Packaging Composable Research Software Libraries

phylotrackpy is a Python phylogeny tracker.

opytional makes working with values that might be None safer and easier.

interval-search provides predicate-based binary and doubling search implementations.

hstrat enables phylogenetic inference on distributed digital evolution populations.

@article{moreno2022hereditary,
  author = {Moreno, Matthew Andres and Dolson, Emily and Ofria, Charles},
  doi = {https://doi.org/10.1162/isal_a_00550},
  journal = {Proceedings of the ALIFE 2022: The 2022 Conference on Artificial Life},
  month = {7},
  pages = {64--74},
  title = {{Hereditary Stratigraphy: Genome Annotations to Enable Phylogenetic Inference over Distributed Populations}},
  volume = {Proceedings of the ALIFE 2022: The 2022 Conference on Artificial Life},
  year = {2022}
}

alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data.

Hands-on, asynchronous 4 day tutorial series covering foundational web development competencies, C++ development with the Empirical library, and compiling for the web with Emscripten.

teeplot automatically saves a copy of rendered Jupyter notebook plots.

A genetic programming implementation designed for large-scale artificial life applications. Organized as a header-only C++ library. Inspired by Alex Lalejini’s SignalGP.

C++ library that wraps intra-thread, inter-thread, and inter-process communication in a uniform, modular, object-oriented interface, with a focus on asynchronous high-performance computing applications.

C++ library for digital evolution simulations studying digital multicellularity and fraternal major evolutionary transitions in individuality.

keyname helps easily pack and unpack metadata in a filename.

Empirical is a library of tools for developing useful, efficient, reliable, and available scientific software. The provided code is header-only and encapsulated into the emp namespace, so it is simple to incorporate into existing projects.

@software{Ofria_Empirical_C_library_2020,
  author = {Ofria, Charles and Moreno, Matthew Andres and Dolson, Emily and Lalejini, Alex and Rodriguez Papa, Santiago and Fenton, Jake and Perry, Katherine and Jorgensen, Steven and hoffmanriley and grenewode and Baldwin Edwards, Oliver and Stredwick, Jason and cgnitash and theycallmeHeem and Vostinar, Anya and Moreno, Ryan and Schossau, Jory and Zaman, Luis and djrain},
  doi = {10.5281/zenodo.4141943},
  license = {MIT},
  month = {10},
  title = {{Empirical: C++ library for efficient, reliable, and accessible scientific software}},
  url = {https://github.com/devosoft/Empirical},
  version = {0.0.4},
  year = {2020}
}