## Astronomy and astrophysics

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [Astropy](https://www.astropy.org/) | no · yes | highly active · highly active | Community-led core Python package and ecosystem for astronomy, built to standardize fundamental representations such as units, coordinates, time, tables, and FITS-centric I/O. |
| [SunPy](https://sunpy.org/) | no · yes | active · active | Open-source Python environment for solar data analysis, built around domain-specific maps, coordinates, data access, and visualization for heliophysics. |
| [yt](https://yt-project.org/) | no · yes | moderate · moderate | Open-source framework for analysis and visualization of volumetric simulation and observational data, especially strong in astrophysics but used in other gridded-data domains as well. |
| [CASA](https://casa.nrao.edu/) | partial · partial | moderate · moderate | Primary data-processing and analysis software suite for major radio observatories such as ALMA and the VLA, with scriptable calibration, imaging, and analysis workflows. |

## Biology, bioinformatics, and systems biology

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [Bioconductor](https://www.bioconductor.org/) | no · yes | highly active · highly active | Large open-source R ecosystem for bioinformatics, designed around repeatable analysis workflows, shared data structures, and coordinated package releases. |
| [Scanpy + AnnData](https://scanpy.readthedocs.io/en/stable/) | no · yes | active · active | Single-cell analysis toolkit coupled to an annotated matrix data model that has become a de facto standard in Python single-cell workflows. |
| [Galaxy](https://galaxyproject.org/) | partial · partial | active · highly active | Open-source platform for accessible, reproducible, and transparent computational research, especially prominent in bioinformatics workflow sharing. |
| [QIIME 2](https://qiime2.org/) | partial · yes | active · active | Community-developed microbiome and multi-omics platform built around artifacts, semantic types, plugins, and provenance tracking. |
| [Biopython](https://biopython.org/) | no · yes | moderate · moderate | Foundational open-source Python toolkit for computational molecular biology, spanning sequence I/O, alignment, BLAST/Entrez access, motifs, structures, and more. |
| [SBML](https://sbml.org/) | yes · partial | moderate · moderate | Systems Biology Markup Language, a widely supported open standard for representing and exchanging computational models of biological systems. |
| [COPASI](https://copasi.org/) | partial · partial | moderate · moderate | Biochemical-system simulation and analysis tool that supports ODE, stochastic, and parameter-estimation workflows and interoperates strongly with SBML. |
| [CellML + OpenCOR](https://cellml.org/) | yes · partial | little · little | Open XML-based model language for mathematical biology, coupled to an open modeling/simulation environment for editing, simulating, and analyzing CellML models. |

## Chemistry and molecular science

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [RDKit](https://www.rdkit.org/) | partial · yes | active · moderate | Open-source cheminformatics toolkit that standardizes molecular representations, descriptors, fingerprints, reactions, and substructure queries. |
| [OpenMM](https://openmm.org/) | partial · yes | active · moderate | Open-source toolkit for high-performance molecular simulation with strong Python interfaces and GPU execution. |
| [ASE](https://ase-lib.org/) | no · yes | moderate · moderate | Atomic Simulation Environment, a Python framework for constructing, running, and analyzing atomistic simulations across many calculators and codes. |
| [Psi4](https://psicode.org/) | partial · yes | moderate · little | Open-source quantum-chemistry package with simple input files, a strong Python interface, and a large method-development ecosystem. |
| [Open Babel](https://openbabel.org/) | partial · yes | little · little | Open chemical toolbox for conversion, analysis, and manipulation of molecular data across a very large set of chemistry file formats. |

## Climate, weather, ocean, and Earth-system science

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [xarray](https://xarray.dev/) | no · yes | highly active · active | Python library for labeled N-dimensional arrays and datasets that has become central to Earth-system and geoscientific data workflows. |
| [WRF](https://www2.mmm.ucar.edu/wrf/users/) | partial · partial | active · active | Community weather-research and forecasting model whose standardized namelists and case workflows make it one of the most widely shared regional atmospheric modeling environments. |
| [netCDF + CF Conventions](https://www.unidata.ucar.edu/software/netcdf/) | partial · partial | moderate · moderate | Array-oriented scientific data format plus metadata conventions that together form one of the core exchange standards for climate and Earth-science computation. |
| [CESM](https://www.cesm.ucar.edu/) | partial · partial | moderate · moderate | Flagship community Earth-system model for coupled atmosphere-ocean-land-sea ice simulations, stewarded through the NCAR/NSF community-model tradition. |
| [MITgcm](https://mitgcm.org/) | partial · partial | moderate · moderate | General circulation model ecosystem for oceanic and atmospheric fluid dynamics with a long tradition in method development, adjoints, and idealized scientific experiments. |
| [ROMS](https://www.myroms.org/) | partial · partial | moderate · moderate | Regional Ocean Modeling System with strong support for coastal/ocean dynamics, tangent-linear and adjoint formulations, and community-shared experiment setups. |

## Engineering, control, and built-environment modeling

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [EnergyPlus](https://energyplus.net/) | yes · yes | highly active · active | Open-source whole-building energy simulation engine whose input data files provide a standardized, shareable representation of building systems and operating assumptions. |
| [Modelica + OpenModelica](https://modelica.org/modelicalanguage) | yes · partial | active · moderate | Equation-based acausal modeling language and open implementation ecosystem that may be the clearest engineering analogue to Dynare-style declarative scientific modeling. |
| [FMI](https://fmi-standard.org/) | partial · partial | moderate · moderate | Functional Mock-up Interface, a free standard for exchanging dynamic simulation models and co-simulation units across tools. |
| [OpenSees](https://opensees.berkeley.edu/) | yes · yes | moderate · little | Open framework for simulating structural and geotechnical systems, especially under earthquake loading, with shareable model scripts in Tcl and Python ecosystems. |

## Geoscience, seismology, hydrology, and geospatial analysis

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [ObsPy](https://www.obspy.org/) | no · yes | moderate · moderate | Python toolbox for seismology and seismological observatories, covering waveform I/O, metadata, signal processing, event handling, and related workflows. |
| [MODFLOW](https://www.usgs.gov/software/modflow-6-usgs-modular-hydrologic-model) | partial · partial | moderate · moderate | USGS modular hydrologic model family and current MODFLOW 6 core, an international standard environment for groundwater simulation. |
| [GMT](https://www.generic-mapping-tools.org/) | partial · partial | moderate · moderate | Generic Mapping Tools, a long-lived scripting environment for geoscientific cartography and spatial visualization. |

## Mathematics, symbolic computation, and formalized mathematics

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [Lean + mathlib](https://lean-lang.org/) | no · partial | highly active · highly active | Open-source theorem prover and programming language paired with a large community mathematics library for writing machine-checked definitions, theorems, and proofs. |
| [Rocq / Coq](https://rocq-prover.org/) | no · partial | highly active · active | Interactive theorem prover and formal language ecosystem for machine-checked mathematics, specifications, and certified programs. |
| [SymPy](https://www.sympy.org/) | no · yes | active · active | Pure-Python symbolic mathematics library and computer algebra system widely used for algebra, calculus, equation solving, and symbolic manipulation. |
| [SageMath](https://www.sagemath.org/) | no · yes | active · active | Broad open-source mathematics software system that integrates many mathematical packages behind a coherent Python-based interface. |
| [GAP](https://www.gap-system.org/) | no · partial | active · moderate | Open-source system and language for computational discrete algebra, especially computational group theory. |
| [PARI/GP](https://pari.math.u-bordeaux.fr/) | no · partial | active · moderate | Long-running open-source computer algebra system and GP language focused on fast computation in number theory and related symbolic/numeric mathematics. |
| [Singular](https://www.singular.uni-kl.de/) | no · partial | active · little | Open-source computer algebra system for polynomial computations with particular strength in commutative algebra, algebraic geometry, and singularity theory. |
| [Macaulay2](https://macaulay2.com/) | no · partial | moderate · moderate | Research-oriented mathematics software system for commutative algebra, algebraic geometry, and related fields. |

## Neuroscience and neuroinformatics

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [BIDS](https://bids.neuroimaging.io/) | partial · partial | active · active | Brain Imaging Data Structure, a community specification for organizing and describing neuroimaging and related data. |
| [NWB](https://nwb.org/) | partial · yes | active · active | Neurodata Without Borders, a data standard and tool ecosystem for sharing, archiving, and analyzing neurophysiology data. |
| [NEURON](https://nrn.readthedocs.io/) | yes · yes | active · moderate | Long-lived simulator for neurons and neural networks, with model definition via Python, HOC, and the NMODL mechanism-description language. |
| [NeuroML](https://neuroml.org/) | yes · partial | little · little | Open language and ecosystem for describing detailed models of neural systems in a portable, exchange-oriented form. |

## Physics, multiphysics, materials, and nuclear science

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [ROOT](https://root.cern/) | partial · yes | highly active · highly active | Open-source data-analysis framework and file/data model ecosystem that became a de facto standard in high-energy physics. |
| [LAMMPS](https://lammps.org/) | partial · yes | highly active · active | Large, extensible molecular-dynamics package with text-script workflows and broad support for atomistic, coarse-grained, and materials simulations. |
| [GROMACS](https://www.gromacs.org/) | partial · partial | active · active | High-performance open-source molecular-dynamics suite widely used for biomolecular and related atomistic simulations. |
| [Geant4](https://geant4.web.cern.ch/) | partial · yes | active · moderate | Open-source toolkit for simulating the passage of particles through matter, used across detector physics, medical applications, space science, and radiation transport. |
| [FEniCSx / UFL](https://fenicsproject.org/) | yes · yes | active · active | Finite-element computing ecosystem whose UFL component is a genuine embedded declarative language for variational forms and weak-form PDE models. |
| [Quantum ESPRESSO](https://www.quantum-espresso.org/) | partial · partial | active · moderate | Major open-source suite for plane-wave density-functional theory and related quantum simulations of materials. |
| [OpenFOAM](https://openfoam.org/) | partial · partial | active · highly active | Open-source CFD framework with a large library of solvers and utilities built around reusable case structures, dictionaries, meshes, and physical models. |
| [MOOSE](https://mooseframework.inl.gov/) | partial · partial | moderate · moderate | Open-source multiphysics finite-element application framework that supports many domain applications through modular kernels, materials, and structured input files. |
| [OpenMC](https://openmc.org/) | partial · yes | moderate · moderate | Community-developed Monte Carlo neutron/photon transport code with strong Python and XML-based model-building workflows. |

## Statistics and probabilistic modeling

| Project | DDSL/API | Activity (maint. · community) | Short description |
|:---|:---|:---|:---|
| [Stan](https://mc-stan.org/) | yes · yes | highly active · highly active | Probabilistic programming language and multi-interface inference ecosystem for Bayesian data analysis. |
| [PyMC](https://www.pymc.io/) | yes · yes | highly active · highly active | Python-based Bayesian modeling and probabilistic programming environment built around an embedded model-specification style. |