Team:UCSD Software/Project
From 2014.igem.org
Topics
Project Description
Abstract
Genetic circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. SBiDer, a web tool developed by the UCSD Software iGEM team, will leverage existing devices to construct a database with consideration for the function of each device interpreted as boolean logic. The data can be queried by the user through SBiDer's visual interface to explore circuit designs. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. Basic validation of the circuit performance is also provided within in the interface. SBiDer's web of information can be expanded through user-generated additions to the database to improve the efficiency of the application and the accuracy of the models.Future Directions
Synthetic genetic circuits created by synthetic biologists have yielded exciting applications such as biofuels production and cancer killing bacteria. These circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. Although there are many genetic devices that have been built, re-using these devices often requires a time-consuming review of the literature. The UCSD Software iGEM team will address this challenge by creating a web-tool that leverages existing genetic devices to create complex genetic circuits.Web Application
We will connect known genetic devices together via device input and outputs to create a network of devices that can interact. We define a genetic device as a DNA construct transformed into cells that can cause expression of some protein in response to stimuli (or input). We will develop a web interface to facilitate access to the complex network that we have constructed. Our Web interface makes extensive use of Cytoscape, an open source bioinformatics software package for metabolic network visualization and simulation. In addition, the interface will generate SBOL Visual Images, a standard language that is easily understood by synthetic biologists all over the world. Users can also update our database with additional devices through this interface. Using the Cynetshare framework, users can share their circuit designs.
Traversal/Search
- Learnt HTML
- Went over everyone else's codes
- SQL cleanup
- Wrote code for BFS and DFS
- Learn Python the Hard Way
- Prepared presentation for expanded BFS on Monday
- Continued shifting through CyNetShare code and annotate functions
- Learnt Bioservices for Miriam
- Read papers to fill in database
- scheme for UUID
- add implicit output list to device table
- promoter sequence database (biobrick registry)
- insert_into_database fix
- determine necessary data for device input
- Worked on traversal algorithm
- Continued debugging network
- Updated database
- Learnt Angular.js main functions to use for the website
- Went over more CyNetShare code
- Read a few articles about visualizing data using JSON files and different techniques to do so
Database (the foundation)
- Created database structure
- Normalization complete
- Working on algorithm
- Reading on petri nets
- Learning about designing wiki
- Populating new database
- Learnt more about Petri Nets
- Learnt more about SQL and its functions
- Met with Joaquin and Fred to brainstorm the traversal algorithm
- Edited the Petri Net traversal to accept multiple inputs
- Formatted integration of Bolean logic and multiple outputs
- Busy with Final Exams
- Began outlining Web part of presentation
- Designed a new structure for the database and the traversal
- Improved BFS algorithm
- Populated database
- Kept journal clean
- Incorporated NetworkX into script
- Began Boolean Satisfiability Problem
- Worked on designing a specific JSON file to visualize database with CyNetShare
- Played around with more JSON data to add more key values and data
- Enabled CyNetShare on his server
- Cleaned up web dev part of master branch
- Met with Joaquin and Huwate (Kwat), improved database structure, finished database normalization, prepared for presentation and traversal algorithm
Modeling
- Cleaned the database and commented on everyone's data
- Worked on search algorithm
- Read about Petri nets
- Tried to modify traverse algorithm to fit Petri Net model
- Edited the database
- Fixed errors in traversal
- Continued to clean up database
- Added NOT gate entries to AND gates involving repressors
- Contributed to website portion of presentations
- Learnt scale vector graphs for possible plotting
- Filled database PowerPoint presentation
- Filled database section
- Improved BFS algorithm
- Populated database
- Kept journal clean
- Worked on presentation
- Incorporated NetworkX into script
- Began Boolean Satisfiability Problem
- Worked on designing a specific JSON file to visualize database with CyNetShare
- Looked over database
- Thought about possible website designs
- Played around with JSON data
- Edited more database information
- Enabled CyNetShare on his server
- Cleaned up web dev part of master branch