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…
Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry.
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.
Pharmacology agent for ADME/PK profiling of drug candidates from SMILES. Computes drug-likeness (Lipinski Ro5, Veber rules), QED, SA Score, ADME predictions (BBB permeability,…
Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMILES to molecul — from…
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.
Structure safety-first, evidence-based physiotherapy reasoning for a patient case. Use for vaka/case prompts involving symptoms, examination findings, surgery or injury, triage,…
Route physiotherapy/FTR evidence, cases, programs and documentation through safety checks. Prefer medical-evidence-research and physio-clinical-copilot when available; keep…
Structure a physiotherapy initial assessment so the subjective drives the objective and the plan follows from both — the history that localises the problem, the red and yellow…
Appraise rehabilitation PDFs, DOI/PMID, bias, effects and clinical relevance. Use for makale değerlendirme; prefer medical-evidence-research when available.
Use when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels,…
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。
Direct research projects by gathering team feedback and delegating implementation tasks. Writes publication-quality scientific text and coordinates bioinformaticians, software…
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…
Profile a medical-imaging dataset before any modelling decision is made — the acquisition grid, voxel spacing and orientation spread, the intensity domain, which label values are…
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.
Performs pseudo-bulk differential gene expression analysis using DESeq2 or edgeR. Aggregates single-cell counts to sample-level pseudo-bulk data, then identifies differentially…
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).
Plan, configure, validate, and document portable public-bioinformatics data acquisition. Use for GEO/GSE/GDS, SRA/ENA, TCGA/GDC, GTEx, DepMap, public expression matrices, raw…
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.
Generate ~5 actionable research topic recommendations by querying PubMed E-utilities; use when a user provides a research direction/constraints and needs evidence-backed topic…
Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or…
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelin — from…
Use when running molecular quantum chemistry calculations in Python. Computes single-point energies, optimized geometries, vibrational frequencies, and population analysis using…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological — from…
Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET…
Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata…
Use when after feature clustering has been applied to co-eluting LC-MS features and mass-to-charge ratio matching to KEGG has produced an annotated table with adduct assignments.
Rapid topic mastery for video/content prep. Takes a topic → generates 5 research questions → parallel PubMed + web search → outputs McKinsey-style brief in 5 minutes.
Query the QuickGO and Evidence & Conclusion Ontology (ECO) REST API. Use this when you need to map genes to biological processes, molecular functions, or cellular components, find…
Use when when annotating .msp mass spectrometry files with chemical structure metadata and you need fast, offline molecular transformations (SMILES↔InChI, canonical SMILES…
Computes all numeric RDKit molecular descriptors from SMILES strings, filtering out NaN, constant, and infinite values to produce a clean feature matrix.