraries with Boltz. Use when docking, scoring, or ranking a supplied SMILES or compound library against a target; also returns free Tier-1…
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation — from science/biology-medicine
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation — from science/biology-medicine
Calculate precise buffer recipes with accurate mass and volume measurements for molecular biology and biochemistry.
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment.
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment.
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment.
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts),…
Generate phylogenies from genome assemblies using BUSCO/compleasm-based single-copy orthologs with scheduler-aware workflow generation — from science/biology-medicine
Guide to interpreting BUSCO completeness statuses: why Duplicated BUSCOs count as complete, parsing output files, computing/comparing completeness across proteomes/genomes, common…
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome. — from science/biology-medicine
Use when targeting Cancer Cell or deciding whether a cancer-biology manuscript fits this venue. Encodes the journal's fit, framing, method-and-evidence bar, house style,…
Use when you have a query mass spectrum and a set of candidate molecular structures, and you need to prioritize candidates by their likelihood of matching the query.
Submit compact cBioPortal API requests for studies, molecular profiles, mutations, clinical data, and samples.
Use when you have structural input data (SMILES or molecular geometry files) for N-Me derived unsaturated sterol lipids and need to generate a predicted CCS dataset indexed by…
Use when targeting Cell (Cell Press) or deciding whether a cell/molecular-biology manuscript fits this flagship venue.
Use first, before any writing, to stress-test whether a study clears Cell's bar — a complete, mechanistic, hypothesis-driven story with converging evidence.
Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template…
Shared author-guideline skill for Cell Press journals that food & nutrition researchers publish in: Cell, Cell Metabolism, Cell Host & Microbe, Molecular Cell, Immunity, Current…
Use when targeting Cell Stem Cell or deciding whether a stem-cell or regenerative-biology manuscript fits this Cell Press venue.
Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to…
Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex…
Submit, monitor, and manage compute jobs on UAB Cheaha (Slurm HPC cluster with CPU/GPU partitions). Use when the user wants to run CPU-intensive or GPU-intensive workloads, train…
Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR s — from…
Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures.
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR stu — from…
Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.
Submit compact ChEMBL API requests for activity, molecule, target, mechanism, and text-search endpoints.
Develop, test, and extend ChemGraph -- an agentic framework for automated molecular simulations using LLMs, LangGraph, ASE, and MCP servers
Ionic, covalent, and metallic bonding, Lewis structures, VSEPR theory, molecular geometry, polarity, and intermolecular forces.
Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes…
Use when you have generated a GNPS molecular network (classical or feature-based
Use when when you have mass-to-charge (m/z) values from mass spectrometry imaging or other MS experiments and need to assign molecular formulae with high precision, especially in…
Use when after a machine learning model has generated predicted molecular structures (connectivity graphs and molecular formulas) from 1D NMR spectra.
Use when you have .msp spectral library files with compound names but lack standardized chemical identifiers (SMILES, InChI, InChI Key, CAS number, IUPAC names, or molecular…
Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared…
Use when you have MS/MS spectra with high chemical noise (spurious ions arising from incomplete ionization, in-source fragmentation, or instrument artifacts) and you possess…
Use when you have MS/MS spectra contaminated with chemical noise (spurious fragment ions that do not correspond to real chemical bonds or rearrangements), a known or predicted…
Use when you have LC-MS/MS data preprocessed with MZmine2 into an MGF file (containing MS1 and MS2 spectra) and a feature table (peak areas per sample), and you want to relate MS1…
Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar…
Use when when you have an unknown metabolite compound with mass spectral data, have retrieved candidate structures from a molecular structure database (PubChem, HMDB), and have…
Use when you have retrieved multiple candidate structures from a molecular structure database (e.g., PubChem, HMDB) for an unknown compound, and you have predictions of…
Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds.
Use when after applying biotransformation rules to generate candidate product structures from input molecules, when the same transformed structure can be produced via multiple…
Use when when you have a set of molecular structures (N-Me derived unsaturated sterol lipids or structurally similar organic molecules with C=C bonds) represented as SMILES or…
Use when you have SMILES strings or molecular structure files (e.g., from a synthetic drug database) and need to feed them into a deep learning model like PS2MS, NEIMS, or DeepEI…
Use when when you have raw molecular structures in SMILES or SDF format that must be prepared as input to a descriptor-based classifier (e.g., BitterPredict).
Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography — from…
Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography — from…