CE-13.10

Title: 

GUI for Qiime (Visual Qiime)

Author(s): 

Sunil Kumar Rai

Oral Defence Date: 

05/29/2013

Location: 

TH 434

Committee: 

CS Professors Marguerite Murphy and Dragutin Petkovic; Biology Professors Edward Connor and Jose de la Torre

Abstract: 

Qiime is open source software developed by the Knight Lab at the University of Colorado in Boulder. It is used for comparing and analyzing microbial communities, primarily based on high throughput amplicon sequencing data like SSU rRNA. Qiime also supports other types of data like shotgun metagenomic data. However there are some major drawbacks with using this software: Qiime does not have a graphical interface, which makes it difficult for researchers to use it, especially ones who do not have computer background, because users need to remember the names of all the scripts for each phase of the Qiime workflow. Qiime is not platform independent software, a Qiime virtual box is required on Windows machines. In order to overcome these limitations, we have developed an application called Visual Qiime. It provides a solution to both of the problems discussed above by providing a Web based graphical interface to use Qiime running on a powerful remote server. The major advantage of using Visual Qiime is that it can be used on any platform and users do not have to remember the names of scripts for various phases of the Qiime workflow. Also users do not have to install and configure the software on a local machine and results are obtained much faster too. A survey-based usability study was conducted with 20 participants and a majority of them responded that the application was useful and easy to use.

Keywords: 

GUI, Qiime, PHP

Copyright: 

Sunil Kumar Rai