Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
Evaluate research artifacts against NDSS badge criteria (Available, Functional, Reproduced) by checking DOI, documentation, exercisability, and reproducibility requirements.
Analyze geospatial data using geopandas with proper coordinate projections. Use when calculating distances between geographic features, performing spatial filtering, or working with plate boundaries and earthquake data.
Matched filtering techniques for gravitational wave detection. Use when searching for signals in detector data using template waveforms, including both time-domain and frequency-domain approaches. Works with PyCBC for generating templates and performing matched filtering.
Hex grid spatial utilities for offset coordinate systems. Use when working with hexagonal grids, calculating distances, finding neighbors, or spatial queries on hex maps.
Data conditioning techniques for gravitational wave detector data. Use when preprocessing raw detector strain data before matched filtering, including high-pass filtering, resampling, removing filter wraparound artifacts, and estimating power spectral density (PSD). Works with PyCBC TimeSeries data.
Analyzes 3D mesh files (STL) to calculate geometric properties (volume, components) and extract attribute data. Use this skill to process noisy 3D scan data and filter debris.
An overview of the python package for running the GaMMA earthquake phase association algorithm. The algorithm expects phase picks data and station data as input and produces (through unsupervised clustering) earthquake events with source information like earthquake location, origin time and magnitude. The skill explains commonly used functions and the expected input/output format.
Read and process GLM output files. Use when you need to extract temperature data from NetCDF output, convert depth coordinates, or calculate RMSE against observations.
Analyze images and multi-frame sequences using OpenAI GPT vision models
Analyze images and multi-frame sequences using OpenAI GPT series
Count occurrences of an object in the image using computer vision algorithm.
Solving finite-horizon LQR via dynamic programming for MPC.
Define custom distance/similarity metrics for clustering and ML algorithms. Use when working with DBSCAN, sklearn, or scipy distance functions with application-specific metrics.
Generate dynamic-object binary masks after global motion compensation, output CSR sparse format.
Combine multiple segment detection results into a unified list. Use when you need to merge segments from different detectors, prepare removal lists for video processing, or consolidate detection outputs.
Standardize video sampling and frame indexing so interval instructions and mask frames stay aligned with a valid key/index scheme.
Calibrate GLM parameters for water temperature simulation. Use when you need to adjust model parameters to minimize RMSE between simulated and observed temperatures.
Detect pauses and silence in audio using local dynamic thresholds. Use when you need to find natural pauses in lectures, board-writing silences, or breaks between sections. Uses local context comparison to avoid false positives from volume variation.
Use this skill when reading sensor data from CSV files, writing simulation results to CSV, processing time-series data with pandas, or handling missing values in datasets.
Perform statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
OmicVerse plotting: volcano, venn, boxplot, embedding, density, heatmap families, dotplot, convex hull, stacked bar, and Forbidden City color palettes.
