Software

I have started to make the code I write publicly available in git repositories. The software published there ranges in complexity, but I very much agree with the stance that sharing code whenever possible strengthens academia.

Points of (possible) interest include:

• I am responsible for the Type VI Secretion System (T6SS) subcomponent of NUFEB, an agent based model of microbial communities
• To make NUFEB more usable, I am also developing:
  • A python package nufebmgr which allows programmatic setup of NUFEB scenarios, using a higher level of biological abstractions rather than ‘molecular dyanmics speak’
  • A graphical user interface nufeb-designer, powered by nufebmgr, which allows point and click setups of NUFEB scenarios
• a standalone (no server or network access required) ‘virtual lab’ which allows students to explore elements of ecology, aligned roughly to Middle School curriculum standards, by playing with pre-solved NUFEB simulations Link
• an application to create sensibly formatted text from a commercial CFD program’s exported data
• an ImageJ macro and example code used to analyze activated sludge particle morphologies
• a Jupyter notebook-based system to interactively teach basic metagenomic data analysis and visualization.

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