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 # PanGEMMA
 
-We are rewriting and modernizing the much beloved GEMMA tool that is core to GeneNetwork.org. The idea is to upgrade the software, and keep 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 have really finished!
+We are rewriting and modernizing the much beloved GEMMA tool that is core to GeneNetwork.org. The idea is to upgrade the software, and keep 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 have really finished! For some reason we painted ourselves into a corner (indeed).
 
-We want to keep the heart of GEMMA 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)).
+Importantly, we want to keep the heart of GEMMA 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 propagator 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. See also [propagators](https://groups.csail.mit.edu/mac/users/gjs/propagators/) and [examples](https://github.com/namin/propagators/blob/master/examples/multiple-dwelling.scm).
+What we will do is create components and wire them together, allowing for sharing memory between components using Linux mmap techniques --- mostly using lmdb that is supported on non-Linux platforms. Each component may have multiple implementations. We will introduce a DSL for orchestration and we may introduce a propagator 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. See also [propagators](https://groups.csail.mit.edu/mac/users/gjs/propagators/) and [examples](https://github.com/namin/propagators/blob/master/examples/multiple-dwelling.scm).
 
-Propagators are [Unix pipes on steroids](https://github.com/pjotrp/ruby-propagator-network/blob/main/README.md).
+I wrote a piece with examples on propagators too. Propagators are [Unix pipes on steroids](https://github.com/pjotrp/ruby-propagator-network/blob/main/README.md).
 
 We want PanGEMMA to be able to run on high-performance computing (HPC) architectures, including GPUs. This implies the core project can have few dependencies and should easily compile from C.
 
@@ -167,7 +167,7 @@ We recently introduced an lmdb version of the genotype file. This new genotype f
 
 ## Example
 
-I created a very minimalistic example in Ruby with a simple round-robin scheduler:
+    I created a very minimalistic example in Ruby with a simple round-robin scheduler:
 
 => https://github.com/pjotrp/ruby-propagator-network/blob/main/propagator.rb
 
@@ -205,4 +205,4 @@ ZeroMQ provides a minimalistic message passing interface in most languages. It w
 
 ## Sharing data in RAM
 
-There are several methods for sharing data between threads and processes. First we can first use Linux copy on write for instantiated processes. The Linux kernel als has shared memory support and, more interesting, memory mapping support --- which is also used in lmdb.
+There are several methods for sharing data between threads and processes. First we can first use Linux copy on write for instantiated processes. The Linux kernel als has shared memory support and, more interesting, memory mapping support --- which is also used in lmdb. Lmdb is multi-platform and works on non-POSIX systems. It is very fast, but may need tweaking, for example by disabling read-ahead with MDB_NORDAHEAD. We'll get to that.