From 09bfc65a992f249b7f95802254fb6b9cf950e8d7 Mon Sep 17 00:00:00 2001
From: Rui Ribeiro <rui.ribeiro@icloud.com>
Date: Wed, 9 Mar 2022 17:39:24 +0100
Subject: [PATCH] pre-release

---
 .../SSBtoolkit-Tutorial1-checkpoint.ipynb     |  2 +-
 .../SSBtoolkit-Tutorial2-checkpoint.ipynb     |  3 ++-
 .../SSBtoolkit-Tutorial3A-checkpoint.ipynb    |  3 ++-
 ...oolkit-Tutorial3B-tauRAMD-checkpoint.ipynb |  2 +-
 README.md                                     | 23 +++++++++++++++++++
 SSBtoolkit-Tutorial1.ipynb                    |  2 +-
 SSBtoolkit-Tutorial2.ipynb                    |  3 ++-
 SSBtoolkit-Tutorial3A.ipynb                   |  3 ++-
 SSBtoolkit-Tutorial3B-tauRAMD.ipynb           |  2 +-
 docs/ssb_toolkit.md                           |  2 +-
 10 files changed, 36 insertions(+), 9 deletions(-)

diff --git a/.ipynb_checkpoints/SSBtoolkit-Tutorial1-checkpoint.ipynb b/.ipynb_checkpoints/SSBtoolkit-Tutorial1-checkpoint.ipynb
index 891f0ec..d93b89b 100644
--- a/.ipynb_checkpoints/SSBtoolkit-Tutorial1-checkpoint.ipynb
+++ b/.ipynb_checkpoints/SSBtoolkit-Tutorial1-checkpoint.ipynb
@@ -12,7 +12,7 @@
     "\n",
     "<br><br><br><br>\n",
     "\n",
-    "# Simulating dose-response curves from agonist affinity values\n",
+    "# Simulation of dose-response curves from affinity values\n",
     "\n",
     "In this tutorial we will simulate a mathematical model of a signaling pathway to obtain dose-response curves, from wich  *potency (EC<sub>50</sub>)* values of agonists can be infered. \n",
     "\n",
diff --git a/.ipynb_checkpoints/SSBtoolkit-Tutorial2-checkpoint.ipynb b/.ipynb_checkpoints/SSBtoolkit-Tutorial2-checkpoint.ipynb
index 044c3cd..f71f5a6 100644
--- a/.ipynb_checkpoints/SSBtoolkit-Tutorial2-checkpoint.ipynb
+++ b/.ipynb_checkpoints/SSBtoolkit-Tutorial2-checkpoint.ipynb
@@ -11,8 +11,9 @@
     "</div> \n",
     "\n",
     "<br><br><br><br>\n",
+    "<br>\n",
     "\n",
-    "# Predicting dose-response curves of antagonists\n",
+    "# Simulation of dose-response curves of antagonists\n",
     "\n",
     "In this tutorial we will simulate a mathematical model of a signaling pathway to obtain dose-response curves of antagonists, from wich their *potencies (IC$_{50}$)* can be infered. \n",
     "\n",
diff --git a/.ipynb_checkpoints/SSBtoolkit-Tutorial3A-checkpoint.ipynb b/.ipynb_checkpoints/SSBtoolkit-Tutorial3A-checkpoint.ipynb
index ee851b3..a752599 100644
--- a/.ipynb_checkpoints/SSBtoolkit-Tutorial3A-checkpoint.ipynb
+++ b/.ipynb_checkpoints/SSBtoolkit-Tutorial3A-checkpoint.ipynb
@@ -11,8 +11,9 @@
     "</div>  \n",
     "\n",
     "<br><br><br><br>\n",
+    "<br>\n",
     "\n",
-    "# Simulating dose-response curves from ligand kinetic values\n",
+    "# Simulation of  dose-response curves from kinetic values\n",
     "\n",
     "In this tutorial we will simulate mathematical model of a signaling pathway to obtain dose-response curves, and consequently, predict the *efficacy (EC$_{50}$)* of drugs. \n",
     "\n",
diff --git a/.ipynb_checkpoints/SSBtoolkit-Tutorial3B-tauRAMD-checkpoint.ipynb b/.ipynb_checkpoints/SSBtoolkit-Tutorial3B-tauRAMD-checkpoint.ipynb
index 21dc63f..7e01490 100644
--- a/.ipynb_checkpoints/SSBtoolkit-Tutorial3B-tauRAMD-checkpoint.ipynb
+++ b/.ipynb_checkpoints/SSBtoolkit-Tutorial3B-tauRAMD-checkpoint.ipynb
@@ -12,7 +12,7 @@
     "<br><br><br><br>\n",
     "<br>\n",
     "\n",
-    "# Predicting dose-response cruves from data acquired with tauRAMD \n",
+    "# Simulation of dose-response cruves from data acquired with tauRAMD \n",
     "\n",
     "\n",
     "In this notebook we will a simulate mathematical model of a signaling pathway to obtain dose-response curves using kinetic values obtained with the <b>tauRAMD</b> tool.\n",
diff --git a/README.md b/README.md
index 50ac3f2..c826145 100644
--- a/README.md
+++ b/README.md
@@ -32,3 +32,26 @@ How to do:
 5. [Exploring SSB pathways associated to disease variants](SSBtoolkit-Tutorial4_OXTR.ipynb)
 
 
+
+
+## Cite Us
+If you use or adapt the SSBtoolkit for your own research projects please cite us.
+
+```
+@article{XXX,
+    title={XXX},
+    author={XXX},
+    publisher={XXX},
+    note={\url{XXX}},
+    year={XXX}
+}
+```
+
+## Acknowledgments
+
+EU Human Brain Project (SGA1 and SGA2): This open source software was developed in part in the Human Brain Project funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No 720270 and No. 78907 (Human Brain Project SGA1 and SGA2).
+
+<div style="padding-bottom:50px">
+<img src="https://res.cloudinary.com/djz27k5hg/image/upload/v1637657234/logos/HBP_horizontal_logo_qtcyzn.png" width="300" align='left' style="margin-left:50px">
+    <img src="https://res.cloudinary.com/djz27k5hg/image/upload/v1642677502/logos/COFUNDED_EU_j2ktlp.jpg" width="300" align='left' style="margin-left:50px">
+</div>  
\ No newline at end of file
diff --git a/SSBtoolkit-Tutorial1.ipynb b/SSBtoolkit-Tutorial1.ipynb
index 891f0ec..d93b89b 100644
--- a/SSBtoolkit-Tutorial1.ipynb
+++ b/SSBtoolkit-Tutorial1.ipynb
@@ -12,7 +12,7 @@
     "\n",
     "<br><br><br><br>\n",
     "\n",
-    "# Simulating dose-response curves from agonist affinity values\n",
+    "# Simulation of dose-response curves from affinity values\n",
     "\n",
     "In this tutorial we will simulate a mathematical model of a signaling pathway to obtain dose-response curves, from wich  *potency (EC<sub>50</sub>)* values of agonists can be infered. \n",
     "\n",
diff --git a/SSBtoolkit-Tutorial2.ipynb b/SSBtoolkit-Tutorial2.ipynb
index 044c3cd..f71f5a6 100644
--- a/SSBtoolkit-Tutorial2.ipynb
+++ b/SSBtoolkit-Tutorial2.ipynb
@@ -11,8 +11,9 @@
     "</div> \n",
     "\n",
     "<br><br><br><br>\n",
+    "<br>\n",
     "\n",
-    "# Predicting dose-response curves of antagonists\n",
+    "# Simulation of dose-response curves of antagonists\n",
     "\n",
     "In this tutorial we will simulate a mathematical model of a signaling pathway to obtain dose-response curves of antagonists, from wich their *potencies (IC$_{50}$)* can be infered. \n",
     "\n",
diff --git a/SSBtoolkit-Tutorial3A.ipynb b/SSBtoolkit-Tutorial3A.ipynb
index ee851b3..a752599 100644
--- a/SSBtoolkit-Tutorial3A.ipynb
+++ b/SSBtoolkit-Tutorial3A.ipynb
@@ -11,8 +11,9 @@
     "</div>  \n",
     "\n",
     "<br><br><br><br>\n",
+    "<br>\n",
     "\n",
-    "# Simulating dose-response curves from ligand kinetic values\n",
+    "# Simulation of  dose-response curves from kinetic values\n",
     "\n",
     "In this tutorial we will simulate mathematical model of a signaling pathway to obtain dose-response curves, and consequently, predict the *efficacy (EC$_{50}$)* of drugs. \n",
     "\n",
diff --git a/SSBtoolkit-Tutorial3B-tauRAMD.ipynb b/SSBtoolkit-Tutorial3B-tauRAMD.ipynb
index 21dc63f..7e01490 100644
--- a/SSBtoolkit-Tutorial3B-tauRAMD.ipynb
+++ b/SSBtoolkit-Tutorial3B-tauRAMD.ipynb
@@ -12,7 +12,7 @@
     "<br><br><br><br>\n",
     "<br>\n",
     "\n",
-    "# Predicting dose-response cruves from data acquired with tauRAMD \n",
+    "# Simulation of dose-response cruves from data acquired with tauRAMD \n",
     "\n",
     "\n",
     "In this notebook we will a simulate mathematical model of a signaling pathway to obtain dose-response curves using kinetic values obtained with the <b>tauRAMD</b> tool.\n",
diff --git a/docs/ssb_toolkit.md b/docs/ssb_toolkit.md
index b916f50..87aa9d3 100644
--- a/docs/ssb_toolkit.md
+++ b/docs/ssb_toolkit.md
@@ -126,7 +126,7 @@ All the three signaling pathways were developed using the [PySB](https://pysb.or
 To predict a dose-response curve from the simulation of signaling pathways, individual simulations of the pathway according to an array of ligand concentrations must be performed first. The dose-response curve is, then, obtained by fitting a logistic regression (eq.4) to the maximum response values from each individual simulation. In the end, a curve of the response in function of the ligand concentration is obtained (Fig.7). The response of a signaling pathway is, naturally, represented by the increase or decrease of one of the species described by the model. Therefore, for each signaling pathway we defined, by default, a reference species. While cAMP was chosen as reference species for the G<sub>s</sub> and G<sub>i/o</sub> pathway, for the G<sub>q/11</sub> pathway we chose IP<sub>3</sub> , Fig.5.
 <br /> <br />
 <figure>
-<img src="./img/fig7.png" alt='equation' width="800" >
+<img src="./img/fig7.png" alt='scheme' width="800" >
 <figcaptation align='center'>Fig. 7 - Conceptual scheme for predicting dose-response through signaling pathways’ simulation. For each concentration value the signaling model is simulated obtaining in the end several curve of the concentration of a specific species of the pathway as function of time. After, the maximum value of each curve is selected and plotted, resulting, in the end, in the dose-response curve.</figcaptation >
 </figure>
 <br /> <br />
-- 
GitLab