Senior Design Projects

ECS193 A/B Winter & Spring 2019

Computational Analysis and Visualization of Complex Biochemical Systems

Name Miguel Valderrama
Affiliation Department of Microbiology and Molecular Genetics

Project's details

Project title Computational Analysis and Visualization of Complex Biochemical Systems
Background Relating the phenotype of an organism to its genome is one of the “Grand Challenges” in modern biology. This includes for instance, relating a disease such as diabetes or cancer to the causative changes in the organisms DNA -mutations- or changes in the organisms environment -toxins, chemicals-. Our lab has developed a theoretical framework that relates the genotype and environment of an organism to the behavior of its underlying biochemical systems ( the phenotype ).
Description We have been working on a computational toolbox for analysis and visualization of these important relationships. The current version of the toolbox consists of two elements: a stand-alone library, written in the C language for speed and parallelization, and a python module that provides access to the functions contained in the C-library and provides visualization capabilities. Additionally, the functionality of the toolbox can be accessed via a user-friendly interface based on Ipython Notebook widgets. Students working on this project will have the possibility to make contributions on three different aspects: 1. Improving Software Distribution: A Docker image ( ) to guarantee software usage in different operating systems has been created. The current size of this image is 3.12 GB, which can be excessive for some users. We believe that the size of this docker image can be dramatically minimized by using different techniques ( e.g. docker-slim ). 2. Updating Both Python Code & User Interface: the python module of the software is written in python 2.7, which will not be maintained past 2020 ( ). In order to guarantee usability of our software in the future, both the python module and the user interface need to be updated to run on python 3 and on the newest version of the Jupyter Notebook ( ). 3. Extending Toolbox Capabilities: several new functionalities are currently under development ( e.g. calculation of the volume of polytopes in a high-dimensional space to assess phenotype robustness ). Students working on this project will have the possibility to contribute to the development of these new functionalities.
Deliverable 1. A slim Docker image. 2. Compatibility of our software with python 3. 3. An updated user interface based on Jupyter widgets. 4. The team is expected to develop at least one new capability for the toolbox.
Skill set desirable • Intermediate to advanced Python knowledge. • Basic understanding of linear algebra is a plus. • Interest on modeling of biochemical networks is a plus.
Phone number N/A
Client time availability 30-60 min weekly or more
IP requirement Open source project
Attachment Click here
Selected N/A
Stuff N/A