From 20a0090b46c83922466150671b110861552dce7d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 17 Apr 2024 02:16:10 -0500
Subject: Mgamma: added pages to track issues

---
 issues/mgamma/mgamma-cli.gmi    | 1 +
 issues/mgamma/mgamma-design.gmi | 9 +++++++++
 issues/mgamma/mgamma-readme.gmi | 6 ++++++
 3 files changed, 16 insertions(+)
 create mode 100644 issues/mgamma/mgamma-cli.gmi
 create mode 100644 issues/mgamma/mgamma-design.gmi
 create mode 100644 issues/mgamma/mgamma-readme.gmi

diff --git a/issues/mgamma/mgamma-cli.gmi b/issues/mgamma/mgamma-cli.gmi
new file mode 100644
index 0000000..d530f7f
--- /dev/null
+++ b/issues/mgamma/mgamma-cli.gmi
@@ -0,0 +1 @@
+# MGAMMA CLI
diff --git a/issues/mgamma/mgamma-design.gmi b/issues/mgamma/mgamma-design.gmi
new file mode 100644
index 0000000..23e02d5
--- /dev/null
+++ b/issues/mgamma/mgamma-design.gmi
@@ -0,0 +1,9 @@
+# MGAMMA design philosophy
+
+We have a lot of experience running and hacking the GEMMA tool in GeneNetwork.org:
+
+=> https://github.com/genetics-statistics/GEMMA
+
+GEMMA proves to give great GWA results and has a decent speed for a single threaded implementation - even though the matrix calls to openblas use multiple threads. The source code base of GEMMA, however, proves hard to build on. This is why we are creating a next generation tool that has a focus on *performance and hackability*.
+
+After several attempts using R, D, Julia, python, Ruby we have in 2023 settled on Guile+C+Zig. Guile provides a REPL and great hackabability. C+Zig we'll use for performance. The other languages are all great, but we think we can work faster in this setup.
diff --git a/issues/mgamma/mgamma-readme.gmi b/issues/mgamma/mgamma-readme.gmi
new file mode 100644
index 0000000..3af51a4
--- /dev/null
+++ b/issues/mgamma/mgamma-readme.gmi
@@ -0,0 +1,6 @@
+# MGAMMA
+
+In this project we are attempting a new LMM runner. This page indexes items we are working on.
+
+=> ./mgamma-design design philosophy
+=> ./mgamma-cli command line interface
-- 
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