update with settings

Author: manulera

README.md

@@ -28,10 +28,10 @@ git submodule update --init --recursive
 # activate virtual environment
 source .venv/bin/activate
 # start dev server
-mkdocs serve
+mkdocs serve -a localhost:8001
 ```
 
-Go to http://127.0.0.1:8000/ and you should see the page.
+Go to http://127.0.0.1:8001/ and you should see the page.
 
 ## Adding content
 

docs/assets/settings.png

@@ -11,6 +11,7 @@ At the top of the page, you have four tabs:
 * `Description`: to add / see a plain text description for your cloning strategy.
 * `Sequence`: A sequence viewer, to see the sequences you have loaded, and their features. When using the [primer designer](./primer_design.md), this tab also allows you to select part of sequences for primer design, such as what regions you want to amplify from a plasmid, or what region you want to replace in the genome (for homologous recombination).
 * `Data model`: shows part of the data model that you can download as a `.json` file, in case you are interested on how will that look.
+* `Settings`: to set global application settinsg. For now, includes parameters to calculate melting temperature and other thermodynamic properties in the [primer table](./primers.md#the-primer-table) and for [primer design](./primer_design.md).
 
 ## Use sequences for cloning and genome engineering
 

docs/interface.md

@@ -2,6 +2,9 @@
 
 In some of these videos, the interface might be slightly different, but the functionality is basically the same.
 
+!!! info "Parameters used to calculate melting temperature for primer design"
+    You can set the parameters used to calculate melting temperature in the [Settings tab](./settings.md).
+
 ## Primer design for homologous recombination
 
 <div class="video-sizer">

docs/primer_design.md

@@ -26,6 +26,10 @@ You can export primers to a `.csv` or `.tsv` file by clicking on the `Download p
 
 ## The primer table
 
+
+!!! info "Parameters used to calculate melting temperature and other thermodynamic properties"
+    You can set the parameters used to calculate and display melting temperature and other thermodynamic properties in the primer table and for [primer design](./primer_design.md) in the [Settings tab](./settings.md).
+
 The primer table shows properties of the primers, and the icons on the left side of the table allow you to edit or delete the primer, and see extra info about it.
 
 If the primers are used in a PCR or oligonucleotide hybridization, the information for the binding part is shown first, and the information for the full primer is shown in parenthesis. For example, below the primer `vector_forward` has a total length of 36bps, but only 19 bind to its template in the PCR, so the table shows `19 (36)` in the `Length` column.

docs/primers.md

@@ -0,0 +1,15 @@
+# Settings
+
+## Primer thermodynamic settings
+
+You can set the parameters used to calculate melting temperature and other thermodynamic properties in the [primer table](./primers.md#the-primer-table) and for [primer design](./primer_design.md) in the `Settings` tab.
+
+For now, you can specify:
+
+- The concentration of the primer in the PCR or hybridization reaction (default 50 nM)
+- The monovalent cation concentration (default 50 mM)
+- The divalent cation concentration (default 1.5 mM)
+
+<div markdown style="max-width: 600px" class="img-container">
+![](assets/settings.png)
+</div>

docs/settings.md

@@ -47,6 +47,7 @@ nav:
   - The OpenCloning interface: interface.md
   - Primers: primers.md
   - Exporting sequences and workflows: exporting.md
+  - Settings: settings.md
   - Supported methods:
       - 🛠 Cre/LoxP: methods/cre_loxp.md
       - CRISPR-HDR: methods/crispr_hdr.md