Computational Biology @ University of Nebraska-Lincoln

Mentors: Student: Xiaodong Zhao

<p>With ccNetViz, this large graph render library using WebGL, I'll add edge animations on it. Including color animations, speed control and other fancy animations like wavy curve, dotted line and liquid fluid effects.</p> <p>These animations will be totally customizable and we'll also offer some high quality presets for user to choose.</p> <p>Finally, documentation for edge animation will be complete and we'll also have a demo page to show all function of edge animation.</p>

Mentors: Student: Aman Dave

<p>The project is based upon Flux Balance Analysis, which is a model used for simulating metabolism. It is used in genome-scale reconstructions of metabolic networks. This project aims at building a web-based pipeline which will help in analysis. The user will be able to submit an SBML model, a representation format based on XML helping in the biological process, select one of the analysis methods and in turn, get a result which will be produced after passing the input through the pipeline.</p> <p>The pipeline will send the input to the COBRAPy microservice, which will return the result through node.js express routes and the results will be displayed via ReactJS frontend.</p>

Mentors: Student: Caner Akdaş

<h4>Advanced Node, Edge, Arrow Plugin Library</h4> <p>This plugin draws the desired types of nodes and arrows on a non-visible canvas. These dynamically drawn images are created in the browser as Blob type images and visualization of ccNetViz as texture.</p> <p>These pre-prepared shapes will be added to the plugin.</p> <p>The library will be able to draw the desired node and arrow graphs without compromising performance. Also, the plugin doesn't affect the core library still keep the core of library lightweight.</p> <p>With this plugin ccNetViz can:</p> <ul> <li>Basic geometric node and arrow styles</li> <li>Interactive animations for node and arrow styles<ul> <li>Color transition effect</li> <li>Shape transition effect</li> </ul> </li> <li>Custom node and arrow styles<ul> <li>Statistical node styles<ul> <li>Gauge chart</li> <li>Pie chart</li> <li>Doughnut chart</li> <li>Radial histogram, etc.</li> </ul> </li> </ul> </li> </ul> <p>With these developments, settings will be prepared and documented to enable the user to use them easily.</p>

Mentors: Student: Mohamed Shadab

<p>Ordinary differential equations are widely used for modelling biological networks and processes of kinetics. The idea of the project is to create a web application that allows a user to submit an SBML model and select methods of analysis and receive results. The different kind of analysis methods that will be available for use are Steady State Analysis, Parameter Fitting, Simulation.</p>

Mentors: Student: Himanshu Jotwani

<p>The Purpose of this project is to add advanced label formatting features to the ccNetviz library for graph Visualizations without affecting the performance , at the same time adding corresponding UNIT tests to the components added.</p>