LICENSE and manor fixes.

Author: lenak01

DuWTill/Contact.aspx

@@ -9,10 +9,10 @@
     <address>
         Australian Centre for Plant Functional Genomics <br />
         School of Agriculture, Food and Wine <br />
-        University of Adelaide, Waite Campus
+        University of Adelaide, Waite Campus <br />
+        <a href="http://www.adelaide.edu.au">www.adelaide.edu.au</a>
     </address>
     <address>
-        Plant Genomics Centre|Hartley Grove|Urrbrae SA 5064 <br />
-        <a href="http://www.acpfg.com.au">www.acpfg.com.au</a>
+        Plant Genomics Centre | Hartley Grove | Urrbrae SA 5064 <br />
     </address>
 </asp:Content>

DuWTill/Site.Master

@@ -30,7 +30,7 @@
         <div class="navbar navbar-inverse">
             <a class="navbar-brand align-top" href="http://www.sa.gov.au" style="padding: 0px 15px 0px 15px">
                 <asp:Image ID="govSA" runat="server" ImageUrl="~/Content/gov-sa-logo.png" Height="50px" /></a>
-            <a class="navbar-brand align-top" href="http://www.acpfg.com.au" style="padding: 0px 15px 0px 0px">
+            <a class="navbar-brand align-top" style="padding: 0px 15px 0px 0px">
                 <asp:Image ID="Image1" runat="server" ImageUrl="~/Content/ACPFG Logo White.png" /></a>
             <div class="container">
                 <div class="navbar-header">
@@ -73,12 +73,12 @@
                 <a href="http://www.unitus.it"><asp:Image runat="server" ImageUrl="~/Content/uni-tuscia-logo.png" Height="50px" /></a>
             </div>
             <div class="col-md-4 text-right">
-                <a href="http://www.acpfg.com.au"><asp:Image runat="server" ImageUrl="~/Content/acpfg_logo.png" Height="50px" /></a>
+                <a><asp:Image runat="server" ImageUrl="~/Content/acpfg_logo.png" Height="50px" /></a>
             </div>
         </div>
         <br />
         <p class="text-center small"><a href="~/About" runat="server">About</a>&nbsp;|&nbsp;<a href="~/Contact" runat="server">Contact</a>&nbsp;|&nbsp;
-            ©&nbsp;Copyright&nbsp;2014-2017&nbsp;<a href="http://www.acpfg.com.au/">Australian&nbsp;Centre&nbsp;for&nbsp;Plant&nbsp;Functional&nbsp;Genomics</a>
+            ©&nbsp;Copyright&nbsp;2014-2017&nbsp;<a>Australian&nbsp;Centre&nbsp;for&nbsp;Plant&nbsp;Functional&nbsp;Genomics</a>
         </p>
 	</footer>
 </body>

LICENSE.md

@@ -0,0 +1,4 @@
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International License</a>.
+
+
+Third-party packages are distributed with the Software (see `packages.config` in each project for the list). Each package is licensed to you by its owner. We are not responsible for, nor grant any licenses to, third-party packages. You agree to comply with the license terms for these packages as part of accessing the Software.

README.md

@@ -2,14 +2,14 @@
 DuWTill is a simple Web client to the database of mutations in the South Australian Durum Wheat Tilling (DuWTill) collection created as part of a joint project between Australian Centre for Plant Functional Genomics (ACPFG), University of Saskatchewan and Università degli Studi della Tuscia for the project “A Molecular Diversity Drive for Precision-Engineered Wheat”.
 
 ## Data content
-Seeds of an advanced durum breeding line, UAD0951096_F2:5, were mutagenized with 0.7% EMS and 500 mutant plants were grown through one further generation to seed. In the next generation (M2) DNA from 100 of these plants and the unmutagenized control (UAD0951096_F2:5) were sequenced (Illumina, 2x150 bp) following reduction by exome capture using the 106.9 Mb [Roche NimbleGen SeqCap](https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/shareddesigns.html) Wheat Exome Design. 
+Seeds of an advanced durum breeding line, UAD0951096_F2:5 (which has given rise to the commercially grown cultivar DBA-Aurora), were mutagenized with 0.7% EMS and 500 mutant plants were grown through one further generation to seed. In the next generation (M2) DNA from 100 of these plants and the unmutagenized control (UAD0951096_F2:5) were sequenced (Illumina, 2x150 bp) following reduction by exome capture using the 106.9 Mb [Roche NimbleGen SeqCap](https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/shareddesigns.html) Wheat Exome Design. 
 
-To improve variant calling, a novel consolidated Durum Exome Capture Reference (DECaR) was built: reads from the unmutagenized control sample were mapped into two publically available durum wheat whole genome assemblies of [Svevo](https://www.interomics.eu/durum-wheat-genome) and [Kronos EI v1](https://opendata.earlham.ac.uk/opendata/data/Triticum_turgidum/EI/v1.1/), and then combined with assembled unmapped control reads. The resulting reference was 484.5 Mbp.
+To improve variant calling, a novel consolidated Durum Exome Capture Reference (DECaR) was built: reads from the unmutagenized control sample were mapped into two publically available durum wheat whole genome assemblies of [Svevo](https://www.interomics.eu/durum-wheat-genome) and [Kronos EI v1](https://opendata.earlham.ac.uk/opendata/data/Triticum_turgidum/EI/v1.1/), and then combined with assembled unmapped control reads. The resulting reference was 484.5 Mbp. The pipeline is described [here](https://github.com/CroBiAd/TILLinG-mutants).
 
 Reads of the 100 exome-captured samples were aligned to DECaR. Any variation from DECaR was considered a mutation if it was present in only one mutant sample and non-polymorphic between the control and DECaR. We also demanded a mutation to be covered by at least three reads, and had sufficient coverage for the control allele in at least 50 other mutant samples. DECaR also allowed us to predict zygosity of the mutations discovered.
 
 For further details and to cite:
->Mario Fruzangohar, Elena Kalashyan, Priyanka Kalambettu, Jennifer Ens, Krysta Wiebe, Curtis J. Pozniak, Penny J. Tricker, Ute Baumann "Novel Informatics Tools to Support Functional Annotation of the durum wheat genome." (In preparation)
+>Mario Fruzangohar, Elena Kalashyan, Priyanka Kalambettu, Jennifer Ens, Krysta Wiebe, Curtis J. Pozniak, Penny J. Tricker, Ute Baumann "Novel Informatics Tools to Support Functional Annotation of the durum wheat genome." (In review)
 
 ## DuWTill Web Server
 The identified mutations are accessible on a public DuWTill Web server http://duwtill.acpfg.com.au.

WebTilling.sln

@@ -1,4 +1,3 @@
-
 Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio 14
 VisualStudioVersion = 14.0.25420.1
@@ -9,6 +8,7 @@ Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "YourDB", "YourDB\YourDB.csp
 EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{493896D5-8008-44A1-A57C-ECC6D5811A83}"
 	ProjectSection(SolutionItems) = preProject
+		LICENSE.md = LICENSE.md
 		README.md = README.md
 	EndProjectSection
 EndProject
@@ -31,4 +31,3 @@ Global
 		HideSolutionNode = FALSE
 	EndGlobalSection
 EndGlobal
-