From aebf0683a7c5146c25995355a82b361056bad598 Mon Sep 17 00:00:00 2001
From: ADDALemos <alexandre_dal@hotmail.com>
Date: Fri, 9 Dec 2016 22:35:52 +0000
Subject: [PATCH 01/10] Create gh-pages branch via GitHub

---
 index.html  | 12 ++++++++++--
 params.json |  2 +-
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/index.html b/index.html
index 1899f9c..3fa8167 100644
--- a/index.html
+++ b/index.html
@@ -69,11 +69,14 @@ <h1>
 
 <p>An ASP solver (contained in the source folder) and available at:</p>
 
-<p><a href="https://github.com/potassco/clingo">clingo</a>
-Use the Quince McCluskey algorithm available at:</p>
+<p><a href="https://github.com/potassco/clingo">clingo</a></p>
+
+<p>Use the Quince McCluskey algorithm available at:</p>
 
 <p><a href="https://github.com/pfpacket/Quine-McCluskey">Quine-McCluskey</a> (to compile requires the Boost C++ Libraries <a href="http://www.boost.org/">boost.org</a></p>
 
+<hr>
+
 <h2>
 <a id="data-sets" class="anchor" href="#data-sets" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Data Sets</h2>
 
@@ -100,6 +103,11 @@ <h1>
 
 <p>If you have any comments or questions, please <a href="mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=%5BRepairing%20Boolean%20regulatory%20networks%5D">contact us</a>.</p>
 
+<h1>
+<a id="previous-work" class="anchor" href="#previous-work" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Previous Work</h1>
+
+<p><a href="http://web.ist.utl.pt/%7Ealexandre.lemos/rbn/">Repairing Steady State Boolean Regulatory Network</a></p>
+
       <footer class="site-footer">
         <span class="site-footer-owner"><a href="https://github.com/ADDALemos/RBN">Repairing Boolean Networks using ASP</a> is maintained by <a href="https://github.com/ADDALemos">ADDALemos</a>.</span>
 
diff --git a/params.json b/params.json
index 85527d6..63434cc 100644
--- a/params.json
+++ b/params.json
@@ -1,6 +1,6 @@
 {
   "name": "Repairing Boolean Networks using ASP",
   "tagline": "",
-  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generete the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series has only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\nUse the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries [boost.org](http://www.boost.org/)\r\n\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady are available two data sets originaly obtain from .\r\nAs the model did not have functions associated with them, all nodes are explained by the same function. Where a node is present if it has at least one activator and has no inbitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly genereted using the available on the folder scripts. The model was genereted using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).",
+  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generete the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series has only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\n\r\nUse the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries [boost.org](http://www.boost.org/)\r\n\r\n***\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady are available two data sets originaly obtain from .\r\nAs the model did not have functions associated with them, all nodes are explained by the same function. Where a node is present if it has at least one activator and has no inbitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly genereted using the available on the folder scripts. The model was genereted using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).\r\n\r\n# Previous Work\r\n[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)",
   "note": "Don't delete this file! It's used internally to help with page regeneration."
 }
\ No newline at end of file

From b7c742af393f52a9808dc3d6fc744ce31c716296 Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Tue, 13 Dec 2016 23:08:33 +0000
Subject: [PATCH 02/10] Create gh-pages branch via GitHub

---
 index.html  | 14 +++++++-------
 params.json |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/index.html b/index.html
index 3fa8167..bb5fbca 100644
--- a/index.html
+++ b/index.html
@@ -32,7 +32,7 @@ <h1>
 <a id="how-to-run-the-project" class="anchor" href="#how-to-run-the-project" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>How to run the project</h1>
 
 <p><code>./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]</code>
-This will generete the repair models in the examples folder.</p>
+This will generate the repair models in the examples folder.</p>
 
 <h2>
 <a id="arguments-of-the-program" class="anchor" href="#arguments-of-the-program" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Arguments of the program</h2>
@@ -40,7 +40,7 @@ <h2>
 <h3>
 <a id="type" class="anchor" href="#type" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Type:</h3>
 
-<p>If the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series has only two columns with the same values.</p>
+<p>If the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.</p>
 
 <h3>
 <a id="available-repair-operations" class="anchor" href="#available-repair-operations" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Available repair operations:</h3>
@@ -60,7 +60,7 @@ <h3>
 <h3>
 <a id="experimental-values" class="anchor" href="#experimental-values" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Experimental values</h3>
 
-<p>The program can deal with 0 or more observations. The observations correspond to a time-series and is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.</p>
+<p>The program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.</p>
 
 <hr>
 
@@ -71,7 +71,7 @@ <h1>
 
 <p><a href="https://github.com/potassco/clingo">clingo</a></p>
 
-<p>Use the Quince McCluskey algorithm available at:</p>
+<p>Uses the Quince McCluskey algorithm available at:</p>
 
 <p><a href="https://github.com/pfpacket/Quine-McCluskey">Quine-McCluskey</a> (to compile requires the Boost C++ Libraries <a href="http://www.boost.org/">boost.org</a></p>
 
@@ -83,13 +83,13 @@ <h2>
 <h3>
 <a id="steady-state" class="anchor" href="#steady-state" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Steady State</h3>
 
-<p>In the folder examples/steady are available two data sets originaly obtain from .
-As the model did not have functions associated with them, all nodes are explained by the same function. Where a node is present if it has at least one activator and has no inbitors.</p>
+<p>In the folder examples/steady two data sets originaly obtained from  are available.
+As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inbitors.</p>
 
 <h3>
 <a id="time-series" class="anchor" href="#time-series" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Time-series</h3>
 
-<p>The data sets in the folder examples/time were randomly genereted using the available on the folder scripts. The model was genereted using the script available at <a href="https://github.com/ptgm/BoolNetR2GINsim">BoolNetR2GINsim</a>.</p>
+<p>The data sets in the folder examples/time were randomly genereted using the program available on the folder scripts. The model was generated using the script available at <a href="https://github.com/ptgm/BoolNetR2GINsim">BoolNetR2GINsim</a>.</p>
 
 <hr>
 
diff --git a/params.json b/params.json
index 63434cc..d131bc1 100644
--- a/params.json
+++ b/params.json
@@ -1,6 +1,6 @@
 {
   "name": "Repairing Boolean Networks using ASP",
   "tagline": "",
-  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generete the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series has only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\n\r\nUse the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries [boost.org](http://www.boost.org/)\r\n\r\n***\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady are available two data sets originaly obtain from .\r\nAs the model did not have functions associated with them, all nodes are explained by the same function. Where a node is present if it has at least one activator and has no inbitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly genereted using the available on the folder scripts. The model was genereted using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).\r\n\r\n# Previous Work\r\n[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)",
+  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generate the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\n\r\nUses the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries [boost.org](http://www.boost.org/)\r\n\r\n***\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady two data sets originaly obtained from  are available.\r\nAs the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inbitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly genereted using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).\r\n\r\n# Previous Work\r\n[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)",
   "note": "Don't delete this file! It's used internally to help with page regeneration."
 }
\ No newline at end of file

From 6d533f5dd19ca8266279c7f0bfb21464e1e5d283 Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Wed, 14 Dec 2016 16:46:59 +0000
Subject: [PATCH 03/10] Create gh-pages branch via GitHub

---
 index.html  | 8 ++++----
 params.json | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/index.html b/index.html
index bb5fbca..6a75889 100644
--- a/index.html
+++ b/index.html
@@ -73,7 +73,7 @@ <h1>
 
 <p>Uses the Quince McCluskey algorithm available at:</p>
 
-<p><a href="https://github.com/pfpacket/Quine-McCluskey">Quine-McCluskey</a> (to compile requires the Boost C++ Libraries <a href="http://www.boost.org/">boost.org</a></p>
+<p><a href="https://github.com/pfpacket/Quine-McCluskey">Quine-McCluskey</a> (to compile requires the Boost C++ Libraries) <a href="http://www.boost.org/">boost.org</a></p>
 
 <hr>
 
@@ -83,13 +83,13 @@ <h2>
 <h3>
 <a id="steady-state" class="anchor" href="#steady-state" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Steady State</h3>
 
-<p>In the folder examples/steady two data sets originaly obtained from  are available.
-As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inbitors.</p>
+<p>In the folder examples/steady two data sets originally obtained from  are available.
+As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.</p>
 
 <h3>
 <a id="time-series" class="anchor" href="#time-series" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Time-series</h3>
 
-<p>The data sets in the folder examples/time were randomly genereted using the program available on the folder scripts. The model was generated using the script available at <a href="https://github.com/ptgm/BoolNetR2GINsim">BoolNetR2GINsim</a>.</p>
+<p>The data sets in the folder examples/time were randomly generated using the program available on the folder scripts. The model was generated using the script available at <a href="https://github.com/ptgm/BoolNetR2GINsim">BoolNetR2GINsim</a>.</p>
 
 <hr>
 
diff --git a/params.json b/params.json
index d131bc1..8da63d4 100644
--- a/params.json
+++ b/params.json
@@ -1,6 +1,6 @@
 {
   "name": "Repairing Boolean Networks using ASP",
   "tagline": "",
-  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generate the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\n\r\nUses the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries [boost.org](http://www.boost.org/)\r\n\r\n***\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady two data sets originaly obtained from  are available.\r\nAs the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inbitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly genereted using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).\r\n\r\n# Previous Work\r\n[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)",
+  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generate the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\n\r\nUses the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries) [boost.org](http://www.boost.org/)\r\n\r\n***\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady two data sets originally obtained from  are available.\r\nAs the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly generated using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).\r\n\r\n# Previous Work\r\n[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)",
   "note": "Don't delete this file! It's used internally to help with page regeneration."
 }
\ No newline at end of file

From 1857f51fbbe7d2519433ac37f0ef4de3a800ccbc Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Mon, 2 Jan 2017 19:00:08 +0000
Subject: [PATCH 04/10] Set theme jekyll-theme-cayman and migrate Page
 Generator content

---
 _config.yml                  |   8 +
 index.html                   | 121 ----------
 index.md                     |  56 +++++
 params.json                  |   6 -
 stylesheets/github-light.css | 124 ----------
 stylesheets/normalize.css    | 424 -----------------------------------
 stylesheets/stylesheet.css   | 245 --------------------
 7 files changed, 64 insertions(+), 920 deletions(-)
 create mode 100644 _config.yml
 delete mode 100644 index.html
 create mode 100644 index.md
 delete mode 100644 params.json
 delete mode 100644 stylesheets/github-light.css
 delete mode 100644 stylesheets/normalize.css
 delete mode 100644 stylesheets/stylesheet.css

diff --git a/_config.yml b/_config.yml
new file mode 100644
index 0000000..8ea79b0
--- /dev/null
+++ b/_config.yml
@@ -0,0 +1,8 @@
+title: Repairing Boolean Networks using ASP
+description: 
+google_analytics: 
+show_downloads: true
+theme: jekyll-theme-cayman
+
+gems:
+  - jekyll-mentions
diff --git a/index.html b/index.html
deleted file mode 100644
index 6a75889..0000000
--- a/index.html
+++ /dev/null
@@ -1,121 +0,0 @@
-<!DOCTYPE html>
-<html lang="en-us">
-  <head>
-    <meta charset="UTF-8">
-    <title>Repairing Boolean Networks using ASP by ADDALemos</title>
-    <meta name="viewport" content="width=device-width, initial-scale=1">
-    <link rel="stylesheet" type="text/css" href="stylesheets/normalize.css" media="screen">
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
-    <link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
-    <link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
-  </head>
-  <body>
-    <section class="page-header">
-      <h1 class="project-name">Repairing Boolean Networks using ASP</h1>
-      <h2 class="project-tagline"></h2>
-      <a href="https://github.com/ADDALemos/RBN" class="btn">View on GitHub</a>
-      <a href="https://github.com/ADDALemos/RBN/zipball/master" class="btn">Download .zip</a>
-      <a href="https://github.com/ADDALemos/RBN/tarball/master" class="btn">Download .tar.gz</a>
-    </section>
-
-    <section class="main-content">
-      <h1>
-<a id="abstract" class="anchor" href="#abstract" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Abstract</h1>
-
-<hr>
-
-<p>Bla</p>
-
-<hr>
-
-<h1>
-<a id="how-to-run-the-project" class="anchor" href="#how-to-run-the-project" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>How to run the project</h1>
-
-<p><code>./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]</code>
-This will generate the repair models in the examples folder.</p>
-
-<h2>
-<a id="arguments-of-the-program" class="anchor" href="#arguments-of-the-program" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Arguments of the program</h2>
-
-<h3>
-<a id="type" class="anchor" href="#type" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Type:</h3>
-
-<p>If the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.</p>
-
-<h3>
-<a id="available-repair-operations" class="anchor" href="#available-repair-operations" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Available repair operations:</h3>
-
-<ul>
-<li>Repair e - removes regulator</li>
-<li>Repair i - negates a regulator</li>
-<li>Repair g - changes AND function to OR function
-Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.</li>
-</ul>
-
-<h3>
-<a id="model" class="anchor" href="#model" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Model</h3>
-
-<p>The model has to be encoded in Boolsim (<a href="http://www.colomoto.org/formats/boolsim.html">format</a>). </p>
-
-<h3>
-<a id="experimental-values" class="anchor" href="#experimental-values" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Experimental values</h3>
-
-<p>The program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.</p>
-
-<hr>
-
-<h1>
-<a id="dependencies" class="anchor" href="#dependencies" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Dependencies</h1>
-
-<p>An ASP solver (contained in the source folder) and available at:</p>
-
-<p><a href="https://github.com/potassco/clingo">clingo</a></p>
-
-<p>Uses the Quince McCluskey algorithm available at:</p>
-
-<p><a href="https://github.com/pfpacket/Quine-McCluskey">Quine-McCluskey</a> (to compile requires the Boost C++ Libraries) <a href="http://www.boost.org/">boost.org</a></p>
-
-<hr>
-
-<h2>
-<a id="data-sets" class="anchor" href="#data-sets" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Data Sets</h2>
-
-<h3>
-<a id="steady-state" class="anchor" href="#steady-state" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Steady State</h3>
-
-<p>In the folder examples/steady two data sets originally obtained from  are available.
-As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.</p>
-
-<h3>
-<a id="time-series" class="anchor" href="#time-series" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Time-series</h3>
-
-<p>The data sets in the folder examples/time were randomly generated using the program available on the folder scripts. The model was generated using the script available at <a href="https://github.com/ptgm/BoolNetR2GINsim">BoolNetR2GINsim</a>.</p>
-
-<hr>
-
-<h1>
-<a id="authors" class="anchor" href="#authors" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Authors</h1>
-
-<p>Alexandre Lemos, <a href="http://pedromonteiro.org/">Pedro T. Monteiro</a> and <a href="http://sat.inesc-id.pt/%7Eines/">Inês Lynce</a>.</p>
-
-<h1>
-<a id="contacts" class="anchor" href="#contacts" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Contacts:</h1>
-
-<p>If you have any comments or questions, please <a href="mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=%5BRepairing%20Boolean%20regulatory%20networks%5D">contact us</a>.</p>
-
-<h1>
-<a id="previous-work" class="anchor" href="#previous-work" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Previous Work</h1>
-
-<p><a href="http://web.ist.utl.pt/%7Ealexandre.lemos/rbn/">Repairing Steady State Boolean Regulatory Network</a></p>
-
-      <footer class="site-footer">
-        <span class="site-footer-owner"><a href="https://github.com/ADDALemos/RBN">Repairing Boolean Networks using ASP</a> is maintained by <a href="https://github.com/ADDALemos">ADDALemos</a>.</span>
-
-        <span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong">Jason Long</a>.</span>
-      </footer>
-
-    </section>
-
-  
-  </body>
-</html>
diff --git a/index.md b/index.md
new file mode 100644
index 0000000..ecabfa1
--- /dev/null
+++ b/index.md
@@ -0,0 +1,56 @@
+# Abstract 
+***
+Bla
+
+***
+# How to run the project
+
+`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`
+This will generate the repair models in the examples folder.
+
+## Arguments of the program
+### Type:
+
+If the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.
+
+### Available repair operations:
+
+* Repair e - removes regulator
+* Repair i - negates a regulator
+* Repair g - changes AND function to OR function
+Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.
+
+### Model
+
+The model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). 
+
+### Experimental values
+
+The program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.
+
+
+***
+# Dependencies
+An ASP solver (contained in the source folder) and available at:
+
+[clingo](https://github.com/potassco/clingo)
+
+Uses the Quince McCluskey algorithm available at:
+
+[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries) [boost.org](http://www.boost.org/)
+
+***
+## Data Sets
+### Steady State
+In the folder examples/steady two data sets originally obtained from  are available.
+As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.
+### Time-series
+The data sets in the folder examples/time were randomly generated using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).
+***
+# Authors
+Alexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).
+# Contacts:
+If you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).
+
+# Previous Work
+[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)
\ No newline at end of file
diff --git a/params.json b/params.json
deleted file mode 100644
index 8da63d4..0000000
--- a/params.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
-  "name": "Repairing Boolean Networks using ASP",
-  "tagline": "",
-  "body": "# Abstract \r\n***\r\nBla\r\n\r\n***\r\n# How to run the project\r\n\r\n`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`\r\nThis will generate the repair models in the examples folder.\r\n\r\n## Arguments of the program\r\n### Type:\r\n\r\nIf the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.\r\n\r\n### Available repair operations:\r\n\r\n* Repair e - removes regulator\r\n* Repair i - negates a regulator\r\n* Repair g - changes AND function to OR function\r\nNote: All the combinations of repairs are allowed, and they need to be written in alphabetical order.\r\n\r\n### Model\r\n\r\nThe model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). \r\n\r\n### Experimental values\r\n\r\nThe program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.\r\n\r\n\r\n***\r\n# Dependencies\r\nAn ASP solver (contained in the source folder) and available at:\r\n\r\n[clingo](https://github.com/potassco/clingo)\r\n\r\nUses the Quince McCluskey algorithm available at:\r\n\r\n[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries) [boost.org](http://www.boost.org/)\r\n\r\n***\r\n## Data Sets\r\n### Steady State\r\nIn the folder examples/steady two data sets originally obtained from  are available.\r\nAs the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.\r\n### Time-series\r\nThe data sets in the folder examples/time were randomly generated using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).\r\n***\r\n# Authors\r\nAlexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).\r\n# Contacts:\r\nIf you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).\r\n\r\n# Previous Work\r\n[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)",
-  "note": "Don't delete this file! It's used internally to help with page regeneration."
-}
\ No newline at end of file
diff --git a/stylesheets/github-light.css b/stylesheets/github-light.css
deleted file mode 100644
index 0c6b24d..0000000
--- a/stylesheets/github-light.css
+++ /dev/null
@@ -1,124 +0,0 @@
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-The MIT License (MIT)
-
-Copyright (c) 2016 GitHub, Inc.
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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diff --git a/stylesheets/normalize.css b/stylesheets/normalize.css
deleted file mode 100644
index 30366a6..0000000
--- a/stylesheets/normalize.css
+++ /dev/null
@@ -1,424 +0,0 @@
-/*! normalize.css v3.0.2 | MIT License | git.io/normalize */
-
-/**
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- * 2. Prevent iOS text size adjust after orientation change, without disabling
- *    user zoom.
- */
-
-html {
-  font-family: sans-serif; /* 1 */
-  -ms-text-size-adjust: 100%; /* 2 */
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- */
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diff --git a/stylesheets/stylesheet.css b/stylesheets/stylesheet.css
deleted file mode 100644
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+++ /dev/null
@@ -1,245 +0,0 @@
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-  border-radius: 0.3rem;
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-  .btn + .btn {
-    margin-left: 1rem; }
-
-.btn:hover {
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From 5a3d07be1b06cac212749cba2aa7a152350f1b4c Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Mon, 2 Jan 2017 19:04:04 +0000
Subject: [PATCH 05/10] Steady state and examples

---
 index.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/index.md b/index.md
index ecabfa1..f5b5e31 100644
--- a/index.md
+++ b/index.md
@@ -5,13 +5,13 @@ Bla
 ***
 # How to run the project
 
-`./Converter type [asynchronous|synchronous] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`
+`./Converter type [asynchronous|synchronous|steady_state] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`
 This will generate the repair models in the examples folder.
 
 ## Arguments of the program
 ### Type:
 
-If the model is asynchronous or synchronous. For steady state, please consider the synchronous where the time-series have only two columns with the same values.
+If the model is asynchronous, synchronous or is in steady state.
 
 ### Available repair operations:
 
@@ -19,7 +19,7 @@ If the model is asynchronous or synchronous. For steady state, please consider t
 * Repair i - negates a regulator
 * Repair g - changes AND function to OR function
 Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.
-
+Some examples with small networks are available in the folder: `examples/repairs`.
 ### Model
 
 The model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). 
@@ -53,4 +53,4 @@ Alexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce
 If you have any comments or questions, please [contact us](mailto:ines.lynce@tecnico.ulisboa.pt;alexandre.lemos@tecnico.ulisboa.pt;pedro.tiago.monteiro@tecnico.pt;?subject=[Repairing%20Boolean%20regulatory%20networks]).
 
 # Previous Work
-[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)
\ No newline at end of file
+[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)

From 34af22b440cdc3c1a3c5bf6f31288e8ec25e443f Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Mon, 2 Jan 2017 19:04:58 +0000
Subject: [PATCH 06/10] Set theme jekyll-theme-cayman


From e69a5281c8ee2eda370d8953e7a9bb399141b3e1 Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Mon, 2 Jan 2017 19:06:30 +0000
Subject: [PATCH 07/10] Set theme jekyll-theme-cayman


From f92d7e4165e784d9e5517d29fc924501275868ca Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Mon, 2 Jan 2017 19:07:52 +0000
Subject: [PATCH 08/10] Update index.md

---
 index.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/index.md b/index.md
index f5b5e31..60fc430 100644
--- a/index.md
+++ b/index.md
@@ -20,6 +20,7 @@ If the model is asynchronous, synchronous or is in steady state.
 * Repair g - changes AND function to OR function
 Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.
 Some examples with small networks are available in the folder: `examples/repairs`.
+
 ### Model
 
 The model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). 

From ce1286979f490cb56baf1be9bfca018cf00232fd Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Tue, 3 Jan 2017 11:28:45 +0000
Subject: [PATCH 09/10] spacing error

---
 index.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/index.md b/index.md
index 60fc430..1619f4b 100644
--- a/index.md
+++ b/index.md
@@ -18,8 +18,10 @@ If the model is asynchronous, synchronous or is in steady state.
 * Repair e - removes regulator
 * Repair i - negates a regulator
 * Repair g - changes AND function to OR function
+
 Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.
-Some examples with small networks are available in the folder: `examples/repairs`.
+
+Some examples with small networks are available in the folder: `examples/repairs`, showing the effects of the repair operations.
 
 ### Model
 

From 6d079ecc03a4be9b3160de3126ab58623de4b26f Mon Sep 17 00:00:00 2001
From: Alexandre Lemos <alexandre_dal@hotmail.com>
Date: Tue, 3 Jan 2017 12:41:39 +0000
Subject: [PATCH 10/10] Update index.md

---
 index.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/index.md b/index.md
index 1619f4b..6bdcc69 100644
--- a/index.md
+++ b/index.md
@@ -21,7 +21,7 @@ If the model is asynchronous, synchronous or is in steady state.
 
 Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.
 
-Some examples with small networks are available in the folder: `examples/repairs`, showing the effects of the repair operations.
+Some examples with small networks are available in the folder: `examples/steady/repairs`, showing the effects of the repair operations.
 
 ### Model
 
@@ -45,10 +45,10 @@ Uses the Quince McCluskey algorithm available at:
 ***
 ## Data Sets
 ### Steady State
-In the folder examples/steady two data sets originally obtained from  are available.
+In the folder `examples/steady/ecoli` two data sets originally obtained from  are available.
 As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.
 ### Time-series
-The data sets in the folder examples/time were randomly generated using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).
+The data sets in the folder `examples/time` were randomly generated using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).
 ***
 # Authors
 Alexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).