Update tutorial "Analyze data"

- complete steps 1 & 2
- review footer & head
- separate toc from head

MASH-FRET/.release_version.json

@@ -1,4 +1,4 @@
 {
 "tag" : "1.1.2",
-"prev_commit_hash" : "2818ba3"
+"prev_commit_hash" : "12275c2"
 }

docs/_includes/tutorial_footer.html

@@ -1,11 +1,13 @@
-<p><span class="fs-3">
+<p style="margin-left:auto; margin-right:auto; text-align:center;"><span class="fs-3">
 {% for node in pages_list %}
 	{% if node.parent == page.parent %}
-		<a href="{{ node.url | absolute_url}}#steps_bottom" class="{% if node.url == page.url %}btn btn-green mr-4{% else %}btn mr-4{% endif %}">STEP {{ node.nav_order }}</a>
+		{% assign prev_nav_order = page.nav_order | minus: 1 %}
+		{% assign next_nav_order = page.nav_order | plus: 1 %}
+		{% if node.nav_order == prev_nav_order %}
+			<a href="{{ node.url | absolute_url}}#tutorials_steps" class="btn btn-green mr-4"><< PREVIOUS: {{ node.subtitle }}</a>
+		{% elsif node.nav_order == next_nav_order %}
+			<a href="{{ node.url | absolute_url}}#tutorials_steps" class="btn btn-green mr-4">NEXT: {{ node.subtitle }} >></a>
+		{% endif %}
 	{% endif %}
 {% endfor %}
 </span></p>
-
----
-
-<span id="steps_bottom"></span>

docs/_includes/tutorial_head.html

@@ -1,40 +1,22 @@
 {% assign pages_list = site.html_pages | sort:"nav_order" %}
-<ul>
-{% for node in pages_list %}
-	{% if page.grand_parent %}
-		{% if node.parent == page.parent %}
-			<li>
-			{% if node.url == page.url %}
-				<strong>Step {{ node.nav_order }}: {{ node.title }}</strong>
-			{% else %}
-				<a href="{{ node.url | absolute_url}}">Step {{ node.nav_order }}: {{ node.title }}</a>
-			{% endif %}
-			</li>
-		{% endif %}
-
-	{% else %}
-		{% if node.parent == page.url %}
-			<li><a href="{{ node.url | absolute_url}}">Step {{ node.nav_order }}: {{ node.title }}</a></li>
-		{% endif %}
-	{% endif %}
-{% endfor %}
-</ul>
-
+<span id="tutorials_steps" class="fs-3"></span>
 {% if page.grand_parent %}
 
-<span id="steps"></span>
-
----
-
-<p><span class="fs-3">
+<p style="margin-left:auto; margin-right:auto; text-align:center;"><span class="fs-3">
 {% for node in pages_list %}
 	{% if node.parent == page.parent %}
-		<a href="{{ node.url | absolute_url}}#steps" class="{% if node.url == page.url %}btn btn-green mr-4{% else %}btn mr-4{% endif %}">STEP {{ node.nav_order }}</a>
+		{% assign prev_nav_order = page.nav_order | minus: 1 %}
+		{% assign next_nav_order = page.nav_order | plus: 1 %}
+		{% if node.nav_order == prev_nav_order %}
+			<a href="{{ node.url | absolute_url}}#tutorials_steps" class="btn btn-green mr-4"><< PREVIOUS: {{ node.subtitle }}</a>
+		{% elsif node.nav_order == next_nav_order %}
+			<a href="{{ node.url | absolute_url}}#tutorials_steps" class="btn btn-green mr-4">NEXT: {{ node.subtitle }} >></a>
+		{% endif %}
 	{% endif %}
 {% endfor %}
 </span></p>
 
-# STEP {{ page.nav_order }}: {{ page.title }}
+# STEP {{ page.nav_order }}: {{ page.subtitle }}
 {: .no_toc }
 
 {% endif %}

docs/_includes/tutorial_toc.html

@@ -0,0 +1,21 @@
+{% assign pages_list = site.html_pages | sort:"nav_order" %}
+<ul>
+{% for node in pages_list %}
+	{% if page.grand_parent %}
+		{% if node.parent == page.parent %}
+			<li>
+			{% if node.url == page.url %}
+				<strong>Step {{ node.nav_order }}: {{ node.subtitle }}</strong>
+			{% else %}
+				<a href="{{ node.url | absolute_url}}">Step {{ node.nav_order }}: {{ node.subtitle }}</a>
+			{% endif %}
+			</li>
+		{% endif %}
+
+	{% else %}
+		{% if node.parent == page.url %}
+			<li><a href="{{ node.url | absolute_url}}">Step {{ node.nav_order }}: {{ node.subtitle }}</a></li>
+		{% endif %}
+	{% endif %}
+{% endfor %}
+</ul>

docs/assets/images/equations/equations.txt

@@ -85,23 +85,23 @@ Signal-to-noise ratio (equation 08):
 
 >> FRET calculations:
 Multi-color FRET (equation 01):
-	E_{D,A}^{*} = {}\frac{I_{A,em}^{D,ex}}{\left [ 1 - \sum_{k>A} \left ( E_{A,k}^{*}  \right ) \right ] \times \sum_{k} \left ( I_{k,em}^{D,ex}  \right )} - \sum_{k>D}^{A-1} \left \{E_{D,k}^{*} \times \prod_{k'> k}^{A} \left [E_{k,k'}^{*} \times \prod_{k''> k'}^{A} \left (E_{k',k''}^{*}  \right )  \right ]  \right \}
+	E_{D,A,\_}^{*} = {}\frac{I_{A,em}^{D,ex}}{\left [ 1 - \sum_{k>A} \left ( E_{A,k,\_}^{*}  \right ) \right ] \times \sum_{k} \left ( I_{k,em}^{D,ex}  \right )} - \sum_{k>D}^{A-1} \left \{E_{D,k,\_}^{*} \times \prod_{k'> k}^{A} \left [E_{k,k',\_}^{*} \times \prod_{k''> k'}^{A} \left (E_{k',k'',\_}^{*}  \right )  \right ]  \right \}
 2-color FRET (equation 02):
-	E_{K-1,K}^{*}= \fract{I_{K-1,em}^{K,ex}}{\sum_{k \geq K-1} \left ( I_{K-1,em}^{K,ex} \right )}
+	E_{K-1,K,\_}^{*}=E_{K-1,K}^{*}= \fract{I_{K-1,em}^{K,ex}}{\sum_{k \geq K-1} \left ( I_{K-1,em}^{K,ex} \right )}
 	or (equation 02b)
-	E_{D,A}^{*}= \frac{I_{A,em}^{D,ex}}{\sum_{k \geq D} \left ( I_{k,em}^{D,ex} \right )}
+	E_{D,A,\_}^{*}=E_{D,A}^{*}= \frac{I_{A,em}^{D,ex}}{\sum_{k \geq D} \left ( I_{k,em}^{D,ex} \right )}
 giving (equation 03):
 	E_{K-1,K}^{*}= \frac{I_{K,em}^{K-1,ex}}{I_{K,em}^{K-1,ex}+I_{K-1,em}^{K-1,ex}}
 	or (equation 03b)
 	E_{D,A}^{*}= \frac{I_{A,em}^{D,ex}}{I_{A,em}^{D,ex}+I_{D,em}^{D,ex}}
 3-colorFRET (equation 04)
-	E_{K-2,K-1}^{*} = \frac{ I_{K-1,em}^{K-2,ex} }{ \left [ 1 - \sum_{k>K-1}\left ( E_{K-1,k}^{*} \right ) \right ] \times \sum_{k \geq  K-2}\left ( I_{k,em}^{K-2,ex} \right )  }
+	E_{K-2,K-1,\_}^{*} = \frac{ I_{K-1,em}^{K-2,ex} }{ \left [ 1 - \sum_{k>K-1}\left ( E_{K-1,k,\_}^{*} \right ) \right ] \times \sum_{k \geq  K-2}\left ( I_{k,em}^{K-2,ex} \right )  }
 and (equation 05)
-	E_{K-2,K}^{*} = \frac{ I_{K,em}^{K-2ex} }{ \sum_{k\geq K-2}\left ( I_{k,em}^{K-2,ex} \right ) - \sum_{k> K-2}\left [ E_{K-2,k}^{*} \times \prod_{k'>k} \left ( E_{k,k'}^{*} \right ) \right ]}
+	E_{K-2,K,\_}^{*} = \frac{ I_{K,em}^{K-2ex} }{ \sum_{k\geq K-2}\left ( I_{k,em}^{K-2,ex} \right ) - \sum_{k> K-2}\left [ E_{K-2,k,\_}^{*} \times \prod_{k'>k} \left ( E_{k,k',\_}^{*} \right ) \right ]}
 giving (equation 06)
-	E_{K-2,K-1}^{*} = \frac{I_{K-1,em}^{K-2,ex}}{\left ( 1 - E_{K-1,K}^{*} \right ) \times \left ( I_{K,em}^{K-2,ex} + I_{K-1,em}^{K-2,ex} + I_{K-2,em}^{K-2,ex} \right )}
+	E_{K-2,K-1,\_}^{*} = \frac{I_{K-1,em}^{K-2,ex}}{\left ( 1 - E_{K-1,K,\_}^{*} \right ) \times \left ( I_{K,em}^{K-2,ex} + I_{K-1,em}^{K-2,ex} + I_{K-2,em}^{K-2,ex} \right )}
 and (equation 07)
-	E_{K-2,K}^{*} = \frac{I_{K,em}^{K-2,ex}}{ I_{K,em}^{K-2,ex} + I_{K-1,em}^{K-2,ex} + I_{K-2,em}^{K-2,ex}} - E_{K-2,K-1}^{*}\times E_{K-1,K}^{*}
+	E_{K-2,K,\_}^{*} = \frac{I_{K,em}^{K-2,ex}}{ I_{K,em}^{K-2,ex} + I_{K-1,em}^{K-2,ex} + I_{K-2,em}^{K-2,ex}} - E_{K-2,K-1,\_}^{*}\times E_{K-1,K,\_}^{*}
 
 >> Stoichiometry calculation:
 	S_{D} = \frac{\sum_{k}\left (I_{k,em}^{D,ex} \right )}{\sum_{k}\left[ \sum_{k'}\left( I_{k',em}^{k,ex} \right ) \right ]}

docs/tutorials/analyze-data/analyze-data.md

@@ -12,12 +12,13 @@ select_with_child: true
 <img src="../assets/images/logos/logo-tutorials_400px.png" width="170" style="float:right; margin-left: 15px;"/>
 
 # Analyze data
+{: .no_toc }
 
 Follow this procedure to process your single molecule videos (SMVs) or trajectories and characterize the molecule dynamics in your sample.
 
 **Note:** *Skip step 1 if already in possession of intensity-time traces files (ASCII or 
 [mash project](../../output-files/mash-mash-project)).*
 
-{% include tutorial_head.html %}
+{% include tutorial_toc.html %}
 
----		
+---