Use when you receive mass spectrometry data through heterogeneous identifier formats—specifically when the input could be a GNPS Task ID, a Universal Spectrum Identifier (USI), or…
Use when you have experimental MS/MS spectra and need to assign definitive molecular identities by matching against a curated spectral library.
Use when user requests medical/pharmaceutical market sizing, Chinese clinical pathway reconstruction, patient flow waterfall charts, drug usage composition analysis, unmet need…
Implement a generative diffusion model (DDPM or score-based) with noise scheduling, U-Net architecture, training loop, and sampling procedures including DDIM acceleration.
Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real…
Use when when you have loaded aligned peak data (from a preceding molecular networking alignment task) as a structured table with peak intensity, m/z, retention time, and…
Systematically interpret nuclear magnetic resonance spectra (1H, 13C, DEPT, and 2D experiments) to elucidate molecular structure.
Structures microbiology result interpretation with susceptibility patterns and resistance mechanisms.
Structures molecular test interpretation including NGS panels, FISH, and PCR-based assays. Use when interpreting molecular results, reporting genetic variants, or documenting…
Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein…
Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that…
Use when training a contrastive encoder on mass spectrometry imaging (MSI) data in ISO mode (isotope ions from the same molecule).
Use when you have TWIM-MS experimental data with assigned biomolecular class labels (e.g., peptides, lipids, carbohydrates) and arrival time measurements, and you need to compute…
Use when you have a curated dataset of molecular structures (or molecular descriptors) paired with experimentally measured or reference collision cross section values, and you…
Use when when you have SMILES strings representing neutral organic molecules and need to enumerate the likely protonated (e.g., [M+H]+) and deprotonated (e.
Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinc — from…
Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs.
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for…
Use when when your project JSON document contains public identifiers (genome IDs, biosample accessions, etc.) that lack human-readable or linked metadata, and you need to populate…
Use when after enriching a project JSON document with external metadata (e.g., organism names, genome identifiers) or before writing enriched JSON to disk.
Julia package equivalents for 137 K-Dense-AI scientific skills. Maps Python bioinformatics, chemistry, ML, quantum, and data science packages to native Julia ecosystem.
初中生物考试复习 Skill是面向中考复习、考前冲刺的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: junior_biology_exam_review.run.
初中生物快速巩固 Skill是面向每日打卡、同步巩固的产品级 Hermes Skill，年级、册别、单元、知识点和难度通过参数传入。 Workflow: junior_biology_quick_practice.run.
Use when you have a curated training dataset of molecular structures with known CCS values, a target set of ≤10,000 molecules requiring CCS predictions, and need to apply a…
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill.
Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network…
Use when you have paired-end Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited) and need to produce standardized .hic binary contact maps that conform…
Use when you have raw Hi-C FASTQ data and need to generate contact maps at kilobase resolution, or you have pre-generated .hic files and need to annotate structural features…
Use when after completing all per-sample annotation steps (molecular networking, ISDB/spectral matching, SIRIUS/CSI:FingerID, and compounds metadata enhancement with Wikidata IDs…
Open-source FAIR biology data framework. Version artifacts (AnnData, DataFrame, Zarr), track lineage, validate via ontologies (Bionty), query datasets.
Use to satisfy The Lancet's clinical-ethics and research-integrity requirements — ethics-committee approval and informed consent under the Declaration of Helsinki, the Declaration…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakema — from…
Rewrites technical research content into a structured lay summary that cross-disciplinary teams can quickly understand and act on.
Use when you have processed the same set of untargeted LC/HRMS files (mzXML, mzML, or netCDF format) with two or more peak-picking tools and need to validate which tool produces…
Generate a dedicated Obsidian learning vault for any certification, course, or study goal. Creates structured notes with domains, concepts, lessons, scenarios, MoCs, dataview…
Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
Query PubMed and scientific databases for protocols, analyze biological data with Biopython, handle HIPAA-compliant data.
Orchestrates the cell-free DNA / liquid-biopsy pipeline from plasma sequencing to tumor monitoring, forking tumor-naive (screening) vs tumor-informed (MRD), and chaining — from…
Use this bioinformatics data analysis skill to construct a database-driven lncRNA-mRNA regulatory network from target lncRNA and/or gene lists by projecting shared miRNA evidence…
Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization.
Configure the local wisp-science runtime — uv/Python bootstrap, Node+scimaster-cli for bear-* literature skills, pixi for bioinformatics multi-env analysis.
Map GWAS loci to ranked candidate genes using a deterministic multi-skill chain (EFO -> GWAS -> coordinates -> Open Targets L2G/coloc -> eQTL -> burden/coding context), w — from…
Use when when you have generated multiple 3D conformations for a molecule or set of ionized adducts (e.g., via RDKit) and need to retain only the most energetically favorable…
Use when you have molecular descriptors or fingerprints for a set of compounds (e.g., from LC-MS metabolomics) and need to predict a continuous property—such as HPLC retention…
Use when when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages,…
Structures trial budget development with per-patient costs, site fees, and sponsor negotiations. Use when budgeting clinical trials, negotiating site contracts, or tracking…
Applies GCP/ICH principles to clinical research operations with compliance monitoring. Use when ensuring GCP compliance, training on ICH guidelines, or auditing research practices.
Use when when you have a set of candidate molecular formulae for a measured m/z value and need to rank them by how closely their theoretical m/z matches the observed value.
Use when when processing raw FT-ICR transient data (e.g., ESI_NEG_SRFA.d) that requires assignment of molecular formulas to experimental m/z peaks.
Use when after chromatographic peak detection on preprocessed LC-MS data, when you have detected features (peaks) in multiple samples and need to establish which peaks ac — from…
Use when processing feature lists from LC- or GC-HRMS data (in mzML format or as custom feature tables with m/z and molecular formula columns) and you need to flag potential PFAS…
Use when you have a filtered peak list (CSV with m/z values and assigned molecular formulas) from FT-ICR MS and want to infer biochemical transformations occurring in microbial or…
Use when when generating a virtual chemical mixture for LC-MS/MS simulation, or when sampling molecular formulas from a metabolite database (such as HMDB), you need to restrict…
Use when you have raw or processed FT-ICR MS spectra with detected peaks (m/z values) and need to: (1) assign elemental compositions to each peak, (2) filter assignments by mass…
Plan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle distributions, stress-strain…
Bridges a traditional healing concept to modern neuroscience and physiology, naming what's established versus speculative.
Fetch medical references (PubMed, PMC, EuropePMC, RACGP/ACRRM/AMC exam reports, AJGP, AIHW, ClinicalKey, UpToDate, AMH, eTG, Murtagh, plus 8 generic publishers via USyd…
Use medical cv resume builder for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.