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<h1 id="architecture-notes-">Architecture notes:</h1>
<p>Dependencies: This repo uses </p>
<ul>
<li>d3 to create visual components, </li>
<li>webcola to lay them out, </li>
<li>MI-Model to create a common data model for any other potential views of the same protein complex on the same page.</li>
<li>jstoxml to convert the js layout into an SBGN-ML file.</li>
</ul>
<h2 id="design">Design</h2>
<p>This repo has been designed to enable semi-automated layouts of protein complexes in SBGN-ML. </p>
<p>SBGN-ML is the XML representation of Systems Biology Graphical Notation (SBGN), a visual language to represent biochemical interactions.</p>
<p>Original paper describing SBGN: <a href="http://www.nature.com/nbt/journal/v27/n8/full/nbt.1558.html">http://www.nature.com/nbt/journal/v27/n8/full/nbt.1558.html</a> Original paper describing SBGN-ML: <a href="https://academic.oup.com/bioinformatics/article/28/15/2016/236089/Software-support-for-SBGN-maps-SBGN-ML-and-LibSBGN">https://academic.oup.com/bioinformatics/article/28/15/2016/236089/Software-support-for-SBGN-maps-SBGN-ML-and-LibSBGN</a> - It says laying out SBGN is a 'hard problem'.</p>
<p>SBGN has three sub-languages:</p>
<ul>
<li>Process Diagram, depicting entities over time</li>
<li>Entity Relationship</li>
<li>Activity Flow, used for scenarios in which broad details are conveyed without necessarily depicting specific entities.</li>
</ul>
<p>Entity Relationship seems to be most pertinent to depicting the protein complexes shown in the complex viewer.</p>
<p>Specification for SBGN Entity Relationship (ER) Version 2 (August 2015): <a href="http://journal.imbio.de/article.php?aid=264">http://journal.imbio.de/article.php?aid=264</a> pages 16, 17 have info about interactions.</p>
<h3 id="notes-about-the-layout">Notes about the layout</h3>
<p>Given that the layout of SBGN in an automated fashion is considered a hard problem, this viewer allows users to drag and re-arrange automated views until they reach a more pleasing state visul state. Once this is reached they may then download the re-arranged view in a serialised SBGN-ML format, preserving their manual layouts. Skipping the preview/re-arrange step would likely result in messy graphs at this stage, without much more complex (and time-intensive) layout algorithms. </p>
<h2 id="installation">installation</h2>
<p>Please see <a href="../README.md">the main README</a> for installation info.</p>