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authorPjotr Prins2025-04-16 17:26:52 +0200
committerPjotr Prins2025-04-16 17:26:52 +0200
commit921f5d49360b8c1b6bb6c2f440ff6212d58e08d3 (patch)
tree09858878e8f6ba78c6fb633357e0ca23057550f9
parentc92799dc0a32f7a5955cd47bfae98ee1b70190ee (diff)
downloadgn-gemtext-921f5d49360b8c1b6bb6c2f440ff6212d58e08d3.tar.gz
A road map for federating GN
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+# GN Road map
+
+GN is a web service for complex traits. The main version is currently deployed in Memphis TN, mostly targetting mouse and rat.
+Here we define a road map to bring GN to more communities by providing federated services.
+The aim is to have plant.genenetwork.org, nematode.genenetwork.org, big.genenetwork.org running in the coming years.
+
+# Getting an instance up (step 1)
+
+## Deploy a new instance
+
+To test things we can use an existing database or a new one. We can deploy that as a (new) Guix service container.
+
+We'll need to run a few services including:
+
+* GN3
+* GN2
+* Auth (if required)
+* Uploader (if required)
+
+## Get database ready
+
+In the first step we have to upload data for the target community. This can be done by updating the databases with some example datasets. Care has to be taken that search etc. works and that we can do the mapping.
+
+* Add traits
+* Add genotype files
+* Add metadata
+
+# Branding and hosting (Step 2)
+
+Once we have a working database with a number of example use cases we can start rebranding the service and, ideally, host it on location.
+
+# Synchronization (Step 3)
+
+## Move traits into lmdb
+
+This is WIP. We need to adapt the GN3 code to work with lmdb when available.
+
+## Move genotypes into lmdb
+
+This is WIP. We need to adapt the GN3 code to work with lmdb when available.
+
+# Federated metadata (Step 4)
+
+## Move all metadata into RDF
+
+This is WIP and happening. We will need to document.
+
+# Community (Step 5)
+
+## Provide programming examples