Team:UCSD Software/Notebook

From 2014.igem.org

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Revision as of 00:27, 14 October 2014


Week

  • Week 1
  • Week 2
  • Week 3
  • Week 4
  • Week 5
  • Week 6
  • Week 7
  • Week 8
  • Week 9
  • Week 10
  • Week 11
  • Week 12

Entries

Week 1

Kwat
  1. Generated Pydoc
  2. Learnt SQL
  3. Learnt Petri Nets
Lauren
  1. Did Learn Python the Hard Way
  2. Read Python Wiki
Gary
  1. Read Cytoscape.js API
Joaquin
  1. Learnt Boolean Networks
  2. Continued Petri Nets
  3. Learnt Dynamic Programming and Path Traversal
Rohit
  1. Learnt Cytoscape
  2. Learnt Python
  3. Learnt Petri Nets
Fernando
  1. Finished command line interface
  2. Acquired snippet of Linh's database

Week 2

Kwat
  1. Learnt boolean networks
  2. Continued learning Petri Nets
Lauren
  1. Learnt Boolean networks
  2. Continued learning Petri nets
Gary
  1. Continued playing with Cytoscape.js add/remove nodes
Joaquin
  1. Learnt Boolean Networks
  2. Learnt reachability treees
  3. Developed Entity Relationship Diagram
Rohit
  1. Learnt Boolean networks
  2. Found SNAKES- a Python package that utilizes Petri nets
Fernando
  1. Learnt Boolean networks
  2. Disambiguated Linh's device composition

Week 3

Kwat
  1. Learnt SQL
  2. Learnt traversal algorithms
  3. Read assigned papers to populate database
Lauren
  1. Petri net reading
  2. CodeAcademy Python tutorials
  3. BFS/DFS algorithms
  4. Read papers to fill in database
Gary
  1. Learnt basics of Angular.js
Joaquin
  1. SQl columns modification
  2. Read papers to fill in database
Rohit
  1. Learnt SQL
  2. Conceptualized traversal algorithms
  3. Read assigned papers to populate database
Fernando
  1. Found possible approach to weigh our edges using "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements" and its database
Valeriy
  1. Started relearning python to work with the traversal as suggested by Jenhan

Week 4

Kwat
  1. Learnt HTML
  2. Went over everyone else's codes
Lauren
  1. Wrote code for BFS and DFS
  2. Learn Python the Hard Way
  3. Prepared presentation for expanded BFS on Monday
Gary
  1. Continued shifting through CyNetShare code
Joaquin
  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
Rohit
  1. Worked on traversal algorithm
Fernando
  1. Continued debugging network
  2. Updated database
Valeriy
  1. Learnt Angular.js main functions to use for the website
  2. Went over more CyNetShare code

Week 5

Kwat
  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
Lauren
  1. Edited the Petri Net traversal to accept multiple inputs
  2. Formatted integration of Bolean logic and multiple outputs
Gary
  1. Busy with Final Exams
  2. Began outlining Web part of presentation
Joaquin
  1. Designed a new structure for the database and the traversal
Rohit
  1. Improved BFS algorithm
  2. Populated database
  3. Kept journal clean
Fernando
  1. Incorporated NetworkX into script
  2. Began Boolean Satisfiability Problem
Valeriy
  1. Worked on designing a specific JSON file to visualize database with CyNetShare
KP
  1. Enabled CyNetShare on his server
  2. Cleaned up web dev part of master branch

Week 6

Kwat
  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
Lauren
  1. Edited the database
  2. Fixed errors in traversal
Gary
  1. Continued to clean up database
  2. Added NOT gate entries to AND gates involving repressors
Joaquin
  1. Filled database PowerPoint presentation
Rohit
  1. Improved BFS algorithm
  2. Populated database
  3. Kept journal clean
Fernando
  1. Incorporated NetworkX into script
  2. Began Boolean Satisfiability Problem
Valeriy
  1. Worked on designing a specific JSON file to visualize database with CyNetShare
KP
  1. Enabled CyNetShare on his server
  2. Cleaned up web dev part of master branch

Week 7

Kwat
  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
Lauren
  1. Added traversal algorithm to presentation
  2. Wrote project description
Gary
  1. Continued to clean up database
  2. Got CyNetShare running on NetBeans
Joaquin
  1. Worked on presentation
  2. Started script to get JSON information
Rohit
  1. Added minimum spanning tree slides to presentation
  2. Started learning JSON
Fernando
  1. Read Overpowering the Component Problem and Circuit Simulation of Genetic Networks
Valeriy
  1. Designed web app page
  2. Worked on wiki
  3. Added slides to presentation

Week 8

Kwat
  1. Finished parser
  2. Finished database structure
KP
  1. Changed size/shapes of nodes in CyNetShare
  2. Began learning Angular UI Bootstrap
  3. Began working on carousel within CyNetShare
Gary
  1. Added dynamic labels to graph that enumerates lines as they are added
  2. Got CyNetShare running on NetBeans
Joaquin
  1. Finished operon, plasmid I.D.s etc. In database
Rohit
  1. Worked on JSON
  2. Edited presentation
Tiffany
  1. Modified pigeon command generator for plasmid to generate commands for each individual operon
  2. Modified logo
Valeriy
  1. Designed web app page
  2. Worked on wiki
  3. Added slides to presentation

Week 9

Kwat
  1. Got inputs on parser working
  2. Began working on outputs and verifying codes
KP
  1. Remote
Gary
  1. Finished adding line removal buttons to legend
  2. Cleaned up Web Dev branch
Joaquin
  1. Populated working data
Rohit
  1. Worked on JSON
  2. Began learning NetworkX

Week 10

Kwat
  1. Patched codes together
  2. Finished database with Joaquin
KP
  1. Remote
Gary
  1. Validated database
  2. Drafted JSON format
  3. Went remote
Joaquin
  1. Parsed excel file into database
  2. Prepared for presentation
Rohit
  1. Wrote Python script that takes SQL query and outputs JSON
  2. Began learning Cytoscape.js
  3. Began learning igraph

Week 11

Kwat
  1. Worked on poster
  2. Worked on presentation outline
  3. Updated traverse code
  4. Updated Google Drive
KP
  1. Remote
Gary
  1. Remote
Joaquin
  1. Designed master Python
  2. Designed device insert page
Rohit
  1. Read up on network motif algorithms (mfinder, color-coding, Kavosh)
  2. Decided on Kavosh
  3. Began learning CytoKavosh
Fernando
  1. Almost finished JSON graph constructor
Lauren
  1. Verified database code compatibility with network traversal

Week 12

Kwat
  1. Populated and finalized database
  2. Combined visualization property with traverse code
  3. Tested and debugged traversal algorithm
  4. Started working on presentation
KP
  1. Remote
Gary
  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
Joaquin
  1. Populated new database structure
  2. Implemented dictionaries necessary for traversal
Rohit
  1. Continued network analysis with Kavosh
  2. Began validating database
Fernando
  1. Remote
Lauren
  1. Generated DOT file creator to retrieve node coordinates from GraphViz

Week 13

KP
  1. Remote
Gary
  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
Joaquin
  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
Rohit
  1. Rendered full network on CytoScape
  2. Attempted to run Linux VirtualBox on my machine to run CytoKavosh
Fernando
  1. Remote
Lauren
  1. Debugged JSON file creator

Week 14

KP
  1. Remote
Gary
  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
Joaquin
  1. Connected algorithms to servlet between database and SBIDer
  2. Integrated database into file creator
Rohit
  1. VirtualBox did not work
  2. Ran CytoKavosh on CSE lab Linux machines and found motifs
Fernando
  1. Worked on SBML modeling script
  2. Finished QualitativeSpecies class and Modeling class
Lauren
  1. Integrated database into file creator

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