newt 4 updates

faq.html

@@ -27,39 +27,78 @@
 
         <h1>FAQ</h1>
 
+    <hr> 
 	  <p> <b>Q: Is Newt free to use?</b><br>
-            A: Newt is an open source <a target="_blank" href="https://github.com/iVis-at-Bilkent/newt">project</a>, distributed under <a href="http://www.gnu.org/licenses/lgpl.html">GNU Lesser General Public License.</a></p>
+            A: Yes, Newt is an open source <a target="_blank" href="https://github.com/iVis-at-Bilkent/newt">project</a>, distributed under <a href="http://www.gnu.org/licenses/lgpl.html">GNU Lesser General Public License.</a></p>
 
+    <hr> 
 	  <p> <b>Q: Is there anything I need to install to start using Newt?</b><br>
             A: No, Newt is web based and is expected to work on most major browsers with recent releases without any prior installation or set up. If you'd like to <a target="_blank" href="https://github.com/iVis-at-Bilkent/newt/blob/master/README.md#Running%20a%20:Local%20Instance">run/deploy it locally</a> rather than using the sample deployment however, some services need to be started.</p>
 
+    <hr> 
 	  <p> <b>Q: What is the best way to get started with Newt?</b><br>
             A: First, read the <a href="tutorials.html">tutorials page</a> and watch the associated videos.</p>
 
+    <hr> 
 	  <p> <b>Q: What notation is used in Newt to draw biological maps?</b><br>
-            A: Newt supports <a target="_blank" href="http://sbgn.github.io/sbgn/">SBGN</a> Process Description (PD) and Activity Flow (AF) maps. A quick introduction to SBGN can be found <a target="_blank" href="https://sbgn.github.io/learning">here</a>. Users are allowed mix up notation from these two languages at the cost of disabled validation checks during creation. In addition, we support <a target="_blank" href="http://www.pathwaycommons.org/pc2/formats#sif_relations">SIF</a> for those preferring a simplified notation. </p>
-
+            A: Newt supports <a target="_blank" href="http://sbgn.github.io/sbgn/">SBGN</a> Process Description (PD) and 
+            Activity Flow (AF), SIF and SBML notations. A quick introduction to SBGN can be found 
+            <a target="_blank" href="https://sbgn.github.io/learning">here</a>. 
+            For those preferring a simplified notation, <a target="_blank" href="http://www.pathwaycommons.org/pc2/formats#sif_relations">SIF</a>
+            would be a good choice. Finally, a notation based on <a target="_blank" href="https://sbml.org/">SBML</a> is also supported in Newt.
+            Users are also allowed mix up notation from these notations by chaning the map type at the cost of disabled validation 
+            checks during creation. </p>
+    <hr> 
 	  <p> <b>Q: What format does Newt use to save maps?</b><br>
-            A: Newt can read <a target="_blank" href="https://github.com/sbgn/sbgn/wiki/SBGN_ML">SBGNML</a> and <a target="_blank" href="https://www.pathwaycommons.org/pc/sif_interaction_rules.do">SIF</a> files. Models constructed with Newt can be saved in rich SBGNML, with extensions for style and annotations ("File | Save..."), or in plain SBGNML ("Export | SBGN-ML Plain"). In addition, the user can import AF models or SIF from simple, tab-delimited text files. We also support importing from and exporting to <a target="_blank" href="http://www.celldesigner.org/"> CellDesigner </a>, <a target="_blank" href="http://sbml.org/Main_Page">SBML</a>, and <a target="_blank" href="https://pathvisio.org/documentation/GPML">GPML</a> file formats. Details on file operations are explained <a href="tutorials.html#file-operations">here</a>. Maps can also be exported as static (raster or vector) images. </p>
-
+            A: Newt uses a native format (".nwt" file) for all notations supported (which is in fact based on 
+            <a target="_blank" href="https://github.com/sbgn/sbgn/wiki/SBGN_ML">SBGNML</a>). Thus, "File | Save..." stores maps in
+            this format and "File | Open..." expects a ".nwt" file as well. Since ".nwt" file is an extension of SBGNML, however, 
+            plain SBGNML (".sbgn") files will be loaded successfully as PD or AF maps depending on the notation specified inside 
+            the file.
+            <br>
+            Newt can import <a target="_blank" href="https://www.pathwaycommons.org/pc/sif_interaction_rules.do">SIF</a> 
+            or AF files formatted as tab-delimited text. Exporting to a simple tab-delimited format for SIF files is also supported
+            through "Export | SIF".
+            Furthermore, Newt supports import from and export to 
+            <a target="_blank" href="http://www.celldesigner.org/"> CellDesigner </a>, 
+            <a target="_blank" href="http://sbml.org/Main_Page">SBML</a>, and 
+            <a target="_blank" href="https://pathvisio.org/documentation/GPML">GPML</a> file formats via various services. 
+            Details on file operations are explained <a href="tutorials.html#file-operations">here</a>. 
+            <br>
+            Maps can also be exported as static (raster or vector) images. </p>
+
+    <hr> 
 	  <p> <b>Q: Does Newt save styling information (e.g. color, font, custom annotations, etc.)?</b><br>
-            A: Yes, any style information per node/edge/map is saved as an extension to standard SBGNML with file extension ".nwt". Thus, you can restore such information when you load such files back up on Newt but such information might be lost when imported to other tools (since other tools might not support the style extension to SBGNML). If a tool is having difficulty importing our files, try exporting in plain SBGNML ("Export | SBGN-ML Plain") with file extension ".sbgn". </p>
+            A: Yes, any style information per node/edge/map is saved as an extension to standard SBGNML with file extension ".nwt". 
+            Thus, you can restore such information when you load such files back up on Newt but such information might be lost 
+            when imported to other tools (since other tools might not support the style extension to SBGNML). If a tool is having 
+            difficulty importing our files, try exporting in plain SBGNML ("Export | SBGN-ML Plain") with file extension ".sbgn". </p>
 
+    <hr> 
 	  <p> <b>Q: How can I create a reversible reaction in Newt?</b><br>
-            A: Use of a single process for a reversible reaction is <a href="http://sbgn.github.io/sbgn/faq/pd#can-we-represent-reversible-interactions-with-a-single-association-or-dissociation-glyphs">a controversial issue</a> since it can lead to ambiguities when the process has modulators. In Newt, if a map's type is PD, it doesn't allow connecting production edges to both the input and the output ports of a process. However, one can create reversible reactions using SBGN bricks ("Edit | Add from Template..."), but the map will no longer pass PD validation checks. </p>
+            A: Use of a single process for a reversible reaction is 
+            <a href="http://sbgn.github.io/sbgn/faq/pd#can-we-represent-reversible-interactions-with-a-single-association-or-dissociation-glyphs">a controversial issue</a>
+            since it can lead to ambiguities when the process has modulators. In Newt, if a map's type is PD, it doesn't allow 
+            connecting production edges to both the input and the output ports of a process. However, one can create reversible reactions 
+            using SBGN bricks ("Edit | Add Using SBGN Bricks..."), but the map may no longer pass PD validation checks. </p>
 
+    <hr> 
 	  <p> <b>Q: How can I be sure that my map is SBGN compliant?</b><br>
             A: Newt provides both syntactic and semantic (in SBGN PD maps only) validation. As you're creating map objects and interactions, Newt will warn you if they are incompatiable with the current map type. In addition, for SBGN PD maps, we also provide <a href="tutorials.html#semantic-validation">semantic validation</a> with suggestions to fix any problems with your maps with most type of errors in an interactive fashion. </p>
 
+    <hr> 
 	  <p> <b>Q: I uniformly use a certain style (map and object properties such as colors) in my maps. Can I simply keep these preferences across sessions?</b><br>
             A: Newt lets you save <a href="tutorials.html#persisting-preferences">preferences</a> and load them back in your next session, so the look and feel of your maps could be uniform. </p>
 
+    <hr> 
 	  <p> <b>Q: Can I overlay experimental data on my maps in Newt?</b><br>
             A: You can upload and overlay your experiment data (as many sets as desired) using <a href="tutorials.html#experiment-data">a simple tab-delimited file</a>. The valid range for data values as well as colors to be used for mapping may be customized by the user.</p>
 
+    <hr> 
 	  <p> <b>Q: Can I deploy my own Newt instance?</b><br>
             A: Yes, it is rather straightforward to <a target="_blank" href="https://github.com/iVis-at-Bilkent/newt/blob/master/README.md#running-a-local-instance">deploy</a> and maintain a local copy of Newt. In addition, Newt is specifically designed to be easily customizable (modify menu and toolbars, and other functionality) and embeddable within your own website. </p>
 
+    <hr> 
 	  <p> <b>Q: What if I'd like to contribute to Newt development?</b><br>
             A: We'd love to have more resources. Please contact us privately through <a href="contact.html">this form</a>. </p>
 

gallery.html

@@ -46,6 +46,17 @@ <h1>Gallery</h1>
             <br><a href="http://web.newteditor.org/?URL=https://raw.githubusercontent.com/iVis-at-Bilkent/newt/gh-pages/samples/mammalian_cholesterol.nwt">Open in Newt</a>
             </th>
           </tr>
+          <tr>
+            <th class="leftcolumn">
+            <a href="images/g1b_transforming_growth_factor_beta_signaling.png" data-lightbox="image-gallery" data-title="AF map of transforming growth factor-beta (TGFbeta) signaling, doi:10.1002/iub.239"><img class="ssthumbnail" src="images/tg1b.png" style="height: 130px;"/></a>
+            </th>
+            <th>
+            <a href="images/g2b_RTN4-controllers-and-binding-proteins.png" data-lightbox="image-gallery" data-title="SIF map of RTN4 controllers and binding proteins, doi:10.1093/bioinformatics/btt539"><img class="ssthumbnail" src="images/tg2b.png" style="height: 130px;"/></a>
+            </th> 
+            <th class="rightcolumn">
+            <a href="images/g3_ERK_PI3K-Akt_and_Wnt_signalling.png" data-lightbox="image-gallery" data-title="SBML map of ERK, PI3K/Akt and Wnt signalling network, doi:10.1039/c6mb00786d"><img class="ssthumbnail" src="images/tg3b.png" style="height: 130px;"/></a>
+            </th>
+          </tr>
           <tr>
             <th class="leftcolumn">
             <a href="images/g4_atm_mediated_phosphorylation_of_repair_proteins.png" data-lightbox="image-gallery" data-title="ATM mediated phosphorylation of repair proteins"><img class="ssthumbnail" src="images/tg4.png" style="height: 130px;"/></a>
@@ -88,6 +99,24 @@ <h1>Gallery</h1>
             </th> 
             </tr>
         </table>
+
+        <p>Below are some example usage of Newt in the literature:
+          <ul>
+            <li> <a target="_blank" href="https://doi.org/10.1016/j.cell.2023.07.013">Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation</a>
+              (<a target="_blank" href="https://www.cell.com/cms/attachment/4dd261cd-12d0-4ab1-944d-30a6c4b550fd/figs3.jpg">figure</a>)
+            <li> <a target="_blank" href="https://www.nature.com/articles/s41375-022-01792-x">Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors</a>
+              (<a target="_blank" href="https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41375-022-01792-x/MediaObjects/41375_2022_1792_Fig2_HTML.png">figure</a>)
+            <li> <a target="_blank" href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010623">Stochastic dynamics of Type-I interferon responses</a>
+              (<a target="_blank" href="https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=10.1371/journal.pcbi.1010623.g001">figure</a>)
+            <li> <a target="_blank" href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010903">New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells</a>
+              (<a target="_blank" href="https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=10.1371/journal.pcbi.1010903.g006">figure</a>)
+            <li> <a target="_blank" href="https://link.springer.com/article/10.1007/s43393-021-00059-3">Review of construction methods for whole-cell computational models</a>
+              (<a target="_blank" href="https://link.springer.com/article/10.1007/s43393-021-00059-3/figures/3">figure</a>)
+            <li> <a target="_blank" href="https://link.springer.com/chapter/10.1007/978-3-031-42715-2_14">Exploring Identifiability in Hybrid Models of Cell Signaling Pathways</a>
+              (<a target="_blank" href="https://media.springernature.com/lw685/springer-static/image/chp%3A10.1007%2F978-3-031-42715-2_14/MediaObjects/551661_1_En_14_Fig1_HTML.png">figure</a>)
+            </ul>
+        </p>
+
      </div>
     </div>
     <script> writeFooter(); </script>

index.html

@@ -30,7 +30,7 @@
         <h1>Welcome to Newt Pathway Viewer & Editor</h1>
 
         <p>Newt is a free, web based, open source viewer and editor for pathways in <a href="http://sbgn.org/">Systems
-            Biological Graphical Notation (SBGN)</a> and <a
+            Biological Graphical Notation (SBGN)</a>, <a href="https://sbml.org/"> Systems Biology Markup Language (SBML)</a>, and <a
             href="http://www.pathwaycommons.org/pc2/formats#sif_relations">Simple Interaction Format (SIF)</a>. It
           was written with a series of libraries and extensions based on <a
             href="http://js.cytoscape.org/">Cytoscape.js</a> with utmost customization in mind.</p>
@@ -57,26 +57,35 @@ <h1>Welcome to Newt Pathway Viewer & Editor</h1>
           <li> Advanced diagramming through interactive move, resize, and styling of map objects including color
             schemes, re-routing and re-connection of interactions, and grid & alignment guideline support
           <li> Support for experiment data overlay on maps</a>
-          <li> Facilities for querying, viewing, and editing pathways in <a href="http://pathwaycommons.org">Pathway
-              Commons</a>
+          <li> Facilities for querying, viewing, and editing pathways in
+            <a href="http://pathwaycommons.org">Pathway Commons</a>,
+            <a href="https://reactome.org/">Reactome</a>, and 
+            <a href="https://www.wikipathways.org/">WikiPathways</a>,
           <li> Conversion to and from <a target="_blank" href="http://www.celldesigner.org/"> CellDesigner </a>, <a
               target="_blank" href="http://sbml.org/Main_Page">SBML</a>, and <a target="_blank" href="https://pathvisio.org/documentation/GPML">GPML</a> file formats
-          <li> Launching with a remote SBGN model specified as a URL (<a
-              href="http://web.newteditor.org/?URL=https://raw.githubusercontent.com/sbgn/libsbgn/master/test-files/PD/activated_stat1alpha_induction_of_the_irf1_gene.sbgn&mapColorScheme=blue_scale"
-              target="_blank">example</a>) or as a URI (<a
-              href="http://web.newteditor.org/?URI=http://identifiers.org/reactome/R-HSA-6803211&mapColorScheme=opposed_green_brown"
+          <li> Launching with a remote model specified as a URL
+            (<a href="https://web.newteditor.org/?URL=https://reactome.org/ContentService/exporter/event/R-HSA-450531.sbgn&inferNestingOnLoad=true&mapColorScheme=opposed_red_blue&fitLabelsToNodes=true"
+              target="_blank">SBGN</a>,
+            <a href="https://web.newteditor.org/?URL=https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000125.2?filename=BIOMD0000000125_url.xml&inferNestingOnLoad=true&applyLayoutOnURL=true"
+              target="_blank">SBML</a>, or
+            <a href="https://web.newteditor.org/?URL=https://www.wikipathways.org/wikipathways-assets/pathways/WP121/WP121.gpml"
+              target="_blank">GPML</a>), or as a URI
+              (<a href="http://web.newteditor.org/?URI=http://bioregistry.io/reactome:R-HSA-70171&mapColorScheme=opposed_green_brown"
               target="_blank">example</a>)
           <li> Support for <a href="https://sbgnbricks.org/">SBGN bricks</a>
         </ul>
+        <p>Some Newt version 4 features are highlighted in <a href="tutorials-newt4.html">here</a>.</p>
         <h2>Citation</h2>
-        <p>Please cite the following when you use Newt:<br><br>
+        <p>Please cite the following when you use Newt:</p>
 
-          H. Balci, M.C. Siper, N. Saleh, I. Safarli, L. Roy, M. Kilicarslan, R. Ozaydin, A. Mazein, C. Auffray, O. Babur, E. Demir and U. Dogrusoz, <a href="https://doi.org/10.1093/bioinformatics/btaa850">Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps</a>, <b>Bioinformatics</b>, 37(10), pp.1475-1477, 2021.<br><br>
+        <p>H. Balci, M.C. Siper, N. Saleh, I. Safarli, L. Roy, M. Kilicarslan, R. Ozaydin, A. Mazein, C. Auffray, O. Babur, E. Demir and U. Dogrusoz,
+          <a href="https://doi.org/10.1093/bioinformatics/btaa850">Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps</a>,
+          <b>Bioinformatics</b>, 37(10), pp.1475-1477, 2021.</p>
 
-          M. Sari, I. Bahceci, U. Dogrusoz, S.O. Sumer, B.A. Aksoy, O. Babur, E. Demir, <a
-            href="https://doi.org/10.1371/journal.pone.0128985">SBGNViz: a tool for visualization and complexity
-          management of SBGN process description maps</a>, <b>PLoS ONE</b>, 10(6), e0128985, 2015.
-        </p>
+        <p>M. Sari, I. Bahceci, U. Dogrusoz, S.O. Sumer, B.A. Aksoy, O. Babur, E. Demir,
+          <a href="https://doi.org/10.1371/journal.pone.0128985">SBGNViz: a tool for visualization and complexity management of SBGN process description maps</a>,
+          <b>PLoS ONE</b>, 10(6), e0128985, 2015.</p>
+
         <h2>Source code</h2>
         <p>Newt source code can be found on <a href="https://github.com/iVis-at-Bilkent/newt">this</a> Github
           repository.</p>