Team:UCSD Software/Project

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

1. Learnt boolean networks
2. Continued learning Petri Nets
3. Looked for useful Python packages for the project

1. Learnt Boolean networks
2. Continued learning Petri nets

1. Continued playing with Cytoscape.js add/remove nodes

1. Learnt Boolean Networks
2. Learnt reachability treees
3. Developed Entity Relationship Diagram

1. Learnt Boolean networks
2. Found SNAKES- a Python package that utilizes Petri nets

1. Learnt Boolean networks
2. Disambiguated Linh's device composition

Web Application

1. Learnt SQL
2. Learnt traversal algorithms
3. Read assigned papers to populate database
4. Read about past IGEM teams and projects

1. Petri net reading
2. CodeAcademy Python tutorials
3. BFS/DFS algorithms
4. Read papers to fill in database

1. Learnt basics of Angular.js
2. Meet with CyNetShare team
3. Got approval to use CyNetShare code

1. SQl columns modification
2. Read papers to fill in database

1. Learnt SQL
2. Conceptualized traversal algorithms
3. Read assigned papers to populate database

1. Found possible approach to weigh our edges using "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements" and its database

1. Started relearning python to work with the traversal as suggested by Jenhan
2. Read a few chapters from different books about Jquery functions to use for data loading onto the website

Traversal/Search

1. Learnt HTML
2. Went over everyone else's codes
3. SQL cleanup

1. Wrote code for BFS and DFS
2. Learn Python the Hard Way
3. Prepared presentation for expanded BFS on Monday

1. Continued shifting through CyNetShare code and annotate functions

1. Learnt Bioservices for Miriam
2. Read papers to fill in database
3. scheme for UUID
4. add implicit output list to device table
5. promoter sequence database (biobrick registry)
6. insert_into_database fix
7. determine necessary data for device input

1. Worked on traversal algorithm

1. Continued debugging network
2. Updated database

1. Learnt Angular.js main functions to use for the website
2. Went over more CyNetShare code
3. Read a few articles about visualizing data using JSON files and different techniques to do so

Database (the foundation)

1. Created database structure
2. Normalization complete
3. Working on algorithm
4. Reading on petri nets
5. Learning about designing wiki
6. Populating new database
7. Learnt more about Petri Nets
8. Learnt more about SQL and its functions
9. Met with Joaquin and Fred to brainstorm the traversal algorithm

1. Edited the Petri Net traversal to accept multiple inputs
2. Formatted integration of Bolean logic and multiple outputs

1. Busy with Final Exams
2. Began outlining Web part of presentation

1. Designed a new structure for the database and the traversal

1. Improved BFS algorithm
2. Populated database
3. Kept journal clean

1. Incorporated NetworkX into script
2. Began Boolean Satisfiability Problem

1. Worked on designing a specific JSON file to visualize database with CyNetShare
2. Played around with more JSON data to add more key values and data

1. Enabled CyNetShare on his server
2. Cleaned up web dev part of master branch

1. Met with Joaquin and Huwate (Kwat), improved database structure, finished database normalization, prepared for presentation and traversal algorithm

Modeling

1. Cleaned the database and commented on everyone's data
2. Worked on search algorithm
3. Read about Petri nets
4. Tried to modify traverse algorithm to fit Petri Net model

1. Edited the database
2. Fixed errors in traversal

1. Continued to clean up database
2. Added NOT gate entries to AND gates involving repressors
3. Contributed to website portion of presentations
4. Learnt scale vector graphs for possible plotting

1. Filled database PowerPoint presentation
2. Filled database section

1. Improved BFS algorithm
2. Populated database
3. Kept journal clean
4. Worked on presentation

1. Incorporated NetworkX into script
2. Began Boolean Satisfiability Problem

1. Worked on designing a specific JSON file to visualize database with CyNetShare
2. Looked over database
3. Thought about possible website designs
4. Played around with JSON data
5. Edited more database information

1. Enabled CyNetShare on his server
2. Cleaned up web dev part of master branch