2017 Purdue University SROP Program for Undergraduates

About Me

• Major: Cellular Molecular Biology
• Future plans: PhD in Infectious Diseases with a focus on Genetics
• Classes:
    General Biology, General Chemistry, Organic Chemistry, Calculus, Statistics, Microbology, Physics, Biochemistry, Genetics, Ecology and Evolution of Infectious Diseases.
• Awards/Recognitions:
   Research Initiative for Scientific Enhancement (RISE) Research Assistanship: August 2016-July 2017

Project Description

During this summer (2017) I Will be working with two mentors, Dr. Vetria Byrd and Dr. Douglas LaCount. I will be applying concepts from data visualization to represent the interactions between Ebola Virus and Marburg Virus proteins and human proteins. In adition, I will be working on a project identifying the interactions between Zika Virus and the human proteins using a yeast two-hybrid system. Meanwhile we will be also attending to different workshops and seminars that will help us professionally and personally.

Visualization Tools

Visualization Tools (under review)

Cytoscape .

http://www.cytoscape.org/
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., ... & Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research, 13(11), 2498-2504.

Tableau.

https://www.tableau.com.

VisAnt.

http://visant.bu.edu/
Hu, Z., Mellor, J., Wu, J., & DeLisi, C. (2004). VisANT: an online visualization and analysis tool for biological interaction data. BMC bioinformatics, 5(1), 17.

Gephi.

https://gephi.org/
Bastian, M., Heymann, S., & Jacomy, M. (2009). Gephi: an open source software for exploring and manipulating networks. Icwsm, 8, 361-362.

GPS Prot.

http://gpsprot.org/
Fahey, M. E., Bennett, M. J., Mahon, C., Jäger, S., Pache, L., Kumar, D., ... & Frankel, A. D. (2011). GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. BMC bioinformatics, 12(1), 298.

D3.js.

https://d3js.org

Week 1

Research trainings (including CITI program)

Literature review on how to read data visualization papers and how to work with it

Introduction to Data Visualization

Data Visualization Vis Tools Assignment

Week 2

Established milestones for the summer projects

Literature review to identify the tools for data visualization that could be applied to the project

Introduction to HTML and developing our websites

Tour at the Envision Center where we were able to see the different applications of data visualization

Downloaded Cytoscape and literature review on how to use it for protein interactions

Developing our websites

Exercises on Pivot Charts and Tables

Week 3

First data visualization with the Ebola Virus and Marburg Virus and the human proteins

Developing our websites

Annotated bibliography

List of tools that could be useful for the data visualizatiopn project

Week 4

Complete list of Visualization tools

Realize an annotated bibliography

Realize different visualizations with variations in colors, thickness of lines and size of nodes

Last updated: 06/23/2017