Team:UCSD Software/Notebook

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
• Week 13
• Week 14
• Week 15

Entries

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