Team:UCSD Software/Notebook

From 2014.igem.org

Revision as of 10:57, 17 October 2014 by Kspuri (Talk | contribs)


Week

Entries

2014 06 27 – Friday

Updates:

  • Rohit working remotely.
  • Rohit read through existing files in repository and started reading graph traversal papers.

Tasks:

  • Change argparse method to argv method (Huwate (Kwat)).
  • 7pm video call (All).
  • Run PyDot representation and fix command line arguments (Rohit).

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Update journal
  • Inform everyone about meeting schedules
  • Inform everyone about online resources available
  • Make sure everyone knows his/her tasks
  • Read about past igem teams and projects
  • Read the paper: http://pubs.acs.org/doi/abs/10.1021/sb400024s
  • Learn PigeonCAD: http://pigeoncad.org
  • Read about cytoscape.js. http://cytoscape.github.io/cytoscape.js/
  • Read about Qualitative package of SBML: http://co.mbine.org/specifications/sbml.level-3.version-1.qual.version-1.release-1.pdf
  • Read more about synthetic biology theories and past accomplishments.
  • Relate our project to that of others
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project to that of others

Joaquin

  • Read about past igem teams and projects.
  • Read more about synthetic biology theories and past accomplishments.
  • Relate our project

Rohit

  • Working remotely
  • Familiarized himself with all the existing code on Github
  • Began reading graph traversal papers

2014 06 28 – Saturday

Updates:

  • Huwate (Kwat) working in SD all weekend.

Personal Status:

Huwate (Kwat):

  • Read about past igem teams and projects
  • Read the paper: http://pubs.acs.org/doi/abs/10.1021/sb400024s
  • Learn PigeonCAD: http://pigeoncad.org
  • Read about cytoscape.js. http://cytoscape.github.io/cytoscape.js/
  • Read about Qualitative package of SBML: http://co.mbine.org/specifications/sbml.level-3.version-1.qual.version-1.release-1.pdf
  • Read more about synthetic biology theories and past accomplishments.
  • Relate our project to that of others

Joaquin

  • Read about past igem teams and projects.
  • Read about Qualitative package of SBML: http://co.mbine.org/specifications/sbml.level-3.version-1.qual.version-1.release-1.pdf .

2014 06 29 – Sunday

Updates:

  • Huwate (Kwat) working in SD all weekend.
  • Contact Huwate (Kwat) if you needed to understand something or work together.

Tasks:

  • Sunday, have a good weekend :)

Personal Status:

Huwate (Kwat):

  • Read about past igem teams and projects
  • Read the paper: http://pubs.acs.org/doi/abs/10.1021/sb400024s
  • Learn PigeonCAD: http://pigeoncad.org
  • Read about cytoscape.js. http://cytoscape.github.io/cytoscape.js/
  • Read about Qualitative package of SBML: http://co.mbine.org/specifications/sbml.level-3.version-1.qual.version-1.release-1.pdf
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project
  • Reviewing python
  • Learning database system
  • Learning synthetic biology theories
  • Optimizing the schedule so we finish the project on time
  • Read more about synthetic biology theories and concepts
  • Relate our project

2014 06 30 – Monday

Updates:

  • Lauren joined :)
  • Rohit is remote and read assigned reading on algorithms.

Personal Status:

Huwate (Kwat)

  • Reviewing python
  • Learning database system
  • Learning synthetic biology theories
  • Optimizing the schedule so we finish the project on time
  • Read more about synthetic biology theories and concepts
  • Relate our project

Joaquin

  • Read about past igem teams and projects.
  • Reviewing python
  • Learning database system

Lauren:

  • Do Learn Python the Hard Way.
  • Read Python Wiki.

Gary:

  • Read Cytoscape.js API

Rohit:

  • Read up on graph and hypergraph traversal

Tasks:

  • Project catch up and review.
  • Clean up codes.
  • Change argparse to argv.
  • Learn proper code style for python.

2014 07 01 – Tuesday

Updates:

  • Rohit will be in SD around 11.
  • Learned about Entity Relationship Diagrams

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Updating journal and getting everyone’s machine compatible with git, anaconda, and other environments
  • Start coding the database structure
  • Read more about synthetic biology theories and past concepts and accomplishments
  • Read more about synthetic biology theories and concepts
  • Relate our project

Joaquin

  • Learn about code styles for Python
  • Play with Cytoscape
  • Refine codes
  • Generate Pydoc
  • Write program to output Pigeon commands as textfile

Rohit:

  • Began attept to develop parser for Pigeon commands

Tasks:

  • Start looking for potential data sources

2014 07 02 – Wednesday

Updates:

  • Rohit is remote
  • Learned about SBML
  • Algorithms/Graph Rep will be moving to SQL to help develop the database

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Updating journal and getting everyone’s machine compatible with git, anaconda, and other environments
  • Start coding the database structure
  • Read more about synthetic biology theories and past concepts and accomplishments
  • Read more about synthetic biology theories and concepts
  • Relate our project
  • Finish program for Pigeon commands
  • Start looking for potential data sources

Tasks:

  • Learn about SQL
  • Learn about Petri Net Theory
  • Learn about SBML (Jenhan sent us a pdf)
  • Learn more about Dynamic Programming and Path Traversal (MIT course that Justin posted is highly recommended)
  • Begin to conceptualize how we will format our data
  • Think about Entity Relationships
  • Convert the the SBML network into an Entity Relationship Diagram (cannot provide images apparently the files are too big according to gmail, sorry)

2014 07 03 - Thursday

Updates:

  • Acquired snippet of Linh’s Database

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Read emailed papers and also help others understand about their assigned papers
  • Start coding the database structure
  • Help others understand the direction of the project
  • Read more about synthetic biology theories and concepts
  • Relate our project
  • Help everyone to catch up with each other and get the project organized

Tasks:

  • Learn about SQL
  • Learn about Petri Net Theory
  • Learn about SBML (Jenhan sent us a pdf)
  • Learn more about Dynamic Programming and Path Traversal (MIT course that Justin posted is highly recommended)
  • Begin to conceptualize how we will format our data
  • Think about Entity Relationships
  • Convert the the SBML network into an Entity Relationship Diagram (cannot provide images apparently the files are too big according to gmail, sorry)

2014 07 07- Monday

Updates:

  • Continued playing with Cytoscape.js add/remove nodes

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Have a team meeting to understand what implementation we should use for our network
  • there are many many well established models
  • implementation mining!
  • Read up on boolean networks
  • Relate our project
  • Read up petri nets

Joaquin

  • Read up on Boolean networs
  • Read up on Petri nets

Tasks:

  • Learn about SQL
  • Learn about Petri Net Theory
  • Learn about SBML (Jenhan sent us a pdf)
  • Learn more about Dynamic Programming and Path Traversal (MIT course that Justin posted is highly recommended)
  • Begin to conceptualize how we will format our data
  • Think about Entity Relationships
  • Convert the the SBML network into an Entity Relationship Diagram (cannot provide images apparently the files are too big according to gmail, sorry)

2014 07 08- Tuesday

Updates:

  • Pydoc template is ready to be used

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Learn about Petrinets and Boolean network
  • Think of their pros and cons in term of our project
  • Read more about synthetic biology theories and concepts
  • Understand the basic properties of a Petri net
  • Learn more about Petri net analysis, remember to consider path traversal (I recommend looking into Reachability Trees)
  • Given your knowledge of Petri nets develop an Entity Relationship Diagram
  • Try finding a Python package that utilizes Petri nets <\li>

Rohit

  • Read up on Boolean networs
  • Read up on Petri nets

Tasks:

  • Learn about Boolean Networks
  • Learn about Petri Net Theory

2014 07 09- Wednesday

Updates:

  • Consensus was formed when discussing the modelling of transcription networks (we will be using Petri nets)!
  • No coding, still waiting on SQL database
  • Now, SQL and network team should all use this journal to update each other!

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Added documents to google drive and everyone must read those documentation summarizing our plans and implementation details
  • Think of their pros and cons in term of our project
  • Read more about synthetic biology theories and concepts
  • Understand the basic properties of a Petri net
  • Learn more about Petri net analysis, remember to consider path traversal (I recommend looking into Reachability Trees)
  • Given your knowledge of Petri nets develop an Entity Relationship Diagram
  • Try finding a Python package that utilizes Petri nets

Tasks:

  • Understand the basic properties of a Petri net
  • Learn more about Petri net analysis, remember to consider path traversal (I recommend looking into Reachability Trees)
  • Given your knowledge of Petri nets develop an Entity Relationship Diagram
  • Try finding a Python package that utilizes Petri nets
  • Do any reading that you feel is necessary for your understanding of the project

2014 07 10 – Thursday

Tasks:

  • Master Petri Nets!

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project
  • Understand the basic properties of a Petri net
  • Learn more about Petri net analysis, remember to consider path traversal (I recommend looking into Reachability Trees)
  • Given your knowledge of Petri nets develop an Entity Relationship Diagram
  • Try finding a Python package that utilizes Petri nets
  • Learn SNAKES- a Python library that provides and simulates Petri nets- https://code.google.com/p/python-snakes/
  • There also exists a Petri Net Markup Language http://www.pnml.org

2014 07 11 – Friday

Updates:

  • Petri Nets will be our primary method to model the flow of information in our transcription network.

Tasks

  • Ensure that you understand Petri Nets
  • Learn new ways to traverse Peti Nets
  • Communicate with the team to figure out where the project stands now

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project
  • Master SNAKES- a Python library that provides and simulates Petri nets- https://code.google.com/p/python-snakes/
  • There also exists a Petri Net Markup Language http://www.pnml.org

2014 07 14- Monday

Updates:

  • Breadth-First Search and Topological Sort Algorithms are possible traversal algorithms that will be implemented in our design.

Tasks:

  • When visualizing your network don’t mind the details such as device composition, simply denote devices as a node along with transitions and intermediates. For transitions, just write it in conditional probability format. For example, A+B > D the transition will be written as D| A+B which reads as “ D given A+B.” Eventually we will be substituting our transitions with a mathematical functional representing a logic gate.

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Read about past igem teams and projects
  • Relate our project
  • Learn more about shortest path algorithms, from a single source vertex, that allow for multiple sources(inputs such as molecule A+B) and sinks (outputs such as C + D) in a directed graph
  • Attempt to write some simple code implementing an algorithm that you find favorable, then visualize your network(use the code on github unless you know of an alternate method)
  • Learn SNAKES- a Python library that provides and simulates Petri nets- https://code.google.com/p/python-snakes/
  • There also exists a Petri Net Markup Language http://www.pnml.org
  • KEEP IN MIND that our solution must work not only for a specific network, but for all connected or acyclic networks

2014 07 15 – Tuesday

Updates:

  • Every team will be merging their code with the master branch this week, Jenhan will be providing further details

Tasks:

  • Continue learning about single source path traversal algorithms
  • Update your status and meet with team to ensure that we are all on the same page

Personal Status:

Huwate (Kwat)

  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project
  • Learn about Dynamic Programming (it will be a key component in our design)
  • Think of possible ways to weigh our edges
  • Learning dynamic programming
  • Learning about graph traversal algorithms (BFS, DFS, Dijkstra’s)

Rohit

  • Learning dynamic programming
  • Learning about graph traversal algorithms (BFS, DFS, Dijkstra’s)

2014 07 16 – Wednesday

Updates:

  • Learned about Max Flow Algorithm and Hotnet.
  • Learned how to apply loading and exporting cytoscape.js JSON.

Tasks:

  • Retrieve information from literature to help populate the database.
  • Think of a way to weigh our edges.
  • Continue to read about network algorithms.

Personal Status:

Huwate (Kwat)

  • Learning SQL
  • Starting to learn petri nets
  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project
  • Think of a way to weigh our edges
  • Continue to read about network algorithms
  • Establish a good structure for the database
  • Establish a good traversal algorithm
  • Create a network using current database

2014 07 17 – Thursday

Updates:

    Learned about Max Flow Algorithm and Hotnet.
  • Learned how to apply loading and exporting cytoscape.js JSON.

Tasks:

  • Learned about the required attributes for each device:
  • Boolean logic
  • Intermediates(small molecules,TF, ligand, RNA,etc.)
  • Type of Gate(transcription, recombinase, RNA circuit,etc.)
  • Retrieve information from literature to help populate the database
  • Think of a way to weigh our edges
  • Continue to read about network algorithms
  • Establish a good structure for the database
  • Establish a good traversal algorithm
  • Create a network using current database

Personal Status:

Huwate (Kwat):

  • Learning SQL
  • Thinking of ideas to structure the database
  • Learning Petri Nets
  • Learning traversal algorithms
  • Reading assigned papers and retrieving information to update JR’s spreadsheet
  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project

Joaquin:

  • SQL columns modification
  • Determining the required information a client would have to provide in order to insert into and update the network.
  • Reading papers to get fill the google docs

Rohit:

  • Learning SQL
  • Conceptualizing traverse algorithm.
  • Reading assigned papers to fill in google doc table

Gary:

  • Met with CynetShare team.
  • Got approval to use CynetShare code.
  • Read up on angular.js and yeoman.

Lauren:

  • Python tutorials
  • Petri net reading

Valeriy

  • Missed the meeting with the cynetshare people but was updated on it
  • Read a few chapters from different books about jquery functions to possibly use in the future for data loading on the website

2014 07 18 – Friday

Updates:

  • Creating new sql tables for promoter, rbs, cds, and terminators.
  • Huwate (Kwat) is sick.
  • Rohit is remote

Tasks:

  • Update the device component table by Monday.
  • Complete the database filling. Make sure all details are accurate now.

Personal Status:

Huwate (Kwat):

  • Learned about testing python codes
  • With JR and Fred, improved the SQL database structure
  • Currently learning about MySQL
  • Reading about Petri Nets to generate a traversal algorithm
  • Going over all the codes to understand them
  • Read about past igem teams and projects
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments
  • Relate our project

Rohit:

  • Learning SQL
  • Reading up on Petri Nets.
  • Reading up on Traversal Algorithms

Gary:

  • Learned basics of angular.js.

Lauren:

  • Codecademy tutorials
  • Petri net reading
  • Breadth first/depth first searches
  • Reading papers to fill in google doc

Valeriy

  • Started re-learning python to work with the traversal as suggested by Jenhan

2014 07 21 – Monday

Updates:

  • Rohit is remote.
  • Evan gave a speech about iGem.
  • Fred in summer school.

Tasks:

  • Populate database
  • Establish traversal algorithm

Personal Status:

Huwate (Kwat)

  • Write documentation guide for others
  • Learned about testing python codes.
  • With JR and Fred, improved the SQL database structure.
  • Currently learning about MySQL.
  • Reading about Petri Nets to generate a traversal algorithm.
  • Going over all the codes to understand them.
  • Reading about assigned papers to fill the spreadsheet.
  • Read about past igem teams and projects.
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments.
  • Relate our project.
  • Generated code for breadth and depth first searches
  • Reading papers to fill in google doc

Rohit

  • Started writing some code for a basic BFS
  • Reading DAG paper

Joaquin

  • DAG Paper

Lauren

  • Generated code for breadth and depth first searches
  • Reading papers to fill in google doc

Valeriy

  • Cleaned up a lot of my code
  • Still going over python coding

2014 0722 – Tuesday

Updates:

  • Rohit cannot make today’s meeting due to family issues. Please keep him updated through the journal. Thanks :)

Tasks:

  • Populate database
  • Establish traversal algorithm

Personal Status:

Huwate (Kwat)

  • Write documentation guide for others
  • With JR and Fred, improved the SQL database structure.
  • Currently learning about MySQL.
  • Reading about Petri Nets to generate a traversal algorithm.
  • Going over all the codes to understand them.
  • Reading about assigned papers to fill the spreadsheet.
  • Read about past igem teams and projects.
  • Look for useful python packages for our project
  • Read more about synthetic biology theories and past accomplishments.
  • Relate our project.
  • Structuring the database
  • Learning Petri Nets.
  • Working on traversal algorithm
  • Learn Python the hard way

Joaquin

  • Further develop sql. Include promoter and cds table.

Gary:

  • Installed Yeoman(Yo, Bower, and Grunt) via GitBash.
  • Tried to troubleshoot missing “bower_components.”

Lauren:

  • Attempting to expand breadth first search for multiple inputs and outputs
  • Look into hotnets and max flow

Valeriy

  • Installed Yeoman to try to see if we can use it for our application
  • Played around with the files
  • Went over the entire tutorial as well as read a few articles for hints about using yeomen

2014 07 23 – Wednesday

Updates:

  • Rohit is remote

Tasks:

  • Populate database
  • Establish traversal algorithm

Personal Status:

Huwate (Kwat)

  • Structuring the database
  • Learning Petri Nets.
  • Working on traversal algorithm
  • Learn Python the hard way
  • Data mining for devices

Lauren

  • Learn Python the hard way

2014 07 24 – Thursday

Updates:

  • Huwate (Kwat) is sick.

Personal Status:

Huwate (Kwat)

  • SQL clean up
  • Learning petri nets
  • Structuring the database
  • Learning Petri Nets
  • Working on traversal algorithm
  • Learn Python the hard way
  • Sick…:(

Joaquin

  • 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

Gary:

  • Looked through CyNet source code and annotate functions.

Valeriy

  • Read a few articles about visualizing data using json files and also different techniques that people use nowadays to achieve it
  • Still learning about how to fully use CyNetShare
Tasks:
  • Think more about the database structure and the traverse algorithm.

2014 07 25 – Friday

Updates:

  • Gary’s birthday! Happy birthday Gary!!!
  • Huwate (Kwat) is still sick...

Tasks:

  • Read about traverse algorithm.
  • Please update this document.

Personal Status:

Huwate (Kwat)

  • Learn HTML
  • Learn Bioservices for Miram, etc.
  • Structuring the database
  • Learning Petri Nets
  • Working on traversal algorithm
  • Learn Python the hard way
  • Learning more about petri nets
  • Go over everyone’s codes

Joaquin

  • Learn Bioservices for Miram, etc.

Gary:

  • Turned 19.
  • Continued sifting through CyNet code.

Lauren

  • Prepare presentation of expanded breadth first search for monday

Valeriy

  • Took the day to try to learn angular js main functions to use for the website
  • Go over more CyNetShare code

2014 07 28 – Monday

Updates:

  • Huwate (Kwat) is not sick! Back!
  • Food place and time is still undecided.
  • Justin proposed his idea about our t-shirt and logo.
  • Discussed freshness of lapel pins and formal dress.
  • We should take a group photo soon.

Tasks:

  • Update this document.
  • Read about presentation structure.
  • Vote for food.

Personal Status:

Huwate (Kwat)

  • Created presentation structure
  • Fully done with Learn Python the Hard Way exercises and CodeAcademy
  • Still working on improving the existing codes.
  • Started learning about Wiki
  • Started learning about HTML
  • Still learning more about petri nets
  • Cleaned up this journal and and folders

Rohit

  • Reading DAG paper
  • Working on BFS code

Gary:

  • Attempted to run CyNetShare on Netbeans.

Lauren

  • worked with Huwate (Kwat), KP, Gary, and Fernando to prepare presentation structure

Valeriy

  • Learning more about CyNetShare to fully understand what it is capable of
  • Also looking at different ways how to store information into json file
  • Read about using json files to visualize data and what it takes to do that
  • Read up on d3.js to see if we could possibly use it

2014 07 29 – Tuesday

Updates:

  • Fernando has produced a image on the network.

Tasks:

  • Meet with two out of three graduate students to discuss the progress.
  • Update this journal.

Personal Status:

Huwate (Kwat)

  • Starting to learn HTML and CSS for Wiki
  • Together with Fred and Joaquin, designed a new structure for the database and the traversal. We will present this tomorrow
  • Brainstorming about traverse algorithm

Joaquin

  • Together with Fred and Huwate (Kwat), designed a new structure for the database and the traversal. We will present this tomorrow.

Fred

  • Together with Huwate (Kwat) and Joaquin, designed a new structure for the database and the traversal.

Gary

  • Fixing errors with running cy-net-share on netbeans.
  • Reviewed cy-net-share code.
  • Learned use of jquery handlers to upload files.

KP

  • Working on running cy-net-share with our netbeans GlassFish server.
  • This week’s tasks include trying to manipulate the nodes of a sample graph generated by cy-net-share (things like clicking on a node to view an image, etc.)

Rohit

  • Working on BFS search on Petri Nets. Will hopefully present on Thursday.

Lauren

  • Began petri net traversal method and refined the path-merger traversal method. The petri net method emphasizes the transitions more heavily and will integrate more easily with the Boolean logic, but may miss some of the paths that the path-merger method would not.

Valeriy

  • Read about how to make CyNetShare work on NetBeans to help kp and gary
  • Thinking about ways to manipulate the json file that CyNetShare accepts in order to visualize any data we want
  • Thinking about possible website design
  • Reading about running CyNetShare

2014 07 30 – Wednesday

Updates:

  • Meeting with Andreas this morning.
  • Talk to graduate students to update about your progress.
  • Wiki will use this document as the journal. So, it is imperative that we keep good records here if we want to win.
  • Petri Nets is the way!

Tasks:

  • Update this journal: make sure to follow the format (we will parse the entire document later.)

Personal Status:

Huwate (Kwat)

  • Learn more about Petri Nets
  • Learn more about SQL and its functions
  • Meeting with JR and Fred to brainstorm more about the traverse algorithm
  • Data mining for devices

    • Rohit

    • Continuing BFS
    • Exploring other traversal ideas

    Joaquin

    • Reading Data Normalization

    Gary

    • Put running cy-net-share on netbeans on backburner.
    • Read about Ruby.
    • Installed Ruby and compass gem to use sass files on cy-net-share.
    • Attempt to run cy-net-share using grunt.
    • Addressed “missing components” issue and “bower_components”
    • Successfully ran Cy-net-share on grunt without error messages.

    Lauren

    • Created a version of the petri net traversal discussed in the previous meeting. Pulls from dictionaries loosely structured around the network.

    Fred

    • learning about data Normalization

    2014 07 31 – Thursday

    Updates:

    • Database normalization complete
    • Meet with graduate students to update the progress

    Tasks:

    • Implement database model
    • Implement traversal

    Personal Status:

    Huwate (Kwat)

    • Improve database model
    • Learn more about Petri Nets
    • Learn more about SQL and its functions
    • Meeting with JR and Fred to brainstorm more about the traverse algorithm
    • Data mining for devices
    • Edited the petri net traversal to include relays between various transitions. Needs to be edited to integrate the boolean logic more thoroughly.

    Fred

    • Meeting with Joaquin and Huwate (Kwat), improved database structure, finished database normalization, prepared for presentation, and traversal algorithm

    Valeriy

    • Played around with some more json data trying to add more key values and data and figuring out an easier way to add more information to the json file

    Week 1

    Huwate (Kwat)
    1. Generated Pydoc
    2. Learnt SQL
    3. Learnt Petri Nets
    4. Read about past IGEM teams and projects
    5. Read emailed papers and also helped others understand their assigned papers
    6. Read more about synthetic biology theories and concepts
    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
    4. Attempted to develop basic parser for Pigeon commands
    5. Read up on synthetic biology and Pigeon images
    Fernando
    1. Finished command line interface
    2. Acquired snippet of Linh's database

    Week 2

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

    Huwate (Kwat)
    1. Learnt SQL
    2. Learnt traversal algorithms
    3. Read assigned papers to populate database
    4. Read about past IGEM teams and projects
    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
    2. Meet with CyNetShare team
    3. Got approval to use CyNetShare code
    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
    2. Read a few chapters from different books about Jquery functions to use for data loading onto the website

    Week 4

    Huwate (Kwat)
    1. Learnt HTML
    2. Went over everyone else's codes
    3. SQL cleanup
    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 and annotate functions
    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
    3. Read a few articles about visualizing data using JSON files and different techniques to do so

    Week 5

    Huwate (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
    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
    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
    2. Played around with more JSON data to add more key values and data
    KP
    1. Enabled CyNetShare on his server
    2. Cleaned up web dev part of master branch
    Fred
    1. Met with Joaquin and Huwate (Kwat), improved database structure, finished database normalization, prepared for presentation and traversal algorithm

    Week 6

    Huwate (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
    3. Contributed to website portion of presentations
    4. Learnt scale vector graphs for possible plotting
    Joaquin
    1. Filled database PowerPoint presentation
    2. Filled database section
    Rohit
    1. Improved BFS algorithm
    2. Populated database
    3. Kept journal clean
    4. Worked on presentation
    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
    2. Looked over database
    3. Thought about possible website designs
    4. Played around with JSON data
    5. Edited more database information
    KP
    1. Enabled CyNetShare on his server
    2. Cleaned up web dev part of master branch

    Week 7

    Huwate (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. Updated slides for iGEM presentation and added figures explaining overall traversal algorithm
    3. Wrote project description
    Gary
    1. Continued to clean up database
    2. Got CyNetShare running on NetBeans
    3. Discussed implementing Ryan’s modeling to the application
    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
    3. Wrote project description
    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

    Huwate (Kwat)
    1. Finished parser
    2. Finished database structure
    3. Wrote pseudocode for search algorithm
    4. Learnt SQL stored function
    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

    Huwate (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
    3. Revisited learning Cytoscape

    Week 10

    Huwate (Kwat)
    1. Patched codes together
    2. Finished database with Joaquin
    3. Worked on reachability
    4. Worked on convergence
    KP
    1. Remote
    Gary
    1. Validated database
    2. Drafted JSON format
    3. Went remote
    4. Learnt how to use database
    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

    Huwate (Kwat)
    1. Worked on poster
    2. Worked on presentation outline
    3. Updated traverse code
    4. Updated Google Drive
    5. Updated Parser again
    7. Updated reachability analyzer again to not return AND logic
    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

    Huwate (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
    4. Stored equations locally for reference
    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

    Huwate (Kwat)
    1. Worked on reachability
    2. Worked on convergence
      3. 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

    Huwate (Kwat)
    1. Worked on update functions
    2. Worked on documentation
    3. Worked on testers for traversal algorithm
    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

    Week 15

    Huwate (Kwat)
    1. Worked on update functions
    2. Worked on documentation
    3. Worked on testers for traversal algorithm
    KP
    1. No longer remote!
    Gary
    1. Brought all basic functionality online remotely
    Rohit
    1. Made wiki notebook for past 15 weeks
    2. Wrote network analysis/Kavosh documentation
    3. Updated slides to include motifs found with Kavosh and sent to Jenhan/Justin/Ben
    Lauren
    1. New names for pigeon files
    2. Added colors to each species so that no color repeats within a single operon

    Retrieved from "http://2014.igem.org/Team:UCSD_Software/Notebook"