1 files changed, 58 insertions, 5 deletions
diff --git a/docs/gemma.ipynb b/docs/gemma.ipynb
index b7796e3..4c5f9a6 100644
--- a/docs/gemma.ipynb
+++ b/docs/gemma.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Running GEMMA from GN3\n",
+    "# Running GEMMA from GN3\n",
     "\n",
     "This document outlines how to use gemma from Genenetwork3."
    ]
@@ -25,7 +25,9 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -37,21 +39,72 @@
    ],
    "source": [
     "import requests\n",
-    "r = requests.get(\"http://127.0.0.1:8080/gemma/version\")\n",
+    "r = requests.get(\"http://127.0.0.1:8080/api/gemma/version\")\n",
     "print(r.json())"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": []
+   "source": [
+    "## Uploading data\n",
+    "\n",
+    "Before you perform any computation, you need to ensure you have your data uploaded\n",
+    "\n",
+    "TODO"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## K-Computation\n",
+    "\n",
+    "Make sure that your metadata file is up to date!\n",
+    "You need the genofile, traitfile, and snpsfile. You also need a token provided when you first uploaded your metadata file."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Computing K-Values (no loco, no cavariates): \n",
+    "##### POST /gemma/k-compute/:token\n",
+    "The end command will look something like:\n",
+    "\n",
+    "```\n",
+    "gemma-wrapper --json -- -debug \\\n",
+    "                -g genotype-file -p traitfile \\\n",
+    "                -a genotypte-snps -gk > input-hash-k-output-filename\"\n",
+    "```"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "# Demo\n",
+    "import requests\n",
+    "r = requests.post(\"localhost:8080/api/gemma/k-compute/abcde-abcde\")\n",
+    "print(r.json())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### POST /gemma/k-compute/:chromosomes/:token\n",
+    "\n",
+    "Cqmpute K values with chromosomes. The end command will look similar to:\n",
+    "\n",
+    "```\n",
+    "  gemma-wrapper --json --loco 1,2,3,4 \\\n",
+    "                -debug -g genotypefile -p traitfile \\\n",
+    "                -a genotype-snps -gk > k_output_filename.json\n",
+    "```"
+   ]
   }
  ],
  "metadata": {