Query BRENDA Enzyme Database for kinetic parameters (Km, Vmax, kcat, Ki), enzyme classifications, substrate specificity, inhibitors, cofactors, and organism-specific enzyme data via SOAP/REST API. 80,000+ enzyme entries, 7M+ kinetic values. Requires free academic registration. For metabolic pathway modeling use cobrapy-metabolic-modeling; for metabolite structures use hmdb-database.
Deep learning cell and nucleus segmentation from fluorescence and brightfield microscopy images. Uses pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm that segments cells without requiring retraining on new image types. Outputs label masks for downstream morphology measurement and tracking. Use scikit-image watershed for rule-based segmentation; use Cellpose when deep learning generalization across staining conditions is needed.
Computational molecular biology toolkit for sequence manipulation, file I/O (FASTA/GenBank/PDB), NCBI database access (Entrez), BLAST automation, pairwise/multiple sequence alignment, protein structure analysis (Bio.PDB), and phylogenetic tree construction. Use for batch sequence processing, custom bioinformatics pipelines, format conversion, and programmatic PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
Route upstream epistemic deficits and evaluate execution-time risks during AI operations. Scans for unresolved upstream protocol needs, materializes intent into tasks, classifies each for risk signals, delegates low-risk tasks to executor, and surfaces elevated-risk findings for user judgment. Type: (ExecutionBlind, User, EVALUATE, ExecutionContext) → SituatedExecution. Alias: Prosoche(προσοχή).
Python library for analyzing molecular dynamics (MD) trajectories from GROMACS, AMBER, NAMD, CHARMM, and LAMMPS. Reads topology and trajectory files into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, hydrogen bond analysis, PCA, and custom distance/angle calculations across millions of frames. Use for structural analysis after MD simulations; use OpenMM or GROMACS directly for running simulations.
Pythonic wrapper around RDKit with simplified interface and sensible defaults for drug discovery cheminformatics. Use for SMILES parsing, molecular standardization, descriptor computation, fingerprints, similarity search, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformer generation, and molecular visualization. Returns native rdkit.Chem.Mol objects. Prefer datamol over raw RDKit for standard workflows; use RDKit directly for advanced control or custom parameters.
Mass spectrometry data processing with PyOpenMS. Use for LC-MS/MS proteomics and metabolomics workflows — mzML/mzXML file I/O, signal processing (smoothing, peak picking, centroiding), feature detection and linking across samples, peptide/protein identification with FDR control, untargeted metabolomics pipelines. For simple spectral matching and metabolite ID, use matchms instead.
PathML is an open-source toolkit for computational pathology. Use it to process whole-slide images (WSIs): load slides, extract tiles, apply stain normalization and nuclear segmentation preprocessing, extract features, and train machine learning models. Supports H&E and multiplex imaging. Ideal for building end-to-end digital pathology pipelines from raw WSI files to quantitative outputs.
NeuroKit2 is a Python toolkit for neurophysiological signal processing. Process ECG (heart rate, HRV, R-peak detection), EEG (complexity, power spectral density), EMG (muscle activation onset), EDA/GSR (skin conductance, SCR decomposition), PPG (photoplethysmography), and RSP (respiration) signals. Simulate synthetic signals for testing. Alternatives: BioSPPy (older, less maintained), MNE (EEG/MEG specialist), heartpy (ECG only), scipy.signal (raw DSP without biosignal abstraction).
Pipeline for analyzing Neuropixels extracellular electrophysiology recordings. Covers probe geometry loading (ProbeInterface), spike sorting with Kilosort via SpikeInterface, quality metrics computation, unit curation (ISI violations, firing rate, signal-to-noise), and post-sort analysis (PSTH, tuning curves, population decoding) using pandas and matplotlib. Designed for acute and chronic Neuropixels 1.0/2.0/Ultra recordings from rodent and primate experiments.
Query COSMIC (Catalogue Of Somatic Mutations In Cancer) for cancer somatic mutations, gene census data, mutational signatures, drug resistance variants, and cancer gene annotations. REST API v3.1 supports gene/sample/variant queries. Free registration required. For germline clinical variants use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
Retrieve quantitative phenotype measurements across inbred mouse strains from the Mouse Phenome Database (MPD) for metabolic, behavioral, and physiological traits. Query strain means and raw individual measurements for body weight, glucose, blood pressure, behavioral assays, and 40+ additional procedures. Use for QTL analysis support, cross-strain phenotype comparison, and identifying mouse models for metabolic or behavioral traits. For mouse gene-disease-phenotype associations use monarch-database; for mouse genome annotations use ensembl-database.
Our preferred stars for celestial navigation and astronomical reference
Expert patterns for combat systems including hitbox/hurtbox architecture, damage calculation (DamageData class), health components, combat state machines, combo systems, ability cooldowns, and damage popups. Use for action games, RPGs, or fighting games. Trigger keywords: Hitbox, Hurtbox, DamageData, HealthComponent, combat_state, combo_system, ability_cooldown, invincibility_frames, damage_popup.
Expert blueprint for physics queries using RayCast, ShapeCast, and DirectSpaceState. Covers hit detection, volume overlap, mouse picking, and high-performance server-side intersection queries. Use when implementing projectiles, LOS, terrain grounding, or AI sensors. Keywords raycast, shapecast, direct_space_state, intersect_ray, intersect_shape, PhysicsRayQueryParameters, collision mask, mouse picking.
Guide for completing Coq proofs involving arithmetic properties like addition commutativity. This skill should be used when working on Coq proof files that require proving properties about natural number arithmetic using induction, particularly when lemmas like plus_n_O and plus_n_Sm are involved.
Engages structured analysis to explore multiple perspectives and context dependencies before responding. Use when users ask confirmation-seeking questions, make leading statements, request binary choices, or when feeling inclined to quickly agree or disagree without thorough consideration.
Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
Conduct enterprise-grade research with multi-source synthesis, citation tracking, and verification. Use when user needs comprehensive analysis requiring 10+ sources, verified claims, or comparison of approaches. Triggers include "deep research", "comprehensive analysis", "research report", "compare X vs Y", or "analyze trends". Do NOT use for simple lookups, debugging, or questions answerable with 1-2 searches.
Research workflow patterns specific to {project}. Covers research agent coordination, source management, and synthesis strategies.
Use this skill for requests related to web research; it provides a structured approach to conducting comprehensive web research.
Analyzes prose for grammar errors, style inconsistencies, clarity issues, and readability problems. Provides specific suggestions for improvement while preserving the author's unique voice. Use when the user needs help polishing their writing, improving clarity, or maintaining consistent style.
Smart article illustration skill. Analyzes article content and generates illustrations at positions requiring visual aids with multiple style options. Use when user asks to "add illustrations to article", "generate images for article", or "illustrate article".
Generates comprehensive chapter outlines for books, including key topics, subtopics, learning objectives, and estimated word counts. Use this when the user needs help structuring a book chapter or creating a table of contents.
