Software

Please see my GitHub Profile for a complete list of the software I am working on.

Subject Matter #
  1. Public Interest Technology
  2. Computational Biology

Public Interest Technology #

Council Data Project #

Eva Maxfield Brown, To Huynh, Isaac Na, Hawk Ticehurst, Katlyn M.F. Greene, Emily Gilles, Madeleine Farrer, Brian Ledbetter, Nic Weber
Development Status :: 5 - Production/Stable
https://councildataproject.org

Council Data Project is an open-source project dedicated to providing journalists, activists, researchers, and all members of each community we serve with the tools they need to stay informed and hold their councilmembers accountable. By combining and simplifying sources of information on council meetings and actions, CDP ensures that everyone is empowered to participate in local government. For members of the community looking to stay up-to-date, we aim to make finding relevant meetings as easy as possible. For journalists and activists, our tools enable tracking legislation through the council process, transcript search with timestamped transcripts for review and sharing, full voting records querying, and more. And, for civic technology organizations and municipal government offices, we make all of our tools easy to deploy for your own council.

Computational Biology #

AICSImageIO #

Eva Maxfield Brown, et al.
Development Status :: 5 - Production/Stable
https://github.com/AllenCellModeling/aicsimageio

AICSImageIO aims to provide a consistent intuitive API for reading in or out-of-memory image pixel data and metadata for the many existing proprietary microscopy file formats, and, an easy-to-use API for converting from proprietary file formats to an open, common, standard – all using either language agnostic or pure Python tooling.

Automated Cell Toolkit (ACTK) #

Eva Maxfield Brown, Rory Donovan-Maiye, et al.
Development Status :: 7 - Inactive
https://github.com/AllenCellModeling/actk

workflow diagram showing how data was combined and processed prior to analysis (the ACTK pipeline)

A pipeline to process field-of-view (FOV) microscopy images and generate data and render-ready products for the cells in each field. Of note, the data produced by this pipeline can be used directly with the Integrated Cell Model.