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Research

Scientific computing and academic tools.

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astronomy-physics
19

obspy

Seismology data processing with ObsPy. Helps with reading seismic waveforms, filtering/processing time series, fetching data from FDSN services, and earthquake analysis. Use when Claude needs to: (1) Read seismic data formats (MiniSEED, SAC, GSE2, SEGY), (2) Filter or process waveforms, (3) Fetch data from IRIS/USGS/FDSN services, (4) Search for earthquakes by magnitude/location, (5) Plot seismograms or spectrograms, (6) Remove instrument response, (7) Analyze station metadata.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

mplstereonet

Stereonet plots for structural geology using matplotlib. Create lower-hemisphere stereographic projections for orientation data. Use when Claude needs to: (1) Create stereonet plots for structural data, (2) Plot planes as great circles or poles, (3) Plot lineations with trend/plunge, (4) Generate density contours for orientations, (5) Calculate mean orientations and statistics, (6) Analyze fold axes with pi-diagrams, (7) Convert between strike/dip and trend/plunge formats.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

pooch

Data file fetching and caching for geoscience applications. Download sample datasets with automatic caching, checksum verification, and multiple download sources. Use when Claude needs to: (1) Download datasets from URLs or DOIs, (2) Cache files locally with automatic verification, (3) Verify file integrity with SHA256/MD5 hashes, (4) Extract compressed archives (ZIP, TAR, GZIP), (5) Create data registries for reproducible workflows, (6) Fetch from Zenodo or other repositories.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

harmonica

Gravity and magnetic data processing and forward modelling using Fatiando a Terra. Use when Claude needs to: (1) Compute gravity forward models (point masses, prisms, tesseroids), (2) Apply terrain/Bouguer corrections, (3) Grid scattered potential field data with equivalent sources, (4) Perform upward/downward continuation, (5) Calculate magnetic anomalies from magnetized bodies, (6) Apply derivative filters (gradients, tilt angle), (7) Process regional or local gravity surveys.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

lasio

Read, write, and manipulate LAS (Log ASCII Standard) well log files for borehole geophysical and petrophysical data. Use when Claude needs to: (1) Read/parse LAS 1.2 or 2.0 files, (2) Extract well headers or curve data, (3) Convert LAS to DataFrame/CSV/Excel, (4) Create new LAS files from arrays, (5) Modify existing LAS files, (6) Handle problematic or malformed LAS files, (7) Batch process multiple well files.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

pygimli

Multi-method geophysical modelling and inversion framework. Use when Claude needs to: (1) Perform electrical resistivity tomography (ERT) inversion, (2) Run seismic refraction tomography (SRT), (3) Model induced polarization (IP) data, (4) Simulate ground penetrating radar (GPR), (5) Create finite element meshes for geophysical problems, (6) Perform joint inversions of multiple datasets, (7) Forward model geophysical responses, (8) Analyze time-lapse monitoring data.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

segyio

Read, write, and manipulate SEG-Y seismic data files. Fast C library with Python bindings for trace, header, inline, and crossline access. Use when Claude needs to: (1) Read/inspect SEG-Y files, (2) Extract trace data or headers, (3) Access 3D survey data by inline/crossline, (4) Create new SEG-Y files from arrays, (5) Modify existing SEG-Y files, (6) Extract subsets of seismic data, (7) Read/write Seismic Unix format.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

disba

Compute surface wave dispersion curves for layered Earth models using the Thomson-Haskell matrix method with Numba acceleration. Use when Claude needs to: (1) Calculate Rayleigh or Love wave phase velocities, (2) Compute group velocity dispersion, (3) Generate sensitivity kernels for inversion, (4) Forward model dispersion curves from velocity profiles, (5) Compare dispersion between different Earth models, (6) Set up surface wave tomography workflows.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

gemgis

Spatial data processing for geological modelling with GemPy. Use when Claude needs to: (1) Prepare spatial data for GemPy models, (2) Extract interface points from geological maps, (3) Process orientations/dip measurements, (4) Sample DEMs along profiles or cross-sections, (5) Convert between GIS formats and GemPy inputs, (6) Clip/transform vector/raster data for modeling, (7) Create model extents from geospatial bounds.

SteadfastAsArt
SteadfastAsArt
research
open
astronomy-physics
19

gprpy

Process and visualize ground-penetrating radar (GPR) data with signal processing, velocity analysis, and depth conversion. Use when Claude needs to: (1) Load GPR files (.DZT, .DT1, .GPR, .rd3), (2) Apply dewow, gain, and filters to radargrams, (3) Convert two-way travel time to depth, (4) Perform CMP/WARR velocity analysis, (5) Apply topographic corrections, (6) Export processed profiles as images or SEG-Y, (7) Batch process multiple GPR survey lines.

SteadfastAsArt
SteadfastAsArt
research
open
lab-tools
19

bio-tools

Biology research tools reference. Always available inside agent containers.

IDEA-XL
IDEA-XL
research
open
lab-tools
19

vibe-research

Set up and maintain a Vibe Research project with bi-directional sync between experimental code, paper.md, and developer docs. Use when starting a research project, managing experimental code, maintaining research documentation, creating academic papers, writing research logs, updating project docs, migrating an existing project to Vibe Research structure, or when the user mentions vibe research, paper sync, research log, experiment tracking, project migration, partial migration, incremental migration, doc update, or bi-directional sync between code and paper.

Zhangyanbo
Zhangyanbo
research
open
lab-tools
19

openspec-archive-change

Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.

DaRacci
DaRacci
research
open
lab-tools
19

dlisio

Read and parse DLIS (Digital Log Interchange Standard) and LIS (Log Information Standard) well log files. Use when Claude needs to: (1) Read/parse DLIS or LIS files, (2) Extract well log curves as numpy arrays, (3) Access file metadata and origin information, (4) Handle multi-frame or multi-file DLIS, (5) Convert DLIS to LAS or DataFrame, (6) Work with RP66 format well logs, (7) Process array or image log data.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

welly

Subsurface well data analysis toolkit for loading, processing, and analyzing well logs, projects, and formation tops. Built on lasio with enhanced curve processing. Use when Claude needs to: (1) Load wells from LAS files with metadata, (2) Work with multi-well Projects, (3) Process curves (despike, smooth, resample, normalize), (4) Manage formation tops, (5) Export well data to DataFrame/LAS/CSV, (6) Perform cross-well analysis and QC.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

query-kegg

Query KEGG for biological pathways and gene info. Use when user asks about metabolic pathways, signaling pathways, pathway genes, or KEGG IDs. Triggers on "kegg", "pathway", "metabolic pathway", "signaling pathway", "pathway genes".

IDEA-XL
IDEA-XL
research
open
scientific-computing
19

devito

Symbolic PDE solver with automatic code generation for finite-difference computations. Use when Claude needs to: (1) Perform seismic wave propagation modeling, (2) Implement acoustic or elastic wave equations, (3) Run forward modeling for shot gathers, (4) Set up Full Waveform Inversion (FWI) workflows, (5) Implement Reverse Time Migration (RTM), (6) Create absorbing boundary conditions, (7) Generate optimized stencil code for CPUs/GPUs, (8) Solve custom PDEs with finite differences.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

gempy

3D structural geological modeling using implicit methods. Create geological models with faults, folds, and unconformities from surface points and orientations. Use when Claude needs to: (1) Build 3D geological models from surface contacts and orientations, (2) Model faults, unconformities, or intrusions, (3) Compute and visualize subsurface geology, (4) Export models to VTK or numpy arrays, (5) Generate gravity forward models, (6) Create cross-sections or 3D visualizations.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

geostatspy

GSLIB-inspired geostatistics library for variogram analysis, kriging, and simulation. Use when Claude needs to: (1) Calculate experimental variograms, (2) Fit variogram models, (3) Perform simple/ordinary kriging, (4) Run sequential Gaussian simulation (SGSIM), (5) Apply normal score transforms, (6) Decluster spatial data, (7) Generate multiple realizations for uncertainty.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

loopstructural

Build 3D geological models with implicit surfaces, faults, folds, and stratigraphic constraints from structural geology data. Use when Claude needs to: (1) Build 3D geological models from structural data, (2) Model fault networks and displacements, (3) Create folded geology representations, (4) Interpolate geological surfaces, (5) Export models to VTK for visualization, (6) Perform uncertainty analysis on geological models, (7) Evaluate model values on grids.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

pastas

Groundwater time series analysis and modelling using transfer function noise models. Use when Claude needs to: (1) Analyze groundwater level time series, (2) Model well responses to precipitation/pumping, (3) Calibrate aquifer parameters from head data, (4) Forecast or hindcast groundwater levels, (5) Decompose hydrological signals into components, (6) Compare response functions, (7) Perform model diagnostics and uncertainty analysis.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

pyrolite

Geochemistry data analysis and visualization for igneous, metamorphic, and sedimentary rocks. Use when Claude needs to: (1) Create ternary diagrams for compositional data, (2) Plot REE spider diagrams with normalization, (3) Build TAS or other classification diagrams, (4) Apply log-ratio transforms to compositional data, (5) Calculate CIPW norms, (6) Generate Harker variation diagrams, (7) Compute element ratios and anomalies.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

pyvista

3D visualization and mesh analysis for geoscience data using PyVista/VTK. Use when Claude needs to: (1) Create 3D visualizations of geological models, (2) Render seismic volumes or voxel data, (3) Visualize point clouds or well paths, (4) Plot surfaces and meshes in 3D, (5) Read/write VTK, STL, OBJ files, (6) Create cross-sections through 3D models, (7) Export publication-quality figures or interactive HTML.

SteadfastAsArt
SteadfastAsArt
research
open
scientific-computing
19

query-reactome

Query Reactome for biological pathways and reactions. Use when user asks about signaling cascades, biological processes, pathway diagrams, or reaction details. Triggers on "reactome", "signaling cascade", "biological pathway", "pathway diagram", "reaction mechanism".

IDEA-XL
IDEA-XL
research
open
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