diff --git a/.DS_Store b/.DS_Store
index 6bf5e34215cbe74bd4099f84a89a3a2ded899de1..50e9336d55a8a60a263247f1a864a247c02bbe61 100644
Binary files a/.DS_Store and b/.DS_Store differ
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..292ef74f0765043158a7ab2fa88a7efd7785b6ae
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,30 @@
+# System files Mac
+._*
+Thumbs.db
+.DS_Store*
+
+# System files Windows
+Desktop.ini
+
+# Abaqus files
+*.com
+*.dat
+*.inp
+*.ipm
+*.log
+*.odb
+*.odb_f
+*.prt
+*.sim
+*.com
+*.sta
+*.jnl
+*.cae
+
+#other ignores
+/.idea
+/.vagrant
+Makefile
+/__pycache__
+/docs/source
+*.pyc
diff --git a/public/.buildinfo b/public/.buildinfo
old mode 100644
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diff --git a/public/.nojekyll b/public/.nojekyll
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diff --git a/public/HowToRun.html b/public/HowToRun.html
old mode 100644
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index b1240f6b0a27eb9fdd903ee1c81713d259180b80..cf0889fb98f9c37a0aac67babde0fb987f59bb63
--- a/public/HowToRun.html
+++ b/public/HowToRun.html
@@ -109,7 +109,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
diff --git a/public/LoadCase.html b/public/LoadCase.html
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diff --git a/public/Parts.html b/public/Parts.html
old mode 100644
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diff --git a/public/Project_idea.html b/public/Project_idea.html
old mode 100644
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index 4054ddb12615005b1932d48f3b2aed2b77055328..e36c193d2522bb9ceff33ee69d7814907a550d50
--- a/public/Project_idea.html
+++ b/public/Project_idea.html
@@ -100,7 +100,6 @@
<li class="toctree-l1"><a class="reference internal" href="Parts.html">Parts package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleAssembly.html">SpindleAssembly package</a></li>
<li class="toctree-l1"><a class="reference internal" href="SpindleMesh.html">SpindleMesh package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="job.html">job module</a></li>
</ul>
diff --git a/public/SpindleAssembly.html b/public/SpindleAssembly.html
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diff --git a/public/SpindleMesh.html b/public/SpindleMesh.html
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diff --git a/public/Theoretical_background.html b/public/Theoretical_background.html
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diff --git a/public/_images/Cell.pdf b/public/_images/Cell.pdf
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index 0000000000000000000000000000000000000000..fd633c07ed46faaaf29680cb6e8ce9b969250d9e
Binary files /dev/null and b/public/_images/Cell.pdf differ
diff --git a/public/_images/GUIstp1.pdf b/public/_images/GUIstp1.pdf
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diff --git a/public/_images/GUIstp3.pdf b/public/_images/GUIstp3.pdf
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diff --git a/public/_images/MT_structure.pdf b/public/_images/MT_structure.pdf
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diff --git a/public/_images/MTangle.pdf b/public/_images/MTangle.pdf
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diff --git a/public/_images/Spindle_image.svg b/public/_images/Spindle_image.svg
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diff --git a/public/_images/Spindle_mode2.eps b/public/_images/Spindle_mode2.eps
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diff --git a/public/_images/interlinked_zone.pdf b/public/_images/interlinked_zone.pdf
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diff --git a/public/_images/spindle_html.pdf b/public/_images/spindle_html.pdf
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diff --git a/public/_modules/LoadCase/Interaction.html b/public/_modules/LoadCase/Interaction.html
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diff --git a/public/_modules/LoadCase/InteractionHelpers.html b/public/_modules/LoadCase/InteractionHelpers.html
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diff --git a/public/_modules/LoadCase/LoadsAndBCs.html b/public/_modules/LoadCase/LoadsAndBCs.html
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diff --git a/public/_modules/LoadCase/Step.html b/public/_modules/LoadCase/Step.html
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diff --git a/public/_modules/Parts/GeometryBuilder.html b/public/_modules/Parts/GeometryBuilder.html
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diff --git a/public/_modules/Parts/standard_parts.html b/public/_modules/Parts/standard_parts.html
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diff --git a/public/_modules/SpindleAssembly/AddComponents.html b/public/_modules/SpindleAssembly/AddComponents.html
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diff --git a/public/_modules/SpindleAssembly/PositionComponents.html b/public/_modules/SpindleAssembly/PositionComponents.html
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diff --git a/public/_modules/SpindleAssembly/PositionConnectors.html b/public/_modules/SpindleAssembly/PositionConnectors.html
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diff --git a/public/_modules/SpindleAssembly/PositionIpMTs.html b/public/_modules/SpindleAssembly/PositionIpMTs.html
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diff --git a/public/_modules/SpindleAssembly/assembly_random.html b/public/_modules/SpindleAssembly/assembly_random.html
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diff --git a/public/_modules/SpindleMesh/generate_mesh.html b/public/_modules/SpindleMesh/generate_mesh.html
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diff --git a/public/_modules/index.html b/public/_modules/index.html
old mode 100644
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diff --git a/public/_sources/HowToRun.rst.txt b/public/_sources/HowToRun.rst.txt
old mode 100644
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diff --git a/public/_sources/LoadCase.rst.txt b/public/_sources/LoadCase.rst.txt
old mode 100644
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diff --git a/public/_sources/Parts.rst.txt b/public/_sources/Parts.rst.txt
old mode 100644
new mode 100755
diff --git a/public/_sources/Project_idea.rst.txt b/public/_sources/Project_idea.rst.txt
old mode 100644
new mode 100755
diff --git a/public/_sources/SpindleAssembly.rst.txt b/public/_sources/SpindleAssembly.rst.txt
old mode 100644
new mode 100755
diff --git a/public/_sources/SpindleMesh.rst.txt b/public/_sources/SpindleMesh.rst.txt
old mode 100644
new mode 100755
diff --git a/public/_sources/Theoretical_background.rst.txt b/public/_sources/Theoretical_background.rst.txt
old mode 100644
new mode 100755
diff --git a/public/_sources/index.rst.txt b/public/_sources/index.rst.txt
old mode 100644
new mode 100755
index d54470e078c5819a235e3da46997a18e0cec42a2..394963690240ab93c1733a0ce07a5c1b9c0fd57a
--- a/public/_sources/index.rst.txt
+++ b/public/_sources/index.rst.txt
@@ -3,12 +3,12 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-Welcome to the interactive documentation of the Spindle FEA application
-===================================
-
-.. figure:: images/Spindle_mode2.eps
+.. figure:: images/Cell.pdf
:align: center
+Welcome to the interactive documentation of the Spindle FEA application
+=======================================================================
+
This the interactive documentation of the application designed to perform parametric stability modelling of the
mitotic spindle structures within various cell types during mitosis. The application relies on `Abaqus CAE
<https://www.3ds.com/products-services/simulia/products/abaqus/abaquscae/>`_ finite
diff --git a/public/_sources/job.rst.txt b/public/_sources/job.rst.txt
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diff --git a/public/_static/css/theme.css b/public/_static/css/theme.css
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diff --git a/public/_static/documentation_options.js b/public/_static/documentation_options.js
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diff --git a/public/_static/searchtools.js b/public/_static/searchtools.js
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diff --git a/public/_static/underscore-1.3.1.js b/public/_static/underscore-1.3.1.js
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diff --git a/public/_static/underscore.js b/public/_static/underscore.js
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diff --git a/public/_static/up-pressed.png b/public/_static/up-pressed.png
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diff --git a/public/_static/up.png b/public/_static/up.png
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diff --git a/public/_static/websupport.js b/public/_static/websupport.js
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diff --git a/public/genindex.html b/public/genindex.html
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diff --git a/public/index.html b/public/index.html
old mode 100644
new mode 100755
index 68c0263b158f75d2154edad838f68b1a9258df8e..23ddeafc6a927103d9aaa36f2f495a6277df0577
--- a/public/index.html
+++ b/public/index.html
@@ -162,11 +162,11 @@
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
- <div class="section" id="welcome-to-the-interactive-documentation-of-the-spindle-fea-application">
-<h1>Welcome to the interactive documentation of the Spindle FEA application<a class="headerlink" href="#welcome-to-the-interactive-documentation-of-the-spindle-fea-application" title="Permalink to this headline">¶</a></h1>
-<div class="figure align-center">
-<img alt="_images/Spindle_mode2.eps" src="_images/Spindle_mode2.eps" />
+ <div class="figure align-center">
+<img alt="_images/Cell.pdf" src="_images/Cell.pdf" />
</div>
+<div class="section" id="welcome-to-the-interactive-documentation-of-the-spindle-fea-application">
+<h1>Welcome to the interactive documentation of the Spindle FEA application<a class="headerlink" href="#welcome-to-the-interactive-documentation-of-the-spindle-fea-application" title="Permalink to this headline">¶</a></h1>
<p>This the interactive documentation of the application designed to perform parametric stability modelling of the
mitotic spindle structures within various cell types during mitosis. The application relies on <a class="reference external" href="https://www.3ds.com/products-services/simulia/products/abaqus/abaquscae/">Abaqus CAE</a> finite
element code and allows users to design and execute mitotic spindle modelling provided the essential spindle parameter
diff --git a/public/job.html b/public/job.html
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diff --git a/public/modules.html b/public/modules.html
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diff --git a/public/py-modindex.html b/public/py-modindex.html
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diff --git a/public/search.html b/public/search.html
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diff --git a/public/style.css b/public/style.css
deleted file mode 100755
index 3eae4084bda0c2270306b14ac8c1ca732415edc3..0000000000000000000000000000000000000000
--- a/public/style.css
+++ /dev/null
@@ -1,24 +0,0 @@
-body {
- font-family: sans-serif;
- margin: auto;
- max-width: 1280px;
-}
-
-.navbar {
- background-color: #313236;
- border-radius: 2px;
- max-width: 800px;
-}
-
-.navbar a {
- color: #aaa;
- display: inline-block;
- font-size: 15px;
- padding: 10px;
- text-decoration: none;
-}
-
-.navbar a:hover {
- color: #ffffff;
-}
-