Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening and drug discovery.

jackspace14

科学計算

Hmdb Database

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

Supraforge14

LLM・AI

Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.

Supraforge14

デバッグ

Gene Database

Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

Supraforge14

ナレッジベース

Research Management

Manage research documentation in workspace platforms. Structures research findings, sources, and analysis in organized research databases.

Supraforge14

スクリプティング

Killo Golden

根据论文目录下的跟踪文档, 选取最容易实现的未实现任务, 进行科研论文编写工作

loning14

ドキュメント

Paper Writer

Medical/scientific paper writing workflow skill. Manages the full pipeline from literature search to submission-ready manuscript. Creates and manages a project directory with IMRAD-format section files, literature matrix, reference management, and quality checklists. Supports both English and Japanese papers. Triggers: 'write paper', 'paper-write', 'start manuscript', '論文を書く', '論文執筆', '論文プロジェクト', 'manuscript', 'research paper', '原稿作成'.

kgraph5714

デバッグ

Metabolomics Workbench Database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

Supraforge14

科学計算

Etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

jackspace14

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fMRI Skill (Modality Layer)

Use this skill whenever the user wants to perform fMRI preprocessing, first-level analysis, ROI extraction, functional connectivity, effective connectivity, or atlas-based alignment to MNI152 space using either fMRIPrep, HCP-style pipelines, or CONN Toolbox. Triggers include: 'fmri', 'fMRI analysis', 'functional connectivity', 'effective connectivity', 'ROI extraction', 'seed-based correlation', 'PPI', 'DCM', 'atlas alignment', 'MNI152', 'HCP pipeline', 'CONN toolbox', or any request involving BOLD data.

CUHK-AIM-Group14

デバッグ

FreeSurfer Tool

Use this skill whenever the user wants to process structural MRI data (T1w, T2w, FLAIR, etc.) with FreeSurfer, especially for cortical/subcortical segmentation, surface reconstruction, parcellation, cortical thickness, volume statistics, or full recon-all pipeline. Triggers include: 'freesurfer', 'recon-all', 'segment MRI', 'FreeSurfer processing', 'cortical segmentation', 'subcortical segmentation', 'run recon-all', 'freesurfer T1', 'process brain MRI with freesurfer', 'aseg aparc', or any request to run FreeSurfer on NIfTI MRI data for research analysis.

CUHK-AIM-Group14

システム管理

Hcp Skill

Use this skill whenever the user wants an end-to-end workflow for the HCP Young Adult dataset, including dataset download, organization, and multimodal processing of sMRI, fMRI, and DTI. Triggers include: 'HCP Young Adult', 'HCP1200', 'process HCP data', 'HCP sMRI fMRI DTI', or any request to run the full HCP multimodal pipeline. This is the NeuroClaw modality-orchestration layer: it plans WHAT to do and delegates execution to other skills.

CUHK-AIM-Group14

計算化学

Fmriprep Tool

Use this skill whenever the user wants to perform standardized preprocessing of functional MRI (fMRI) and anatomical MRI data using fMRIPrep. Triggers include: 'fmriprep', 'fMRIPrep', 'fMRI preprocessing', 'BIDS fMRI', 'run fmriprep', 'preprocess bold', 'BOLD preprocessing', 'anatomical preprocessing', or any request involving BIDS-organized fMRI datasets.

CUHK-AIM-Group14

LLM・AI

cuhk-aim-group-neuroclaw-skills-research-idea-skill-md

Use this skill whenever the user wants to generate or refine a research idea through literature search and discussion. Triggers include: 'research idea', 'brainstorm idea', 'generate idea', 'research-idea', 'idea generation', 'discuss new direction', or any request to explore literature and output to IDEA.md. This skill is the **mandatory interface-layer idea generator** in NeuroClaw: it calls networking search skills to retrieve recent papers, identifies gaps/trends, then iteratively discusses with the user to finalize a structured idea, always saving the result as IDEA.md.

CUHK-AIM-Group14

データエンジニアリング

Bids Organizer

Use this skill whenever the user wants to automatically organize raw neuroimaging data (DICOM, NIfTI, EEG, etc.) into a valid BIDS (Brain Imaging Data Structure) dataset. Triggers include: 'organize to BIDS', 'BIDS organizer', 'convert to BIDS', 'BIDS conversion', 'bidsify', 'create BIDS dataset', 'raw data to BIDS', or any request to structure data according to BIDS specification.

CUHK-AIM-Group14

バイオインフォマティクス

Scikit Bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Supraforge14

バイオインフォマティクス

Gtars

High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

Supraforge14

バイオインフォマティクス

String Database

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.

Supraforge14

バイオインフォマティクス

Geo Database

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

jackspace14

計算化学

Pdb Database

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

jackspace14

学術

Literature Review

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

jackspace14

学術

Peer Review

Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.

jackspace14

バイオインフォマティクス

Pyopenms

Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.

jackspace14

計算化学

Pytdc

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

jackspace14

計算化学

Diffdock

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

jackspace14

データエンジニアリング

DICOM to NIfTI conversion

Use this skill whenever the user wants to convert DICOM files or folders to NIfTI format (.nii or .nii.gz), extract neuroimaging volumes from clinical DICOM series (MRI, CT, PET, etc.), prepare raw DICOM data for research processing pipelines, anonymize while converting, or batch-convert multiple series/studies. Triggers include: 'DICOM to NIfTI', 'dcm to nii', 'convert dicom to nii.gz', 'dcm2niix', 'extract nii from dicom', 'batch dicom to nifti', 'prepare dicom for freesurfer/fsl/spm', 'anonymized nifti conversion', or any request to transform clinical DICOM data into analysis-ready NIfTI format while preserving orientation, voxel spacing, slice timing (when available), and important metadata in the JSON sidecar.

CUHK-AIM-Group14

科学計算

Deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

jackspace14

デバッグ

Metabolomics Workbench Database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

jackspace14

科学計算

Hmdb Database

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

jackspace14

計算化学

DrugBank Database

Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.

jackspace14

生化学者・生物物理学者

生化学者・生物物理学者

Zinc Database

Hmdb Database

Denario

Gene Database

Research Management

Killo Golden

Paper Writer

Metabolomics Workbench Database

Etetoolkit

fMRI Skill (Modality Layer)

FreeSurfer Tool

Hcp Skill

Fmriprep Tool

cuhk-aim-group-neuroclaw-skills-research-idea-skill-md

Bids Organizer

Scikit Bio

Gtars

String Database

Geo Database

Pdb Database

Literature Review

Peer Review

Pyopenms

Pytdc

Diffdock

DICOM to NIfTI conversion

Deeptools

Metabolomics Workbench Database

Hmdb Database

DrugBank Database