From fc187e5e788efcd000502f46085914c8fa6ebddb Mon Sep 17 00:00:00 2001
From: Yohan Jarosz <yohanjarosz@yahoo.fr>
Date: Tue, 3 Nov 2015 08:48:54 +0100
Subject: [PATCH] breaking changes

---
 _includes/footer.html      |   4 +-
 _includes/header.html      |   4 +-
 fetch_projects.sh          |   2 +-
 index.html                 |  63 +---
 web/bootstrap_project_page |   1 +
 web/imp                    |   1 +
 {projects => web}/index.md |   0
 web/minerva/index.md       | 711 +++++++++++++++++++++++++++++++++++++
 web/minerva/user guide.md  |   8 +
 9 files changed, 740 insertions(+), 54 deletions(-)
 create mode 120000 web/bootstrap_project_page
 create mode 120000 web/imp
 rename {projects => web}/index.md (100%)
 create mode 100644 web/minerva/index.md
 create mode 100644 web/minerva/user guide.md

diff --git a/_includes/footer.html b/_includes/footer.html
index bba9350..119a213 100644
--- a/_includes/footer.html
+++ b/_includes/footer.html
@@ -3,8 +3,8 @@
         <div class="footer-col-wrapper">
           <div class="footer-col  footer-col-1">
             <ul class="list-unstyled list-inline">
-              <li><img style="width: 70px" src="{{ site.baseurl }}/img/logoUni.png"></li>
-              <li><img style="width: 140px" src="{{ site.baseurl }}/img/logoLCSB.jpg"></li>
+              <li><img style="width: 70px" src="https://webdav-r3lab-server.uni.lu/public/biocore/logos/logoUni.png"></li>
+              <li><img style="width: 140px" src="https://webdav-r3lab-server.uni.lu/public/biocore/logos/logoLCSB-long.jpg"></li>
             </ul>
           </div>
 
diff --git a/_includes/header.html b/_includes/header.html
index 6ce99b0..79443ec 100644
--- a/_includes/header.html
+++ b/_includes/header.html
@@ -2,8 +2,8 @@
     <nav class="navbar navbar-inverse">
         <div class="container-fluid">
             {% if page.index %}
-                {% assign brand =  page.index | split:":" %}
-                <a class="navbar-brand" href="{{ site.baseurl }}/projects/{{brand[0]}}">{{brand[1]}}</a>
+                {% assign brand =  page.index | split:"$" %}
+                <a class="navbar-brand" href="{{ site.baseurl }}/web/{{brand[0]}}">{{brand[1]}}</a>
             {% endif %}
             <ul class="nav navbar-nav">
             {% if page.nav %}
diff --git a/fetch_projects.sh b/fetch_projects.sh
index b109cf5..f86bfc0 100755
--- a/fetch_projects.sh
+++ b/fetch_projects.sh
@@ -2,7 +2,7 @@
 
 # directory where reside this script (not working if no simlinks are in the path).
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-PROJECTS_DIR="$DIR/projects"
+PROJECTS_DIR="$DIR/web"
 
 # read config file passed as input
 while IFS=' ' read -r name url ; do
diff --git a/index.html b/index.html
index 7eb5e66..303620f 100644
--- a/index.html
+++ b/index.html
@@ -1,6 +1,6 @@
 ---
 layout: default
-index: ../:R3lab
+index: ../$R3lab
 nav: https://git-r3lab.uni.lu$Gitlab,https://webdav-r3lab.uni.lu$File Storage,https://docker-r3lab.uni.lu$Docker
 ---
 
@@ -9,56 +9,21 @@ nav: https://git-r3lab.uni.lu$Gitlab,https://webdav-r3lab.uni.lu$File Storage,ht
     <div class="jumbotron">
         <h1>Reproducible Research Results</h1>
         <div class="row marketing">
-          <div class="col-lg-6">
-            <h4>Browse public repositories</h4>
-                              <p><span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span>  <a href="/public/biocore">biocore</a></p>
-                              <p><span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span>  <a href="/public/R3lab">R3lab</a></p>
-                              <p><span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span>  <a href="/public/msp">msp</a></p>
-                          </div>
-        </div>
+          <div class="col-lg-6"></div>
         <div class="row marketing">
-          <div class="col-lg-6">
-            <h4>Private repositories - restricted access</h4>
-                              <p><span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span>  <a href="/private/R3">R3</a></p>
-                          </div>
+            <div class="col-lg-6"></div>
         </div>
     </div>
 
-    <div class="well">
-        <p>We provide two types of repositories:<br/>
-              <b>-   Public</b>: Anyone can see and download the data you put there. Useful to share your data with the world.<br/>
-              <b>-   Private</b>: Only allowed people can share data there.
-        </p>
-        <p>If you have question or want to have access <small>(Only people in UNI.lu can ask for write access)</small> <a class="btn btn-sm btn-success" href="mailto:lcsb-sysadmins@uni.lu" role="button">Ask for access</a></p>
+    <div class="jumbotron">
+        <h2>Hosted websites</h2>
+        {% for project in site.pages %}
+           {% if project.type == 'project' %}
+               {% assign index =  project.index | split:"$" %}
+              <p>
+                  <span class="glyphicon glyphicon-circle-arrow-right" aria-hidden="true"></span>  <a href="/web/{{index[0]}}">{{index[1]}}</a>
+                  {{project.description}}
+           {% endif %}
+        {% endfor %}
     </div>
-
-</div> <!-- /container -->
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-<dl class="dl-horizontal">
-{% for project in site.pages %}
-   {% if project.type == 'project' %}
-    <dt><a class="project-link" href="{{ project.url | prepend: site.baseurl }}">{{ project.title }}</a><dt>
-    <dd>{{project.description}}</dd>
-   {% endif %}
-{% endfor %}
-</dl>
+</div>
diff --git a/web/bootstrap_project_page b/web/bootstrap_project_page
new file mode 120000
index 0000000..f5374f0
--- /dev/null
+++ b/web/bootstrap_project_page
@@ -0,0 +1 @@
+/Users/yohan.jarosz/Documents/LCSB/biocore/bootstrap_project_page
\ No newline at end of file
diff --git a/web/imp b/web/imp
new file mode 120000
index 0000000..e5ce546
--- /dev/null
+++ b/web/imp
@@ -0,0 +1 @@
+/Users/yohan.jarosz/Documents/LCSB/biocore/IMP-website
\ No newline at end of file
diff --git a/projects/index.md b/web/index.md
similarity index 100%
rename from projects/index.md
rename to web/index.md
diff --git a/web/minerva/index.md b/web/minerva/index.md
new file mode 100644
index 0000000..a89c292
--- /dev/null
+++ b/web/minerva/index.md
@@ -0,0 +1,711 @@
+---
+layout: page
+title: Minerva
+index: minerva:Miverva Title
+type: project
+nav: userguide:User Guide,userguide2:User Guide 2
+---
+
+#### Licensing:
+
+What type of license? What about Google Maps API license?
+
+#### Debian package description:
+
+MINERVA (**M**olecular **I**nteraction **NE**two**R**k **V**isu**A**lization) platform is a standalone webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format. After installation, the resource is used and managed via a webbrowser, under the address configured …
+
+CellDesigner ([www.sbi.jp/celldesigner](https://www.google.com/url?q=http://www.sbi.jp/celldesigner&amp;sa=D&amp;usg=AFQjCNEtBcIj5pBHUw2BzRNJK25zhsdT2g))
+or SBGN (webref?) format files are accepted. Please, consult the user guide (webref?) for more details.
+
+> DISCLAIMER: to be written up
+
+
+
+
+#### man minerva description:
+
+<dl class="dl-horizontal">
+<dt>NAME</dt>
+<dd>minerva - a webserver for <b>m</b>olecular <b>i</b>nteraction <b>ne</b>two<b>r</b>k<b>v</b>isu<b>a</b>lization</dd>
+
+<dt>SYNOPSIS</dt>
+<dd>mode of use needed</dd>
+
+<dt>DESCRIPTION</dt>
+<dd>as above</dd>
+
+<dt>DISCLAIMER</dt>
+<dd>as above</dd>
+
+<dt>PARAMETERS</dt>
+<dd>mode of use needed</dd>
+
+<dt>OPTIONS</dt>
+<dd>mode of use needed</dd>
+<dt></dt><dd>start</dd>
+<dt></dt><dd>stop</dd>
+<dt></dt><dd>restore</dd>
+<dt></dt><dd>etc ...</dd>
+
+<dt>NOTES</dt>
+
+<dt>SEE ALSO</dt>
+<dd>javac, java, ... </dd>
+
+</dl>
+
+
+# 1. Introduction
+
+MINERVA (**M**olecular **I**nteraction **NE**two**R**k **V**isu**A**lization)  platform is a standalone
+webserver for visualization, exploration and management of molecular networks encoded in SBGN-compliant format (See **Appendix 6.1 source file**).
+
+> Copy from Implementation part of the MINERVA article here.
+
+Visualization of uploaded networks, generated by the platform, is accessible via a web browser to all viewers with the
+weblink to the resource. See **Section 4. User panel** for a description of functionalities available in the map.
+
+# 2. Installation
+
+> …
+
+# 3. Administrator view
+
+Administrator view refers to the set of functionalities for web-based management of the content and configuration of your MINERVA instance.
+
+## 3.1. Login
+Administrator view is accessible via the “ADMIN” button in the bottom left corner of the user view (see below). See also **Section 4 User view**.
+
+![Login view](images/image22.png){:width="800px"}
+
+
+Many projects (maps, networks) can be hosted in parallel on a single MINERVA instance (see <b>Section 4.1.1 Accessing the project**).
+and a user having administrator rights to at least one of them can log via “ADMIN”. After successful login (see below),
+you will have access to the administrator panel to manage your MINERVA instance.
+
+![Successful login](images/image30.png){:width="800px"}
+
+## 3.2. Comments
+This panel allows you to manage comments provided by users of your maps (see <b>Section 4.x User panel - Comments**).
+The panel to the right (<em>Projects</em>) allows you to switch between different maps.
+Current active map will be highlighted. For the current active map, comments will be displayed in the panel to the left.
+The field “Title” is a hyperlink to a given comment in the map.
+
+![Comments](images/image24.png){:width="800px"}
+
+
+Users logged in as administrators have a possibility to remove a comment, as for them an additional button is visible
+on the comment pop-up (see below, 1). You can provide a comment associated with the removed comment (see below, 2)
+and press the “Remove” button (see below, 3).
+
+![Remove Comments](images/image17.png){:width="800px"}
+
+
+The removed comment will no longer be visible among the pinned comments, and its status will be updated in the
+“Comments” panel (see below).
+
+![Removed Comment status](images/image07.png){:width="800px"}
+
+
+## 3.3. Map manager
+
+This panel allows you to add new projects and manage existing ones. In the top left corner, the name of current active
+project is displayed. The panel allows you to (1) add new projects (2) edit them and (3) examine messages generated
+during the upload of the project.
+
+![Map manager](images/image02.png){:width="800px"}
+
+
+### 3.3.1. Add project
+
+The “ADD PROJECT” button invokes a menu allowing you to upload your project and start its generation in the MINERVA platform.
+
+![Add project](images/image23.png){:width="800px"}
+
+#### 3.3.1.1. Fields of the “ADD PROJECT” window
+
+* File - Choose button: invokes a file upload dialog. For a quick start, CellDesigner files are accepted directly. Available options and configurations of the source file are discussed in <b>Section 6.1 Abppendix - Source file**.
+
+* ProjectId: a working name of the uploaded project on the MINERVA platform
+
+* Project name: the name of the uploaded project displayed in the top left corner of the Admin and User panels; your official name of the project
+
+* Complex: this section describes how main map and uploaded submaps (if any) are related. For more details on how to
+upload predefined layouts, data mining datasets, images with biological overview and submaps associated with the main
+ map, see <b>Appendix 6.1 Source file**.
+Ignore it if you submit a single file.
+    * <em>Filename</em>: name of one of multiple files
+    * <em>Name/em>: name of the main map, or a submap, in the project
+    * <em>Root model/em>: a column of checkboxes; only one position must be checked, corresponding to the main map in the project
+    * <em>Mapping file/em>: a column of checkboxes; only one position must be checked, corresponding to the mapping file
+    describing relationships between the main map and the submap(s)
+    * <em>Model type/em>: whether the submap is a pathway, or a list of downstream targets; currently in development and unused
+    * <em>File type/em>:  type of the uploaded file; recognized automatically.
+* Additional layouts: this section describes uploaded additional layouts (element and interaction colorings) to be
+generated and accessible for all users of the project via “Layouts” tab in the “User panel”.
+Ignore it if you submit a single file.
+    * <em>Filename</em>: name of one of custom layout files
+    * <em>Name</em>: name of the layout visible in the project
+    * <em>Description</em>: the text to appear after mouseover on the name of the layout.    
+* Data mining: this section describes data mining candidates uploaded for the project. Ignore it if you submit a single file.
+    * <em>Filename</em>: name of one of data mining files
+    * <em>Name</em>: name of the resource visible in the project
+    * <em>Source</em>: (optional) weblink to the source of the data mining set
+    * <em>Type</em>: currently in development and unused
+* Overview images: this section describes the uploaded overview images and their configuration file. It is a column of
+filenames. Ignore it if you submit a single file.
+* Version: a text field displayed next to the name of your project in the “User panel”.
+* Annotate model automatically: if this checkbox is checked, elements of the uploaded map will be automatically annotated using built in annotators.
+Behavior of the annotators can be configured by clicking the “Advanced” button (see <b>Section 3.3.1.1 Configure automatic annotation**).
+* Verify manuel annotations: if this checkbox is checked, elements and interactions of the uploaded map will be scanned
+for existing annotations; if present these existing annotations will be validated against a set of rules.
+Verification rules can be configured by clicking the “Advanced” button (see <b>Section 3.3.1.2 Verify manual annotations**).
+* Cache data: if this checkbox is checked, all hyperlinks in the project resolved by MIRIAM repository
+(e.g. cross-links to external bioinformatic databases) are resolved and cached.
+* Auto margin: if this checkbox is checked, upon generation of the graphics, empty spaces surrounding elements and interactions will be cropped
+* Display SBGN: if this checkbox is checked, the uploaded model will be displayed in SBGN format,
+instead of default CellDesigner format.
+
+#### 3.3.1.2. Configure automatic annotation
+The “Advanced” button, next to the “Annotate model automatically” checkbox under “ADD PROJECT” button, invokes a dedicated configuration window (see below).
+
+![Configuration window](images/image19.png){:width="800px"}
+
+Clicking on each element type (“Object annotators”) in the left panel, an annotator can be assigned in the right panel
+that will attempt to automatically retrieve information from external bioinformatic databases for each relevant element,
+and annotate them. There are a number annotators available, utilizing either the name, or existing identifier of an object.
+These are:
+<dl class="dl-horizontal">
+
+<dt>Biocompendium</dt>
+<dd>name of an element will be used to retrieve additional information, including: full name, symbols, description and identifiers:
+RefSeq, ENSEMBL, Entrez Gene identifier, HGNC symbol, KEGG, Reactome, Pubmed and others</dd>
+
+<dt>HGNC</dt>
+<dd>HGNC identifier, if present, or, if absent, name of an element will be used to retrieve additional information,
+including full name, symbols, description and identifiers: RefSeq, ENSEMBL and Entrez Gene identifier</dd>
+
+<dt>Uniprot:</dt>
+<dd>Uniprot identifier, if present, will be used to retrieve additional information, including HGNC symbol and identifier, and Entrez Gene identifier</dd>
+
+<dt>Entrez Gene</dt>
+<dd>Entrez Gene identifier, if present, will be used to retrieve additional information, including full name, synonyms,
+description, HGNC symbol and identifier, and ENSEMBL identifier</dd>
+
+<dt>ENSEMBL:</dt>
+<dd>ENSEMBL identifier, if present, will be used to retrieve additional information, including symbol, full name, synonyms,
+HGNC symbol and identifier, and Entrez Gene identifier</dd>
+
+<dt>ChEBI:</dt>
+<dd>Uniprot identifier, if present, will be used to retrieve additional information, including synonyms, parents and
+children in the ChEBI ontology tree</dd>
+
+<dt>Gene Ontology</dt>
+<dd>Uniprot identifier, if present, will be used to retrieve additional information, including full GO definition for
+this identifier.</dd>
+
+</dl>
+
+#### 3.3.1.3. Configure automatic verification
+The “Advanced” button, next to the “Verify manual annotations” checkbox under “ADD PROJECT” button, invokes a dedicated configuration window (see below).
+
+
+![Configuration window](images/image26.png){:width="800px"}
+
+Clicking on each element or interaction type (“Classes”) in the left panel:
+<dl class="dl-horizontal">
+<dt>top right panels</dt>
+<dd>a list of valid MIRIAM identifiers can be assigned. All elements or interactions in the uploaded model, annotated
+with an identifier outside of the “Valid” list will be flagged as warnings</dd>
+
+<dt>bottom rb panels</dt>
+<dd>a list of mandatory MIRIAM identifiers can be assigned. If checkbox “Require annotations” is checked, all elements
+or interactions in the uploaded model, annotated without at least one identifier marked as “Required” list will be
+flagged as warnings.</dd>
+</dl>
+
+#### 3.3.1.4. “Submit” button: project generation
+Clicking “Submit” button at the bottom of the “ADD PROJECT” dialog window will start generation of the project.
+The window will refresh automatically, showing status changes during the process. Any warnings raised during the process
+will cause an “exclamation mark” icon to appear next to the project status. The list of warnings is extended gradually,
+and you need to wait for the project completion to see the full list. You will receive an email notification after the
+generation is complete.
+
+It may happen that the project generation will result in a failure. An icon will be displayed, and a mouseover on it
+will display the reason for failure. Moreover, you will receive an email message detailing the error you have received.
+
+### 3.3.2. Edit project
+
+![Edit project](images/image02.png){:width="800px"}
+
+Clicking on the magnifying glass icon in the last column with the project parameters (see above, 2) will invoke a dialog
+window to modify the configuration of a generated project (see below)
+
+<b>General** is the first configuration tab, allowing edition of basic information about the project.
+Using “Remove” button you can permanently delete the current active project.
+
+![General tab](images/image03.png){:width="800px"}
+
+<b>Layouts** tab allows you to examine and manage layouts (custom colorings of elements and interactions) in the current
+project (see below). Layouts accessible for all users are marked as N/A in the “Owner” column. Below, you can examine
+layouts generated by other users. If you have appropriate privileges (see <b>Section 3.4 User manager**), you can remove
+generated layouts by pressing a respective button in the “Remove” column.
+<div class="alert alert-danger">Removed layouts cannot be restored.</div>
+
+![Layout tab](images/image15.png){:width="800px"}
+
+<b>Data mining** tab allows you to examine and manage data mining files uploaded for the project (see below).
+Using buttons in the “Data” column you can download respective datasets.
+
+![Data mining tab](images/image05.png){:width="800px"}
+
+<b>Users** tab provides a project-level overview of access and management rights of users registered on the platform
+(see below). First two columns (“Drug targeting advanced view” and “Edit suggested connections”) concern functionalities
+under development, they are currently not supported.
+Remaining columns (“Manage comments”, “Manage layouts” and “View project”) correspond to respective user privileges are
+discussed in detail in <b>Section 3.4 User manager**).
+
+![User tab](images/image00.png){:width="800px"}
+
+### 3.3.3. Examine warnings
+
+![Warnings](images/image02.png){:width="800px"}
+
+Clicking on the “exclamation mark” icon (if present) next to the project status description (see above, 3) will display
+the list of warnings raised during the generation of this project (see below).
+
+![Warnings list](images/image10.png){:width="800px"}
+
+
+The list can also be downloaded as a tab-delimited text file. Types and identifiers of the elements and interactions are
+listed in the left column (“No”), while the nature of an error is provided in the right column.
+The table below lists possible errors and their explanations:
+
+
+
+
+<table class="table table-striped">
+<tr>
+    <th>Warning type</th>
+    <th>Explanation</th>
+</tr>
+<tr> <td colspan="2" class="info">Warnings generated by automatic annotation</td></tr>
+<tr>
+    <td>[Annotator] annotation problem</td>
+    <td>[Annotator] (e.g. HGNC) could not retrieve correct information for this element or interaction. The probable reason is wrong manual annotation, or name, of this element or interaction</td>
+</tr>
+<tr>
+    <td>Cannot find information for element.</td>
+    <td>None of the assigned annotators were able to retrieve information for this element or interaction. The probable reason is wrong manual annotation, or name, of this element or interaction</td>
+</tr>
+<tr>
+    <td>Chemical name cannot be found in chebi: [name]</td>
+    <td>ChEBI annotator could not annotate the element or interaction correctly by name, as [name] is not a ChEBI-recognized name. The annotation by manually provided identifier may still be successful.</td>
+</tr>
+<tr>
+    <td>Former symbols list different than default [list]. Ignoring</td>
+    <td>Existing annotation of an element (list of symbols) is different than the [list] retrieved by one of the assigned annotators.</td>
+</tr>
+<tr>
+    <td>New full name different than default [full name]. Ignoring.</td>
+    <td>Existing annotation of an element (full name) is different than the [full name] retrieved by one of the assigned annotators.</td>
+</tr>
+<tr>
+    <td>New symbol different than default [symbol]. Ignoring.</td>
+    <td>Existing annotation of an element (symbol) is different than the [symbol] retrieved by one of the assigned annotators.</td>
+</tr>
+<tr>
+    <td>Synonyms list different than default [list]. Ignoring.</td>
+    <td>Existing annotation of an element (list of synonyms) is different than the [list] retrieved by one of the assigned annotators.</td>
+</tr>
+<tr> <td colspan="2" class="info">Warnings generated by verification of manual annotation</td></tr>
+<tr>
+    <td>contains invalid annotations:[annotation]</td>
+    <td>Configuration in “Validate manual annotations” did not foresee [annotation] as allowed for this element or interaction.</td>
+</tr>
+<tr>
+    <td>misses one of the following annotations:[list].</td>
+    <td>Configuration in “Validate manual annotations” required one of [list] of annotations for this element or interaction, but none was found.</td>
+</tr>
+<tr>
+    <td>misses annotations.</td>
+    <td>No annotation exists for this element or interaction. </td>
+</tr>
+<tr>
+    <td>Unknown miriam uri: [MIRIAM type]</td>
+    <td>An element or interaction was annotated with [MIRIAM type] - this type of identifier is currently not handled.</td>
+</tr>
+
+</table>
+
+
+## 3.4. User manager
+This panel allows you to manage users registered for a given instance of MINERVA platform (see below).
+
+![User manager](images/image20.png){:width="800px"}
+
+Registered users have access to additional functionalities besides accessing the visual content generated by the platform.
+Clicking on the “New user” button (above, 1) invokes the window allowing to set login, password and personal details of
+a new user. The window allows to set privileges of the new user. For a detailed explanation, see below.
+
+![User detail](images/image27.png){:width="800px"}
+
+Clicking on the magnifying glass icon (“User manager” figure above, 2) invokes a panel, allowing to configure privileges
+of a respective user. The panel is identical to the “New user“ window, with the exception of Id and login, which are
+assigned and not editable. The panel is shown in the figure below.
+
+![User detail2](images/image08.png){:width="800px"}
+
+The “User detail” window allows to configure the following parameters for a given registered user:
+
+* <b>Password** of the user
+* <b>Name**, <b>Surname** and <b>Email** details.
+* <b>Global privileges** concern all projects on your MINERVA instance
+    * <b>Add project** checkbox, if checked, grants the user access right to the “Add project” button and permits the user to
+    add new projects.
+    * <b>Custom layouts** field defines how many layouts can be created by a given user across all projects they have access
+    to on your instance of MINERVA platform
+    * <b>Manage configuration** checkbox, if checked, grants the user access right to access “Configuration” tab and permits
+    them to manage the global configuration of your instance of MINERVA platform.
+    * <b>Map management** checkbox, if checked, grants the user right to access “Map manager” tab and manage existing projects
+    * <b>User management** checkbox, if checked, grants the user right to access the “User manager” tab and permits the user
+    to manage users on your instance of MINERVA platform.
+* <b>Project-specific privileges** concern only the project, for which they are configured
+    * <b>Manage comments** checkbox, if checked, grants the user right to the “Comments” tab, and allows them to manage
+    comments for this specific project
+    * <b>Manage layouts** checkbox, if checked, grants the user right to manage layouts of all users for this specific project
+    * <b>View project** checkbox, if checked, grants the user right to view this specific project
+    * <b>Drug targeting advanced view** and <b>Edit suggested connections** are functionalities under development and are not
+    supported at the moment
+* <b>Remove** button removes this registered user from your instance of MINERVA platform
+
+
+## 3.5. Service status
+
+“Service status” tab lists all external services and databases cross-linked by MINERVA platform. The left column contains
+service name hyperlinked to the original website. The right column contains the status of the service. Clicking on
+“Service status” tab invokes a checkup of the services and an update of their status. The checkup may also be invoked
+by the “Refresh” button at the bottom of the window. The figure below illustrates the “Service status” tab.
+
+![Service status](images/image11.png){:width="800px"}
+
+
+## 3.6. Configuration
+“Configuration” tab provides a summary of the current version of your MINERVA instance. Moreover, it allows privileged
+users to configure global parameters of the MINERVA instance. Clicking “Refresh” button (see below, 1) displays the table
+of global parameters, which can be edited set using and “Save” button (see below, 2).
+
+![Configuration 1](images/image29.png){:width="800px"}
+
+![Configuration 2](images/image06.png){:width="800px"}
+
+The list of global MINERVA configuration parameters is displayed in figure above. These are:
+* <b>E-mail address** : e-mail address used for sending notifications about the activity of your MINERVA instance
+- project uploads, comments, etc.
+* <b>E-mail server login**, <b>E-mail server password**, <b>IMAP server** and <b>SMTP server**:
+configuration of your mail server for notification sending.
+* <b>Default project id**: the project that will be displayed by default under the root address of the platform (your.url/MapViewer/)
+* <b>Logo icon**: the filename of your logo icon, displayed in the bottom-right corner of the visualized content.
+* <b>Logo link**(after click): the website to which you will be redirected after clicking on the logo
+* <b>Max distance for clicking on element (px)**: the content visualized by MINERVA platform is interactive, and
+clicked elements or interactions are recognized by the vicinity of the click event. This parameter controls, how close
+to an element or interaction, in pixels, you need to click to select them.
+* <b>Email used for requesting an account**: the “Login” tab in the user interface features a “Request for an account”
+button; clicking the button will auto-generate an message to the e-mail, or list of e-mails separated by a semicolon, provided
+in this field
+* <b>Max number of results in search box**: it may happen that a “Search” query returns a large amount of results.
+This parameter allows to tune the performance of your MINERVA instance by setting the cap for the number of displayed results.
+* <b>Google Analytics** tracking ID used for statistics: MINERVA platform offers integration with Google Analytics to
+track user activity of your MINERVA instance by providing an appropriate Google Analytics ID in this field.
+* <b>Logo description**: the popup text that will be displayed upon mouseover on your logo.
+
+## 3.7. MIRIAM
+
+The “MIRIAM” panel lists all MIRIAM-supported resources
+([http://www.ebi.ac.uk/miriam/main/mdb?section=intro]("https://www.google.com/url?q=http://www.ebi.ac.uk/miriam/main/mdb?section%3Dintro&amp;sa=D&amp;usg=AFQjCNHMlAnK0CQlVQA8mLNmnOMeCX57PA))
+currently handled by MINERVA platform as shown in the figure below.
+In particular:
+
+* <b>Annotation type**: column lists the names of the resources, hyperlinked to the original website
+* <b>Miriam identifier**: column lists corresponding MIRIAM identifiers, hyperlinked to their definition in the MIRIAM registry
+* <b>Valid for elements**: column provides information, for which records this identifier is configured as “valid”
+(see <b>Section 3.3.1.3 Configure automatic verification**)
+* <b>Valid uri** column provides information on the correct format of corresponding MIRIAM identifier
+
+![MIRIAM](images/image28.png){:width="800px"}
+
+
+# 4. User view
+
+User view refers to the visualization and functionalities accessed by users of the content hosted by your MINERVA instance.
+
+## 4.1. Main view
+The main view of the MINERVA platform is summarized in the figure below.
+
+![Main](images/image04.png){:width="800px"}
+
+Main components of this view are
+
+* <b>Display area (1)**: where the contents of the projects are visualized
+* <b>Functional area (2)**: allowing for advanced interaction with explored content
+* <b>Information bar (3)**: containing additional overlay functions
+* <b>Project name(4)**
+* <b>Admin/Export bar (5)**: allowing administrator login and advanced export of the contents
+
+### 4.1.1. Accessing the project
+Your instance of MINERVA platform can host many projects, which are uploaded via the administrator view
+(see <b>Section 3.3.1 Add project). They are accessed by a provided, dedicated web address.
+
+
+### 4.1.2. Exploring the display area
+The content is visualized using Google Maps API, and allows similar pan and zoom functionalities. The content is interactive,
+the user can click on an element or interaction to examine additional details displayed in the left panel (functional area).
+
+The content is by default displayed in a semantic zoom mode, where compartments and areas in the submitted file cover
+underlying elements on higher levels of zoom. This view is generated procedurally, directly from the uploaded content.
+For more details see <b>Section 4.1.3 Content curation**.
+You can turn off the semantic zoom view by going to the “Layouts” tab in the left panel (functional area), and changing
+the view to “Network” (see also <b>Section 4.2.3 Layouts**).
+
+### 4.1.3. Annotating, selecting and downloading the display area
+Right-click in the display area invokes a contextual menu with two options - (see below).
+
+![Annotating](images/image25.png){:width="800px"}
+
+#### 4.1.3.1. Add comment
+
+This functionality allows to annotate contents in the display area. Clicking the “Add comment” button invokes a form that
+can be filled out by the user and sent to the administrators of the project. The field “Pinned” controls, whether the
+comment will be visible in the map (see below, left).
+
+![Annotating](images/image13.png){:width="800px"}
+
+“Type” field is a drop-down menu, listing elements nearby to the click location. This allows to choose and attach the
+comment to a particular element or interaction (see above, right).
+
+After sending, and if the field “Pinned” was set to “Yes”, the comment becomes visible in the display area, as shown below,
+to the left (after checking the “Comments” checkbox, see <b>Section 4.3.2 Comments**).
+
+![Pinning](images/image16.png){:width="800px"}
+
+Clicking on the comment bubble displays annotated element and the text of the comment (see above, right). Name and email
+are not disclosed, they will be accessible only to project and platform administrators (see <b>Section 3.2 Comments**).
+
+#### 4.1.3.2. Select mode.
+Clicking the “Select mode” enables the functionality supported by Google Maps API, allowing to select an arbitrary shape
+in the display area. The shape then can be downloaded in various formats, either as a model (.xml file) or as an image (see below).
+
+![Select mode](images/image18.png){:width="800px"}
+
+* <b>Export as model** produces a file acceptable by either CellDesigner, or pure SBGN editors, containing the editable
+fragment of the selected display area. Importantly, in the case of CellDesigner export, all additional annotations provided
+by MINERVA platform are downloaded as well.
+* <b>Export as image** produces a rectangular image containing the selection. Export to vector graphics is supported,
+allowing to modify and enhance the downloaded image.
+
+### 4.1.4. Content curation
+MINERVA framework handles SBGN-compliant format, produced either by CellDesigner ([http://www.celldesigner.org](https://www.google.com/url?q=http://www.celldesigner.org&amp;sa=D&amp;usg=AFQjCNGP8Z97rb6NBjGK4iCG0VamVYBGXg))
+) or SGBN editors, like SBGN-ED ([https://immersive-analytics.infotech.monash.edu/vanted/addons/sbgn-ed](https://www.google.com/url?q=https://immersive-analytics.infotech.monash.edu/vanted/addons/sbgn-ed/&amp;sa=D&amp;usg=AFQjCNGKO_7rzfjlKgY0bF4SD6sY-uHS-Q)).
+MINERVA relies on such externally curated content.
+
+Moreover, a number of additional functionalities of MINERVA operates on metadata that can be provided in the SBGN-compliant
+file itself. These are the following:
+
+* <b>Processing of existing annotations**: annotations to elements or interactions embedded within CellDesigner file
+(MIRIAM &gt; Add relation) are automatically parsed and processed. They can be used to extensively annotate elements
+(see <b>Section 3.3.1.2 Configure automatic annotation**).
+and they can be verified by MINERVA platform against a set of predefined content-governing rules (see <b>Section 3.3.1.3
+Configure automatic verification**).
+* <b>Procedural generation of semantic zoom** : information on complexes and overlaying compartments is extracted from
+SBGN-compliant files to generate “Pathways and compartments” view, where on the high level of zoom bigger compartments
+overlay smaller ones, and on the middle levels of zoom contents of complexes are masked. Moreover, in CellDesigner, TextArea
+elements can be used to draw named rectangles covering functionally important areas. These will be incorporated into the
+generation of the semantic zoom as well.
+* <b>Cross-platform SBGN translation**: CellDesigner files can be uploaded to be displayed in pure SBGN notation
+(see <b>3.3.1.1 Fields of the “ADD PROJECT” window**), and SBGN-displayed content can be downloaded as
+
+## 4.2. Functional area
+Functional area (the panel to the left from the display area) displays additional information about selected elements and
+interactions, allows to query the content, generate custom layouts and browse submaps.
+
+### 4.2.1. Search
+“Search” tab allows to search for particular elements or interactions in the displayed map. Also, under this tab,
+the panel displays detailed information on selected elements or interactions (see below).
+
+![Search](images/image01.png){:width="800px"}
+
+The panel is used in the following way:
+
+* **Search** field: Type your search query here, separating multiple elements with comma “,”. Search will look for
+similar names and synonyms of elements in the map. To search for an identifier of an interaction, you need to add “reaction:”
+prefix to the searched identifier. The “search” bubbles indicate hits in the display area. They have different colors for
+multiple search items and are clickable, showing information as in the left panel.
+* **Perfect match** tick box: If this box is ticked, terms with an exact match to the query will be returned. In the case of
+large networks or broad queries the search results may be capped to ensure the performance of the system. The limit of
+displaying search results can be configured via the admin view (see **Section 3.6 Configuration**).
+
+
+Direct link to the elements in the display area is possible, as the search query can be provided within the web address of
+the displayed project. An address constructed as follows:
+
+    your.wbrver.address/?search=”search query”
+
+
+is a link executing the search for a given “search query” in the default project of your MINERVA instance. For example, an address
+
+    your.wbrver.address/?search=reaction:xyz123
+
+will directly point to an interaction with id “xyz123”. Referring to a given project on your MINERVA instance requires
+additionally to pass the project identifier in the address, as shown below. Identifiers of projects are accessible using the Admin view.
+
+    your.wbrver.address/?id=”project id”&amp;search=”search query”
+
+
+### 4.2.2. Drug
+**Drug** tab in the functional panel allows to search for known drug targets and display them in the map. Targets will
+be marked by bubbles in the display area. Please, note that they have different shape than the “search” result bubbles.
+
+* **Find targets** field: type your search query here, separating multiple drug names with comma “,”. DrugBank and ChEMBL
+will be queried for known targets to be displayed in the map.
+* Drug description, synonyms and all known targets will be displayed in the left panel.
+
+### 4.2.3. Layouts
+“Layouts” tab allows to display or generate custom coloring of elements and interactions in the map. It is composed of two
+sections - general layouts and custom layouts (see below).
+
+* **View** column contains buttons (“magnifying glass” icon) allowing to switch to a corresponding layout.
+Mouseover over the button displays a short description of the dataset, if provided on upload
+* **Data** column contains buttons, where applicable, allowing to download the dataset used to generate the layout.
+
+![Layouts](images/image14.png){:width="800px"}
+
+In the figure above:
+
+* **General layouts** are layouts accessible for every user viewing the content
+* **Custom layouts** are user-provided layouts, this menu becomes available upon login (see below).
+
+![Layouts](images/image09.png){:width="800px"}
+
+Custom layouts part contains the following elements (above):
+* **List** of uploaded layouts containing
+    * **View**  column with buttons enabling switching between custom layouts
+    * **Data** column with buttons allowing the user to download the dataset used to generate the layout. The users have access only to their respective datasets.
+    * **Edit** column with buttons allowing the user to provide description to the uploaded datasets
+* **Adding** section with “Name” field to annotate and “+Choose” button to upload your custom dataset.
+
+#### 4.2.3.1. Upload custom data - format
+
+**Basic format**
+The basic format of file containing the uploaded data is two-column, tab-separated text file, with the columns “Name” and “Value”.
+
+* **Name** column contains the names of elements to be colored
+* **Value** column contains the values normalized to [-1,1] range.
+
+Basic format will look for names of the elements provided in the “Name” column among the names of elements in a given network
+and for the matching ones will assign them colors: red for negative values, green for positive values, with the saturation
+proportional to the value.
+
+**Advanced format**
+The advanced format allows for by identifier matching, custom color assignment and coloring of interactions.
+Advanced format foresees two parts of the uploaded dataset - header and body.
+
+Header lines have to start with ‘#’. It can contain the following elements:
+
+* **Version** `# VERSION=xyz` - a version of this custom layout
+* **Name** `# NAME=xyz` - a name that will be automatically assigned upon upload
+* **Description** `# DESCRIPTION=xyz` - a description that will be automatically assigned upon upload
+
+Body is a table with a following set of columns:
+
+* **Name**, **Value** - same as in basic layout
+* **Compartment** - name of a compartment in which coloring should take place
+* **Chebi** - ChEBI identifiers of elements to be colored
+* **Entrez genes** - Entrez identifiers of elements to be colored
+* **Gene ontology** - Gene Ontology identifiers of elements to be colored
+* **Ensembl** - Ensembl identifiers of elements to be colored
+* **Hgnc symbol** - HGNC symbols of elements to be colored
+* **Uniprot** - Unprot identifiers of elements to be colored
+* **ReactionIdentifier** - ID of interaction to be colored (interactions coloring only)
+* **LineWidth** - linewidth of the colored interaction (interactions coloring only)
+* **Color** - color of the colored element.
+
+The dataset for upload may be integrated and sparse, i.e. a document may contain all columns at once, and, where irrelevant,
+their content may be left blank. In other words, you can color interactions and elements in the same dataset, leaving blank
+fields in “ReactionIdentifier” and “LineWidth” for elements, and leaving blank fields in “Name” for interactions.
+
+#### 4.2.3.2. Upload custom data - procedure
+After choosing the dataset to upload, pressing “Generate” button will invoke a comment, initiate generation and reduce the
+amount of available custom layouts (see below, left). The progress status will automatically update (see below, right)
+and when the progress reaches 100%, your custom layout is ready to be displayed.
+
+You will be notified by email when your layout is ready. The email will also contain the list of elements in your dataset
+not found in the map.
+
+Important reminder:
+* The number of available layouts is configured in the Admin view (see **Section 3.4. User manager**)
+
+* The number of available layouts is common for all projects hosted on your MINERVA instance. If a user is registered
+in a number of projects and uploads custom datasets in all of them, the global number of available custom layouts will be
+reduced with each uploaded layout.
+
+![Upload](images/image21.png){:width="800px"}
+
+### 4.2.4. Login/Profile
+
+The “Login” tab is visible for an anonymous user, upon immediate access to a project hosted on your MINERVA instance.
+It allows a registered user to type in their login and password, or to request for an account from the administrators of this MINERVA instance.
+Platform administrators can register new users (see **Section 3.4 User manager**) and configure “Request an account” functionality
+(see **Section 3.6. Configuration**)
+
+After login, the tab name changes to “Profile”, displaying information on the registered, logged in user. After the
+successful login the user gains the possibility to upload custom layouts (see **Section 4.2.3. Layouts**).
+
+### 4.2.5. Submaps
+
+The “Submaps” tab summarizes all the submap networks uploaded together and linked to the main network of this project
+hosted by your MINERVA instance. See **Appendix 6.1 Source file** to learn how to upload the submaps together with the main file.
+
+The “Submaps” tab displays the tab with the “Name” column, and the column with the buttons displaying corresponding submaps.
+The submaps show as a pop-up window on top of the main map, and are synchronized with respect to search queries and displaying layouts.
+This means that search results and search target bubbles will be visible in the main map and the displayed submaps.
+Similarly, coloring for layouts are mirrored in the submaps (see figures below).
+
+![Submaps](images/image31.png){:width="800px"}
+
+![Submaps2](images/image12.png){:width="800px"}
+
+
+## 4.3. Information bar
+
+Information bar is the topmost part of the user view, containing the “Show overview” button, “Comment” and “Legend” checkboxes
+and “Clear button”. The “Clear” button clears all search results currently shown in the display area. The remaining functionalities
+are detailed below.
+
+### 4.3.1. Show overview
+
+This button invokes a static image associated with the displayed content. It may be a graphics facilitating the understanding
+of the underlaying network, or any other visual cue that the content curator decided to present. The initial image displayed with the
+“Show overview” button can be linked to:
+
+* another static image to be displayed next
+* a defined area in the displayed content
+* a set of elements or interactions.
+
+Detailed information on how to configure “Show overview” images display is provided in **Appendix 6.1 Source file**.
+
+### 4.3.2. Comments
+
+If this checkbox is checked, the comments provided by users with “Pinned” option set to “Yes” will become visible in the
+display area (see also **Section 4.1.3.1 Add comment**).
+
+### 4.3.3. Legend
+
+If this checkbox is checked, the legend describing element and interaction types will be displayed.
+
+## 4.4. Export
+
+# 5. Disclaimer
+
+# 6. Appendix
+
+## 6.1. Source file
diff --git a/web/minerva/user guide.md b/web/minerva/user guide.md
new file mode 100644
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@@ -0,0 +1,8 @@
+---
+layout: page
+title: Minerva
+index: minerva
+type: subpage
+description: "Minerva website"
+nav: user guide,something else
+---
-- 
GitLab