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update web page to 3.1
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ugurdogrusoz committed Feb 2, 2024
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2 changes: 1 addition & 1 deletion faq.html
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Expand Up @@ -40,7 +40,7 @@ <h1>FAQ</h1>
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>

<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> and <a target="_blank" href="http://sbml.org/Main_Page">SBML</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 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>

<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>
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6 changes: 3 additions & 3 deletions index.html
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Expand Up @@ -59,8 +59,8 @@ <h1>Welcome to Newt Pathway Viewer & Editor</h1>
<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> Conversion to and from <a target="_blank" href="http://www.celldesigner.org/"> CellDesigner </a> and <a
target="_blank" href="http://sbml.org/Main_Page">SBML</a> file formats
<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
Expand All @@ -71,7 +71,7 @@ <h1>Welcome to Newt Pathway Viewer & Editor</h1>
<h2>Citation</h2>
<p>Please cite the following when you use Newt:<br><br>

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>
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>

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
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3 changes: 3 additions & 0 deletions js/scripts.js
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Expand Up @@ -37,6 +37,9 @@ document.write("<h3>Search</h3>");
document.write("<gcse:search>");
document.write("</gcse:search>");
document.write("<h3>Latest News</h3>");
document.write("<h4>GPML support</h4>");
document.write("<h5>February 2, 2024</h5>");
document.write("<p>Newt 3.1 was released to include support for GPML import/export.<br> /></p>");
document.write("<h4>Reactome and BioModels integration</h4>");
document.write("<h5>2022, 2023</h5>");
document.write("<p>Reactome and BioModels pathways now connect to our Newt editor for viewing and editing in SBGN (<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\">Reactome example</a> and <a href=\"https://www.ebi.ac.uk/biomodels/BIOMD0000000125\">BioModels example</a>)<br /></p>");
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4 changes: 2 additions & 2 deletions tutorials.html
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Expand Up @@ -198,7 +198,7 @@ <h3 id="import-export">Import-export
<p> &#9752; Newt can support both milestones 0.2 and 0.3 but opts to 0.2 by default. Persistency in milestone 0.3 is available though through the "Export" menu.
</p>

<p> Newt also supports import and export facilities from and to <a href="https://en.wikipedia.org/wiki/SBML">SBML</a> and <a href="http://www.celldesigner.org/">CellDesigner</a> through "{Import, Export} | {SBML, CellDesigner}".</p>
<p> Newt also supports import and export facilities from and to <a href="https://en.wikipedia.org/wiki/SBML">SBML</a>, <a href="http://www.celldesigner.org/">CellDesigner</a>, and <a href="https://pathvisio.org/documentation/GPML">GPML</a> through "{Import, Export} | {SBML, CellDesigner, GPML}".</p>

<p> In addition, AF models can be imported to Newt from simple tab-delimited files. An example model formatted in this manner follows:</p>
<div style="margin-left: 20px;"><code>
Expand Down Expand Up @@ -401,7 +401,7 @@ <h2 id="querying-pathway-commons">Querying Pathway Commons <a href="#top-of-tuto
<h2 id="references">References
<a href="#top-of-tutorials"><img src="images/back-to-top.svg" height=16px/></a></h2>

[1] 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>, Bioinformatics, to appear, 2020.
[1] 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>, Bioinformatics, 37(10), pp. 1475–1477, 2021.
<br><br>[2] 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>", PLoS ONE, 2015.
<br><br>[3] U. Dogrusoz and B. Genc, "<a href="https://doi.org/10.1016/j.cag.2005.10.015">A Multi-Graph Approach to Complexity Management in Interactive Graph Visualization</a>", Computers & Graphics, 2006.
<br><br>[4] U. Dogrusoz, A. Karacelik, I. Safarli, H. Balci, L. Dervishi, M.C. Siper, "<a href="https://doi.org/10.1371/journal.pone.0197238">Efficient methods and readily customizable libraries for managing complexity of large networks</a>", PLoS ONE, 2018.
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