Submit compact NCBI Datasets v2 requests for assembly, genome, taxonomy, and related metadata endpoints.
Drafts an eCTD-compliant New Drug Application (NDA) for FDA submission under 21 CFR Part 314. Compiles clinical trial data, CMC documentation, nonclinical studies,…
Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.
Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo…
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public data — from…
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Dataflow workflow engine for scalable bioinformatics pipelines. Defines processes (containerized tasks) connected by channels; runs local, HPC (SLURM/SGE), cloud (AWS/GCP/Azure),…
Run or plan bulk RNA-seq FASTQ-to-count processing with sample-sheet, strandedness, genome annotation, alignment or pseudoalignment, MultiQC, and count-matrix QC checks.
Run or plan targeted DNA panel variant workflows that use UMIs, duplex consensus reads, molecular barcodes, low-frequency calling, target coverage, and panel-specific QC.
Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal…
Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API.
Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph…
Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other…
Rules for categorizing notes into planning, programming, and biology directories. Includes keyword matching, file formatting, and special commands like TODO archival.
Use when after applying a quantitative analysis function (e.g., cooltools.insulation, contact frequency calculations) to Hi-C cooler files or other genomic datasets, validate that…
Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants.
Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).
Submit compact AlphaFold Protein Structure Database API requests for prediction, UniProt summary, sequence summary, and annotation lookups.
Submit compact Human Protein Atlas requests for gene JSON, search downloads, and page-level tissue or cell-line lookups.
Submit, poll, and summarize NCBI BLAST Common URL API jobs (Blast.cgi) for nucleotide or protein sequences.
Codex adaptation of the OpenClaw Medical Skills library. Use for biomedical, clinical, healthcare AI, genomics, bioinformatics, drug discovery, pharmacovigilance, clinical trials,…
Use when when a project JSON document contains genome identifiers but lacks corresponding organism name annotations, and you need to link MS/MS mass spectra with genomic context…
Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hier — from…
Clinical research outcome extraction for meta-analysis. Use when users need to extract outcome measures (binary, continuous, or survival data) from clinical research papers for…
Use when code imports `ovito`, or user asks to render molecular snapshots / animations from LAMMPS, XYZ, GSD, PDB, CIF or POSCAR files.
Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragment_paired'] or .
Generates comprehensive academic introductions for biological pathways, including signaling processes, markers, and inhibitors.
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and — from…
Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands).
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and — from…
Use when you have two related compounds (a known reference and its structural analog with unknown modification site), baseline peak annotations from cosine alignment, and newly…
Use when you have raw LC-MS/MS spectra from vendor instruments (mzML, mzXML, MGF, or MSP format) with variable peak quality and intensity distributions, and you plan to perform…
Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover…
Use when when you have loaded aligned peak-alignment data from a molecular networking task and need to distinguish high-confidence, reproducible peak alignments from noise or…
Use when after applying cluster-based filtering with quasi-molecular adducts and frequency thresholds on candidate metabolites from KEGG matching.
Use when after applying cluster-based filtering with quasi-molecular adduct constraints and frequency thresholds on LC-MS feature candidates, when some peaks have been entirely…
Use when you have a pretrained model with documented performance on a bounded input domain (e.g., molecules ≤19 heavy atoms, sequences <1000 bp) and you need to establish whether…
6 pharmaceutical research skills. Trigger: drug discovery, pharmacology, clinical trial design, regulatory filing.
Run phi CLI commands for the dyno protein analysis platform: fetch structures, run folding/inverse-folding pipelines (ESMFold, AlphaFold2, ProteinMPNN), filter and score…
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree.
Use when targeting PLOS Biology (PLOS Biol) or deciding whether a general biology manuscript fits this open-access venue.
Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control.
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF…
Playbook for implementing/porting a new biomolecular model (protein folding, structure prediction, protein language model, diffusion structure head, MSA encoder, etc.) onto…
Run a deterministic physical-validity DRC over molecular docking poses with karyon. Use for pose validity, PoseBusters-style geometric checks,…
Use when after molecular formula assignment has been performed on FT-ICR MS peaks and you need to remove assignments with unacceptable mass error before proceeding to…
Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
PCR、qPCR、测序引物和探针设计 skill。用于设计或验证 primer pair、TaqMan probe、molecular beacon、amplicon、Tm GC 二聚体发夹、SNP/repeat 避让和特异性检查交接。
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute differential expression statistics, especially when the n — from…
Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation — from…
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq.
Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.
Patterns for protein structure prediction using AlphaFold2/ColabFold, structural analysis, model quality assessment, and integration with experimental data.
protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing.
Use when you have SMILES-encoded molecular structures and need to model their behavior under electrospray ionization (ESI) or other ionization methods in mass spectrometry.
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text.
Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies.