From 9033c936673b25f70d059e061cc4295a720f7137 Mon Sep 17 00:00:00 2001
From: Gal Barel <barel@molgen.mpg.de>
Date: Thu, 2 Apr 2020 15:07:23 +0200
Subject: [PATCH] added time and memory warnings in tutorial

---
 Tutorial.ipynb | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/Tutorial.ipynb b/Tutorial.ipynb
index 611b46b..74d228a 100644
--- a/Tutorial.ipynb
+++ b/Tutorial.ipynb
@@ -157,6 +157,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "**Run-time memory warning:** Executing the next funtion will be executed assuming it can use 64 cores (or more). If you're running this on a computer with less cores, make sure to first change the ```num_cores``` argument accordingly. \n",
+    "\n",
     "To generate permutations in a parallel fashion, the user can change the ```num_cores``` argument in the function to be larger than ```1``` and then multiple processes will be generated (as many as the number of given cores).\n",
     "\n",
     "**PLEASE NOTE:** the function takes long to run. It is recommented to use multiple cores and generate at least 100 permutations. This can be done once only and later be repeatedly used.\n",
@@ -484,6 +486,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "NetCore requiers at least 3 inputs:\n",
+    "\n",
+    "* An edge list file for the network\n",
+    "* A weights file for some or all the nodes in the network. In case such file is not avilable than a seed file can be used\n",
+    "* A path for the directory containing all of the permutaions of the network\n",
+    "\n",
     "Running NetCore with the input files will generate two outputs:\n",
     "\n",
     "* ```random_walk_weights.txt``` - a propagation weights file with re-ranking of the nodes in the network according to their weights after the propagation\n",
@@ -503,7 +511,33 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To run NetCore the ```network_propagaion.py``` script must be executed using ```python3``` with at minimum 4 arguments. The user can chose to input either a weights file or a seed file (or both), but at least one must be provided. "
+    "**Run-time memory warning:** NetCore is computes the fractional power of a matrix using [scipy](http://lagrange.univ-lyon1.fr/docs/scipy/0.17.1/generated/scipy.linalg.fractional_matrix_power.html) which might take long and be intesive to process. It is recommened to use a machine with at least 64 cores. \n",
+    "\n",
+    "To run NetCore the ```netcore.py``` script must be executed using ```python3``` with at least 4 arguments. The user can chose to input either a weights file or a seed file (or both), but at least one must be provided. "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Requiered arguments"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "``` -e``` : Network file in an edge list format\n",
+    "\n",
+    "``` -w``` : Weights file for some or all nodes in the network\n",
+    "\n",
+    "*or*\n",
+    "\n",
+    "``` -s``` : Seed file with seed nodes for binary propagation and/or module identification\n",
+    "\n",
+    "``` -pd``` : The path to the directory where the permutation files of the network are stored\n",
+    "\n",
+    "``` -o``` (optional) : Dirctory for output files (if not give, default is the current directory) \n"
    ]
   },
   {