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# PanGEMMA
We are rewriting and modernizing the much beloved GEMMA tool.
The idea it to upgrade the software, but keeping it going using ideas from Hanson and Sussman's book on *Software Design for Flexibility: How to Avoid Programming Yourself into a Corner*.
This is not the first attempt, in fact quite a few efforts have started, but none really finished!
We want to keep the tool heart beating while upgrading the environment taking inspiration from fetal heart development: The human heart is one of the first organs to form and function during embryogenesis. By the end of gestational week 3, passive oxygen diffusion becomes insufficient to support metabolism of the developing embryo, and thus the fetal heart becomes vital for oxygen and nutrient distribution. The initiation of the first heart beat via the *primitive heart tube* begins at gestational day 22, followed by active fetal blood circulation by the end of week 4. The start of early heart development involves several types of progenitor cells that are derived from the mesoderm, proepicardium, and neural crest. This eventually leads to the formation of the 4-chambered heart by gestational week 7 via heart looping and complex cellular interactions in utero (e.g., [Tan and Lewandowski](https://doi.org/10.1159/000501906)).
What we will do is create components and wire them together, allowing for sharing RAM between components. Each component may have multiple implementations. We will introduce a DSL for orchestration and we may introduce a propagated network to run components in parallel and test them for correctness. At the same time, the core functionality of GEMMA will keep going while we swap components in and out.
We want PanGEMMA to be able to run on high peformance computing (HPC) architectures, including GPU targets. This implies the core project can have few dependencies and should easily compile from C.
# Innovation
* Split functionality into components
* Wire components up so they can be tested and replaced
* New components may run in parallel
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