GitHub
pymatgen
Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.
https://github.com/brandmaier/semtree
Recursive Partitioning for Structural Equation Models
@cleerly/cornerstone-tools
[Deprecated] Use Cornerstone3D Instead https://cornerstonejs.org/
biosteam
The Biorefinery Simulation and Techno-Economic Analysis Modules; Life Cycle Assessment; Chemical Process Simulation Under Uncertainty
biobb-pmx
Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
aligator
A versatile and efficient C++ library for real-time constrained trajectory optimization
eo
EOLANG, an Experimental Pure Object-Oriented Programming Language Based on 𝜑-Calculus
GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
https://github.com/lukasturcani/stk
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
mwtab
The mwtab package is a Python library that facilitates reading and writing files in mwTab format used by the Metabolomics Workbench for archival of Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) experimental data.
atomrdf
atomRDF is a python tool for ontology-based creation, manipulation, and querying of structures. atomRDF uses the Computational Material Sample Ontology (CMSO).
minari
A standard format for offline reinforcement learning datasets, with popular reference datasets and related utilities
HOHQMesh
HOHQMesh.jl is a Julia wrapper for the HOHQMesh mesh generator, which allows to produce curved quadrilateral and hexahedral meshes for high-order numerical simulations.
eckity
EC-KitY: A scikit-learn-compatible Python tool kit for doing evolutionary computation.
actinia-core
Actinia Core is an open source REST API for scalable, distributed, high performance processing of geographical data that uses mainly GRASS GIS for computational tasks (DOI: https://doi.org/10.5281/zenodo.5879231) | Tutorial: https://actinia-org.github.io/actinia-core/ | Docker: https://hub.docker.com/r/mundialis/actinia-core
betaMC
betaMC: Generates Monte Carlo confidence intervals for standardized regression coefficients for models fitted by lm().
slmsuite
Python package for high-performance spatial light modulator (SLM) control and holography. Supports features from aberration-corrected 3D point clouds to automated Fourier-domain calibrations.
simpa
The Simulation and Image Processing for Photonics and Acoustics (SIMPA) toolkit.
ansible-collection-toolkit
This Ansible collection provides production-ready Ansible roles used for providing services used in research and by research software engineers, but not exclusively.
compss
COMP Superscalar (COMPSs) is a framework which aims to ease the development and execution of applications for distributed infrastructures, such as Clusters, Grids and Clouds.
pedbp
R package for working with pediatric blood pressures based on age and height
aiida-crystal-dft
AiiDA plugin for the ab initio modeling suite CRYSTAL, developed in Turin University
tasksource
Datasets collection and preprocessings framework for NLP extreme multitask learning
climada_petals
CLIMADA Petals generates different types of hazards and contains more specialized applications than the CLIMADA Core module https://github.com/CLIMADA-project/climada_python.
https://github.com/astropy/pytest-filter-subpackage
Simple pytest plugin to allow sub-packages to test to be selected with e.g. -P io.fits,modeling
rastervision
An open source library and framework for deep learning on satellite and aerial imagery.
fluidx3d
The fastest and most memory efficient lattice Boltzmann CFD software, running on all GPUs and CPUs via OpenCL. Free for non-commercial use.
nplinker
A python framework for microbial natural products data mining by integrating genomics and metabolomics data
autogoal
A Python framework for program synthesis with a focus on Automated Machine Learning.
biobb
Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.
forecast-tools
forecast_tools provides fundamental tools to support the forecasting process in python
pigeons.jl
Sampling from intractable distributions, with support for distributed and parallel methods
mriqc
Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
weaver
Weaver: Workflow Execution Management Service (EMS); Application, Deployment and Execution Service (ADES); OGC API - Processes; WPS; CWL Application Package
pretzel
Javascript full-stack framework for Big Data visualisation and analysis
ampycloud
Python package to determine the sky coverage fraction and base height of cloud layers using ceilometer data
scimlbook
Parallel Computing and Scientific Machine Learning (SciML): Methods and Applications (MIT 18.337J/6.338J)
beobench
A toolkit providing easy and unified access to building control environments for reinforcement learning (RL). No longer actively maintained.
quantum-gates
Noisy Quantum Gates model for simulating the noise of quantum devices.
theft
R package for Tools for Handling Extraction of Features from Time series (theft)
pyorthoani
A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.
clusttraj
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
https://github.com/althonos/lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices.
alpino-query
Library for creating xpath queries by example for Alpino treebanks
Qiskit Dynamics
Qiskit Dynamics: A Python package for simulating the time dynamics of quantum systems - Published in JOSS (2023)
kikuchipy
Toolbox for analysis of electron backscatter diffraction (EBSD) patterns
anesthetic
anesthetic: nested sampling visualisation - Published in JOSS (2019)
qa-catalogue
QA Catalogue – a metadata quality assessment tool for library catalogue records (MARC, PICA, UNIMARC)
ConformalPrediction
Predictive Uncertainty Quantification through Conformal Prediction for Machine Learning models trained in MLJ.
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
corelay
CoRelAy is a tool to compose small-scale (single-machine) analysis pipelines.
Category Encoders
Category Encoders: a scikit-learn-contrib package of transformers for encoding categorical data - Published in JOSS (2018)
gtdbtk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
tensors.jl
Efficient computations with symmetric and non-symmetric tensors with support for automatic differentiation.
pyrtlib
PyRTlib is an attractive educational software to simulate observations from ground-based, airborne, and satellite microwave sensors. It provides a flexible and user-friendly tool to broadly simulate how electromagnetic radiation travels through the atmosphere as it interacts with atmospheric constituents.
