Team:UCSD Software/Teaml

<hl> Kwat </hl>

1. Learnt boolean networks
2. Continued learning Petri Nets

<hl> Lauren </hl>

1. Learnt Boolean networks
2. Continued learning Petri nets

<hl> Gary </hl>

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

<hl> Joaquin </hl>

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

<hl> Rohit </hl>

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

<hl> Fernando </hl>

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

</ol>










<hl> Kwat </hl>

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




<hl> Lauren </hl>

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




<hl> Gary </hl>

1. Learnt basics of Angular.js




<hl> Joaquin </hl>

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

<hl> Rohit </hl>

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




<hl> Fernando </hl>

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




<hl> Valeriy </hl>

1. Started relearning python to work with the traversal as suggested by Jenhan







<hl> Kwat </hl>

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




<hl> Lauren </hl>

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




<hl> Gary </hl>

1. Continued shifting through CyNetShare code




<hl> Joaquin </hl>

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

<hl> Rohit </hl>

1. Worked on traversal algorithm




<hl> Fernando </hl>

1. Continued debugging network
2. Updated database




<hl> Valeriy </hl>

1. Learnt Angular.js main functions to use for the website
2. Went over more CyNetShare code




<hl> Kwat </hl>

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




<hl> Lauren </hl>

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




<hl> Gary </hl>

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




<hl> Joaquin </hl>

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




<hl> Rohit </hl>

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




<hl> Fernando </hl>

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




<hl> Valeriy </hl>

1. Worked on designing a specific JSON file to visualize database with CyNetShare




<hl> KP </hl>

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




<hl> Kwat </hl>

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




<hl> Lauren </hl>

1. Edited the database
2. Fixed errors in traversal




<hl> Gary </hl>

1. Continued to clean up database
2. Added NOT gate entries to AND gates involving repressors




<hl> Joaquin </hl>

1. Filled database PowerPoint presentation







<hl> Rohit </hl>

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




<hl> Fernando </hl>

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




<hl> Valeriy </hl>

1. Worked on designing a specific JSON file to visualize database with CyNetShare




<hl> KP </hl>

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




<hl> Kwat </hl>

1. Made a script that parses a user input, searches graph and returns one more more linear searchable space
2. Learned SNAKES
3. Learned SQL stored function
4. Provided Fernando data for analysis




<hl> Lauren </hl>

1. Added traversal algorithm to presentation
2. Wrote project description




<hl> Gary </hl>

1. Continued to clean up database
2. Got CyNetShare running on NetBeans




<hl> Joaquin </hl>

1. Worked on presentation
2. Started script to get JSON information







<hl> Rohit </hl>

1. Added minimum spanning tree slides to presentation
2. Started learning JSON







<hl> Fernando </hl>

1. Read Overpowering the Component Problem and Circuit Simulation of Genetic Networks







<hl> Valeriy </hl>

1. Designed web app page
2. Worked on wiki
3. Added slides to presentation










<hl> Kwat </hl>

1. Finished parser
2. Finished database structure







<hl> KP </hl>

1. Changed size/shapes of nodes in CyNetShare
2. Began learning Angular UI Bootstrap
3. Began working on carousel within CyNetShare




<hl> Gary </hl>

1. Added dynamic labels to graph that enumerates lines as they are added
2. Got CyNetShare running on NetBeans




<hl> Joaquin </hl>

1. Finished operon, plasmid I.D.s etc. In database










<hl> Rohit </hl>

1. Worked on JSON
2. Edited presentation







<hl> Tiffany</hl>

1. Modified pigeon command generator for plasmid to generate commands for each individual operon
2. Modified logo







<hl> Valeriy </hl>

1. Designed web app page
2. Worked on wiki
3. Added slides to presentation










<hl> Kwat </hl>

1. Got inputs on parser working
2. Began working on outputs and verifying codes







<hl> KP </hl>

1. Remote




<hl> Gary </hl>

1. Finished adding line removal buttons to legend
2. Cleaned up Web Dev branch




<hl> Joaquin </hl>

1. Populated working data










<hl> Rohit </hl>

1. Worked on JSON
2. Began learning NetworkX































<hl> Kwat </hl>

1. Patched codes together
2. Finished database with Joaquin







<hl> KP </hl>

1. Remote




<hl> Gary </hl>

1. Validated database
2. Drafted JSON format
3. Went remote




<hl> Joaquin </hl>

1. Parsed excel file into database
2. Prepared for presentation










<hl> Rohit </hl>

1. Wrote Python script that takes SQL query and outputs JSON
2. Began learning Cytoscape.js
3. Began learning igraph







<hl> Kwat </hl>

1. Worked on poster
2. Worked on presentation outline
3. Updated traverse code
4. Updated Google Drive




<hl> KP </hl>

1. Remote




<hl> Gary </hl>

1. Remote




<hl> Joaquin </hl>

1. Designed master Python
2. Designed device insert page










<hl> Rohit </hl>

1. Read up on network motif algorithms (mfinder, color-coding, Kavosh)
2. Decided on Kavosh
3. Began learning CytoKavosh




<hl> Fernando </hl>

1. Almost finished JSON graph constructor




<hl> Lauren </hl>

1. Verified database code compatibility with network traversal

























<hl> Kwat </hl>

1. Populated and finalized database
2. Combined visualization property with traverse code
3. Tested and debugged traversal algorithm
4. Started working on presentation




<hl> KP </hl>

1. Remote




<hl> Gary </hl>

1. No longer remote
2. Met with Ryan and Jenhan to refine modeling development directoin
3. Decided to use dictionaries of each operon's modeling information




<hl> Joaquin </hl>

1. Populated new database structure
2. Implemented dictionaries necessary for traversal










<hl> Rohit </hl>

1. Continued network analysis with Kavosh
2. Began validating database




<hl> Fernando </hl>

1. Remote




<hl> Lauren </hl>

1. Generated DOT file creator to retrieve node coordinates from GraphViz































<hl> KP </hl>

1. Remote




<hl> Gary </hl>

1. Rendered full network JSON
2. Tweaked HTML and laid down function frameworks for search box
3. Reorganized app HTML for easier styling and positioning




<hl> Joaquin </hl>

1. Fixed operon I.D.s in database creator
2. Fixed operon to output transition mapping
3. Connected positions to JSON creator
4. Worked on Pidgeon







<hl> Rohit </hl>

1. Rendered full network on CytoScape
2. Attempted to run Linux VirtualBox on my machine to run CytoKavosh




<hl> Fernando </hl>

1. Remote




<hl> Lauren </hl>

1. Debugged JSON file creator




























<hl> KP </hl>

1. Remote




<hl> Gary </hl>

1. Connected algorithms and servlet between database and SBIDer
2. Modified GET requests to accept JSON strings instead of JSON files
3. Edited color scheme and style of nodes







<hl> Joaquin </hl>

1. Connected algorithms to servlet between database and SBIDer
2. Integrated database into file creator










<hl> Rohit </hl>

1. VirtualBox did not work
2. Ran CytoKavosh on CSE lab Linux machines and found motifs




<hl> Fernando </hl>

1. Worked on SBML modeling script
2. Finished QualitativeSpecies class and Modeling class




<hl> Lauren </hl>

1. Integrated database into file creator