iGEM 2014 — Team UCSD_Software

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# Team:UCSD Software/Notebook

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## 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
* Week 16
* Week 17
* Week 18
* Week 19

## Entries

### **Week (1) of June 27**

### **2014 06 27 – Friday**

### Updates:

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

![](http://i.imgur.com/pFnR42V.jpg?1)

### Tasks:

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

![](http://i.imgur.com/5xwPPFD.jpg?1)

### 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

#### KP

* Learnt jQuery
* Played around with buttons on an HTML page using jQuery- FUN day!
* Began reading syn bio 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

### **Week (2) of June 30**

### **2014 06 30 – Monday**

### Updates:

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

![](http://i.imgur.com/zViv3Jr.jpg?1)

### 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

#### KP

* Put up a draft website using Bootstrap templates

### 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)

### **Week (3) of July 7**

### **2014 07 07- Monday**

### Updates:

* Continued playing with Cytoscape.js add/remove nodes

![](http://i.imgur.com/oY6gSqr.jpg?1)

![](http://i.imgur.com/xrJ7JcV.jpg?1)

### 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

#### KP

* Read up on Boolean networs
* Learnt/Read up on Cytoscape Js since we plan on deploying our app using that
* 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

#### KP

* Used a basic CytoscapeJS graph to create a sitemap for the draft website
* Played around a little more with Cytoscape JS; familiarized myself with its API

### 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

#### KP

- Read up on entity relationship diagrams
- Spoke to the Cytoscape team at UCSD about using their app to help create our own

### 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

![](http://i.imgur.com/s94ynF5.jpg?1)

### **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

### **Week (4) of July 14**

### **2014 07 14- Monday**

### Updates:

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

![](http://i.imgur.com/2ExW5ga.jpg?1)

### 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.

![](http://i.imgur.com/nu5tLyj.jpg?1)

### 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)

#### KP

* After meeting with the Cytoscape team, decided to use CyNetShare as the foundation for our app
* Consequently, started learning AngularJs, Yeoman, Bower and other such tools used to build CyNetShare

### **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

![](http://i.imgur.com/1Pb5leu.jpg?1)

### 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

#### KP

* Kept working on CyNetShare, trying to understand their code (since it isn't documented)
* Teamed up with Gary to work on CyNetShare, and discussed plans to modify it to suit our own app

#### 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

### **Week (5) of July 21**

### **2014 07 21 – Monday**

### Updates:

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

![](http://i.imgur.com/YT2PQrd.jpg?1)

![](http://i.imgur.com/schqP9e.jpg?1)

### Tasks:

* Populate database
* Establish traversal algorithm

![](http://i.imgur.com/iaor9Jy.jpg?1)

### 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 :)

![](http://i.imgur.com/Yi5m2JN.jpg?1)

### 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

![](http://i.imgur.com/xG1GjPR.jpg?1)

### 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

### **Week (6) of July 28**

### **2014 07 28 – Monday**

### Updates:

* Huwate (Kwat) is not sick! Back!
* 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.

![](http://i.imgur.com/aRFJnem.jpg?1)

### Tasks:

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

![](http://i.imgur.com/6AvILBL.jpg?1)

![](http://i.imgur.com/aku7mxu.jpg?1)

### 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!

![](http://i.imgur.com/98q1pUT.jpg?1)

### 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

![](http://i.imgur.com/3cPbMq7.jpg?1)

### 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 (7) of August 1**

### **2014 08 01 – Friday**

### Updates:

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

![](http://i.imgur.com/gkyOAkv.jpg?1)

### Tasks:

* Stop everything that you are doing for igem and POPULATE the database!

![](http://i.imgur.com/bpq5g7G.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Created database structure.
* Normalization complete.
* Working on algorithm.
* Reading on petri nets.
* Learning about designing wiki
* Populating new database
* Read more about synthetic biology theories and past accomplishments.
* Relate our project.
* Data mining for devices

#### KP

* CyNetShare now runs on our (mine, for now) server so we can make as many changes as we want to (to suit our network)!
* We can now select nodes to display images just like we could in Cytoscape.js (more about this at meeting).
* This will allow us to click on devices to view them in greater detail. Next week I might try to display images in the table instead, so that if you select multiple nodes you can see multiple images.
  I’ll also try running the CyNetShare graph on JSON files provided by Fernando to see if the format is correct.
* Today’s tasks include pushing web dev files to the master branch so that the home page of our website runs normally again (if you try to run it with the files currently in master branch, the CSS appears to be broken as we’re missing a few files). Basically cleaning up the web dev part of the master branch.

#### Gary

* Busy with Final Exams
* Began outlining Web part of presentation.

#### Rohit

* Improving BFS algorithm
* Learning Petri nets
* Populating database
* Keeping journal clean

#### Lauren

* Editing the new petri net traversal. Accepts multiple inputs. Currently formatting integration of boolean logic and multiple outputs.

#### Valeriy

Working on figuring out how to design a specific json file to obtain the information from the database and have it visualized with CyNetshare

### **Week (8) of August 4**

### **2014 08 04 – Monday**

### Updates:

* Database is structured.
* Time to populate the database.
* Only 2 months left until the jamboree, we have to collaborate.

![](http://i.imgur.com/VnrNNT2.jpg?1)

### Tasks:

* Populate the database ASAP.
* STOP everything that you do, and work on the database.
* Setting up the powerpoint structure.

![](http://i.imgur.com/CLQ7vMe.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Made instruction sheet for filling the database.
* Improved algorithm.
* Reading on Petri Nets to use the style within the algorithm.
* Populated my portion of the database.
* Cleaned database up for consistent style.

#### Joaquin

* Instruction sheet for filling in the database sheet.
* Instruction sheet for filling the component sheet.
* Creating a powerpoint structure for database group.

#### Gary

* Populated my portion of the database
* Cleaned database up for consistent style.
* Preparing presentation structure for Web Dev.
* Continuing to address cy-net-share discrepancies.

![](http://i.imgur.com/AfBIRR4.jpg?1)

#### Rohit

* Populated my portion of the database
* Cleaned database up for consistent style

#### Lauren

* Populate the database
* test a preliminary version of the new petri net algorithm on a small database

#### Fred

* worked with Joaquin about presentation
* worked on traversal algorithm
* started making python script for new database

#### Valeriy

* Populated my portion of the database
* Worked on a draft of the website homepage for the presentation
* Read my research papers as well fernandos paper

### **2014 08 05 – Tuesday**

### Updates:

* Database is structured
* Time to populate the database

### Tasks:

* Populate the database please.
* Make sure your partner’s data is correct.
* Fill in powerpoint structure and be ready to present tomorrow.

### Personal Status:Huwate (Kwat) * Cleaned the database and commented on everyone's data * Working on the search algorithm * Reading about Petri Nets * The current search algorithm does not follow Petri Nets model, unfortunately. So I am trying to fix this * I made a folder named whiteboard\_pictures, where all the pictures of the whiteboard can be found * Wiki model: https://2013.igem.org/Team:USTC-Software Gary * Continued to clean up the database. * Added NOT gate entries to AND gates involving repressors. * Contributed to Website portion of presentations. * Learning Scale Vector Graphs for possible plotting. Rohit * Fixing data on database * Working on presentation Joaquin * Filling in database ppt information * Working with everyone to form a coherent and structured ppt. * Filling Database section. Lauren * Edit the database * Fix the errors in the traversal: not accepting multiple outputs, returning incorrect outputs when loops are concerned Valeriy * Looked over the data base * Thinking further about possible website designs * Playing around with json data and having it show up * Still discussing with Joaquin about what we will do to create and pass the json files * Edited more of the database information

### **Week (9) of August 11**

### **2014 08 11 – Monday**

![](http://i.imgur.com/s69i4Rh.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Wrestled with MySQL
* Starting on parsing the sub tree
* Working on search algorithm
* Read articles provided
* Read about petri nets
* Cleaned the database
* Improving spanning tree algorithm
* Cleaned database up for consistent style

#### Rohit

* Improving spanning tree algorithm

#### Joaquin

* Created a database\_to\_pigeon.py that pulls information from the database that is used in pigeon commands
* Talked with yesterday Tiffany about the database\_to\_pigeon.py
* Worked with Tiffany to check her code and how it works with database\_to\_pigeon.py
* Established with Valeriy, Gary and KP information necessary to produce the final CyNetShare visualization. Two files will be created nodes.txt and edges.txt
  nodes.txt will have the following information Node\_ID, Name, Type where type is either intermediate, transition or operon. Type may not be used during the creation of the json but this information may be necessary for CyNetShare. Later the Type can be mapped to the Node\_ID dictionary style
  edges.txt will have the following information Source\_ID, Target\_ID, Math (Probably just for visualization purposes in CyNetShare simply as a text to see a label). Math is only important for transitions nodes. Later the Math can be mapped to the Transition\_Node\_ID.
* Skyped with Fred so he can help me out with the Miriam ID using the Bioservices Module as well as helping to create the nodes.txt and edges.txt for the website team.
* Talked with Jenhan and through a mention transitions tables decided to include the in the database. This may cause some denormalization but it makes it possible to look up specific transitions. This includes a transitions\_input table and a transitions\_output table. The good thing about these tables is that they can be made from data we have already captured and provide a Transition ID for them.
  Transition\_input
  Operon\_ID
  TO\_ID
  Intermediate\_ID
  Transition\_output
  Intermediate\_ID
  TI\_ID
  Operon\_ID
  Made some test data for Valeriy using the test database

#### Gary

* Continued revising slides for the web portion of the presentation.
* Talked with Joaquin to continue finalizing how the web application will receive the node and edge data.

#### Tiffany

* Completed database\_to\_pigeonv2.py (pigeon command generator for plasmids)

#### Valeriy

* Got the rough draft of all the pages ready but still not sure if that will be the final
* Reading up on different web style techniques
* Talked to Joaquin about the json file and how we will use it.
* Further reading about setting up json files

#### KP

* Worked on the presentation (setting up slides of web dev with Gary).
* Reading up on Petri Nets
* AngularJS videos for a better understanding (Source YouTube: “Angular JS in 60ish minutes” by Dan Wahlin).
* Managed to make CyNetShare run on netbeans with Gary, pushed code for the same on GitHub.
* Try to change shapes/sizes of nodes in the CyNetShare network.

### **2014 08 12 – Tuesday**

### Updates:

* Presentation make up
* When out to eat as a group and got an awesome group photo with the sunset!!!

![](http://i.imgur.com/MLZ6JJk.jpg?1)

![](http://i.imgur.com/kQJYUgf.jpg?1)

![](http://i.imgur.com/edxo87Y.jpg?1)

What's a day at the beach without awesome Indian food, eh?

### Tasks:

* Incorporate more of a “story” into the presentation to increase cohesiveness.
* Had great Indian food at the beach and took an almost complete team picture.

![](http://i.imgur.com/2qpLMOz.jpg?1)

Yep, Jenhan makes us work even on beach day...

### Personal Status:

#### Huwate (Kwat)

* Cleaned the database and commented on everyone's data.
* Working on the search algorithm.
* Reading about Petri Nets.
* The current search algorithm does not follow Petri Nets model, unfortunately. So I am trying to fix this.
* I made a folder named whiteboard\_pictures, where all the pictures of the whiteboard can be found.
* Wiki model: https://2013.igem.org/Team:USTC-Software
* Worked on the presentation

#### Joaquin

* Sat down with Gary for 3 hours in Geisel and made up the introduction slides
* Came up with a diagram to represent devices
* Epiphany at 3am about how ER diagrams are meant to capture table-table relationships via key columns. Will include in next slides.
* Worked on the presentation

#### Gary

* Worked with Rohit and Joaquin to build introduction and part of the concluding portions of the presentation.
* Continue cleaning up web portion of the slides.
* Continued practicing slides.

#### Lauren

* Edited the presentation so the example slides were clearer: enlarged figures, added tags to inputs and outputs

#### Valeriy

* Working on the homepage as well as the app page
* Figuring out with Joaquin how to produce the json files for visualization
* Trying to see how to get CyNetShare working on netbeans

### **2014 08 13 – Wednesday**

### Updates:

* Test run 2 of project presentation

### Tasks:

* Properly cite your sources
* If you need some information from the database just ask

### Personal Status:

#### Huwate (Kwat)

* Wrote project description.
* With JR and Fred, created a petri net model for the sample database.
* Organized the folders and codes.
* Thought about the name for the project, SBIDer.
* Allocating tasks for people.
* A lot to work on...

#### Joaquin

* Presentation made me realize that I have to practice my slides a lot more
* Presentation story is slowly getting better. We got this!
* Sat with Tiffany and we defined what her slides meant and what types of questions they tried to answer.
* Really trying to help everyone tie their parts to the project as a whole.

#### Gary

* Unexpectedly presented the entire web portion of slides.
* Aim to continue practicing, being more wary of other parts of the presentation.
* Need to learn more about validation.
* Added basic code for a simple d3.js plot graph

.

#### Lauren

* Edited the slides more to include feedback from the meeting: examples and arrows are clearer

#### Valeriy

* Finished drawing out the layout of most of the website pages
* Working on the home page using html and css
* Reading about possible slider options for the team page

### **2014 08 14 – Thursday**

### Updates:

* Sign up for the iGem roster by tomorrow.

### Tasks:

* Find out what website and network side need from the table.
* Submit project description.

### Personal Status:

#### Huwate (Kwat)

* SBiDer = name? Thoughts?
* Wrote project description.
* With JR and Fred, created a petri net model for the sample database.
* Organized the folders and codes.<\li>* Thought about the name for the project, SBIDer.<\li>* Allocating tasks for people.<\li>* A lot to work on...

#### Lauren:

* Update the slides for the iGEM presentation and add figures explaining the overall traversal algorithm
* Write project description

#### Rohit

* Wrote project description
* Made iGEM account and applied for roster
* Adding sponsor logos to presentation\_logos folder
* Adding slides about minimum spanning trees to presentation

#### Fred

* Read more about petri nets
* With JR and Fred, created a petri net model for the sample database.
* Making a python script to parse database csv
* Started learning SNAKES

#### Gary

* Discussed implementing Ryan’s modeling to the application.
* Need to iron out details about visualizing and acquiring data for the models.

#### Valeriy

* Finishing working on the website design
* Finished the home page with all the links to the other pages
* Working on editing the igem Logo to make it fit with the background

### **2014 08 15 – Friday**

### Updates:

* iGem wiki editing had began. Today, the first team description was input.
* Team name voting started. Please look at the document.

### Tasks:

* Vote on the project name.
* Update the task sheet.
* Update this journal.
* Communicate better and understand the overall project description better.
* Please re-read others’ project description; doing so will help you understand more about the project.

### Personal Status:

#### Huwate (Kwat)

* Making a script that can parse a user input, search the graph, and return one or more linear searchable space.
* Learning SNAKE and graphviz.
* Learning SQL stored function.
* Working on providing Fernando the data he needs for analysis

#### Rohit

* Added MST slides to presentation
* Thinking of idea for project name
* Learning json

#### Gary

* 1am epiphany on how to get CyNetShare running on Netbeans.
* 2am epiphany on how to fix the tables so that they display node/edge data. properly in CyNetShare.
* Continued cleaning database. It’s in poor shape. Considering reading more papers when time allows.
* Finalized design for displaying images with KP and Valeriy.

#### Joaquin

* Continue working on presentation
* Scripting python code to obtain json file information and pass to Rohit

#### Valeriy

* Working on the slider for the team page, and the contact page
* Designing the app page but have to work with gary and kp on it
* thinking about what to add to the wiki page
* Trying to prepare some potential slides for the presentation

### **Week (10) of August 18**

### **2014 08 18 – Monday**

### Updates:

* The project name is voted to be SBIDer!
* We may need a cuter modification to our logo.

![](http://i.imgur.com/59mbUDs.jpg?1)

### Tasks:

* Modify our logo to be a little cuter.
* Search algorithm team need to meet and recap and catch up.
* Meeting on Monday.
* Presentation needs to get better.

![](http://i.imgur.com/vOduIrB.jpg?1)

![](http://i.imgur.com/vOduIrB.jpg?1)

![](http://i.imgur.com/AQDgP24.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Writing a pseudo code for search algorithm.
* (2am) finalized the database in paper, needs to update it tomorrow.
* I need to cooperate with Fred and JR so they start using MySQL instead of SQlte3.
* Sadly, people were busy this weekend and I was not able to visualize the sample database. I must get this done ASAP.
* I need to improve the team description.
* I need to improve the presentation slides, bringing uniformity and a better style.
* I need to read more on petrinetworld.com to look for better ways to do what we do.
* Finally, I need to code the parser that Jenhan asked me to do.

#### Tiffany

* Modified pigeon command generator for plasmid to generate commands for each individual operon
* Modifying logo

#### Rohit

* Learning json- need file information from Joaquin
* Working to improve presentation

#### Gary

* Continued working on d3.js models. Incorporating a way to let users dynamically alter experimental parameters.
* Managed to plot a single line with angular controller to capture constants.

#### KP (weekly update)

* Managed to change size/shapes of nodes in CyNetShare (available shapes for nodes are rectangle, round rectangle, ellipse, triangle, pentagon, hexagon, heptagon, octagon & star). ~This information is important for visualization (would like inputs from the database team about this).
* Reading up on this new and amazing Angular UI Bootstrap source: http://angular-ui.github.io/bootstrap/
* Has a nice carousel option to display images.
* Will try to use a carouse within CyNetShare to display multiple images when multiple nodes are selected by the end of the week.

### **2014 08 19 – Tuesday**

### Updates:

* Database structure finished

### Tasks:

* Please take a look at the database structure. It is finished. No more changes.
* Fill out 199 form if you want academic credit

### Personal Status:

#### Huwate (Kwat)

* Finalized the database structure. FINALLY!
* Writing a pseudo code for search algorithm.
* Improving presenting slides with Joaquin
* Organized the folders and codes.

#### Gary

* Resolved some issues with graph overextending boundaries on render.
* Further compartmentalized function and variables for easier input of point and further development.
* Issues with Git pull destroyed vasts sections of my codebase with meaningless strings. Time consuming task of hunting it down in all files.

#### Rohit

* Generating json image
* Editing presentation
* Need to skype Joaquin tomorrow and discuss database

### **2014 08 20 - Wednesday**

### Updates:

* Database structure finished

### Tasks:

* Please take a look at the database structure. It is finished. No more changes.
* Fill out 199 form if you want academic credit

### Personal Status:

#### Huwate (Kwat)

* Worked with JR on the below things.
* def get\_all\_input\_trans\_ID():
* def get\_all\_operon\_ID():
* def get\_all\_plasmid\_ID():
* def single\_trans\_to\_bool(trans\_ID)
* def single\_operon\_to\_bool(operon\_ID)
* def unlist\_values(to\_list)
* def bool\_trans(interactor):
* def database\_to\_bool\_operon():

#### Joaquin

* def get\_all\_input\_trans\_ID():
* def get\_all\_operon\_ID():
* def get\_all\_plasmid\_ID():
* def single\_trans\_to\_bool(trans\_ID)
* def single\_operon\_to\_bool(operon\_ID)
* def unlist\_values(to\_list)
* def bool\_trans(interactor):
* def database\_to\_bool\_operon():

### **2014 08 21 – Thursday**

### Updates:

* Database structure finished

### Tasks:

* Please take a look at the database structure. It is finished. No more changes.
* Fill out 199 form if you want academic credit

### Personal Status

#### Huwate (Kwat)

* Writing a pseudo code for search algorithm.
* Improving presenting slides with Joaquin
* Learning SQL stored function.

#### Gary

* D3.js graph can now dynamically append lines with the user inputted parameters.

### **2014 08 22 – Friday**

### Updates:

* Database structure finished

### Tasks:

* Please take a look at the database structure. It is finished. No more changes.
* Fill out 199 form if you want academic credit

### Personal Status:

#### Huwate (Kwat)

* Working on parsing. I plan to finish this by the weekend.
* Reviewed presentation.
* Organized google drive.
* Debugging and improving input parsing.

#### Gary

* Added dynamic labels to the graph that is able to enumerate lines as they are added. Axes are static after render, considering a constant value for axes. Normalize data?

### **Week (11) of August 25**

### **2014 08 25 – Monday**

![](http://i.imgur.com/BLu5c1g.jpg?1)

UCSD's modeling team ;)

![](http://i.imgur.com/WhGaRbl.jpg?1)

### Tasks:

* Fill out 199 form if you want academic credit.

### Personal Status:

#### Huwate (Kwat)

* Completed the pseudo code for “User Input Syntax Analyzer and Semantic Evaluatorhttps”: https://docs.google.com/document/d/1dT22MNyL9srF9Fw6f-1rgrmnSyi-DbAbr9lrxme5z0U/edit#heading=h.ktnov6qtgi2b
* Organized google drive.
* Organized journal.
* Reviewed presentation.

#### Gary

* Continued working on a legend for the graph.
* Added functions for removing the lines via buttons.
* Buttons are not running functions properly.

#### Rohit

* Generating json nodes
* Reviewed presentation

#### KP

* Worked on presentation slides for web dev
* Reviewed presentation

### **2014 08 26 – Tuesday**

### Updates:

* iGem apparel options are available. Thanks Justin!
* Great work on presentation guys.

### Tasks:

* Fill out 199 form if you want academic credit.

![](http://i.imgur.com/2lXwq7n.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Debugging and improving input parsing.
* Uploaded pictures from beach curry party.
* Organized the folders and codes.

#### Rohit

* Working on dummy json nodes
* Learning NetworkX

#### Gary

* Final preparations for presentation to Coleman lab.

#### 2014 08 27 – Wednesday

### Updates:

* iGem apparel options are available. Thanks Justin!
* Please fill out 199 by tomorrow.
* Presentation with Professor Coleman went great
* Suggested Graphlab, factor graph

### Tasks:

* Fill out 199 form if you want academic credit.

![](http://i.imgur.com/icPZ4zC.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Spent most of the day looking for better parsers… failure…
* Organized the folders and codes.
* Organized journal.
* Reviewed presentation.

### **2014 08 28 – Thursday**

### Updates:

* Please fill out 199 by tomorrow.

### Tasks:

* Fill out 199 form if you want academic credit.
* Please update this journal

### Personal Status:

#### Huwate (Kwat)

* Spent all day looking for better parsers… failure…
* Improving parser
* Read about Grako, and more parsers… I think I will use YAPPS.

#### Joaquin

* Working on populating the working data

#### Gary

* Finished adding line removal buttons to the legend.
* Need a way to highlight lines.

#### Rohit

* Working on generating JSON nodes
* Learning NetworkX
* Learning Cytoscape

### **2014 08 29 – Friday**

### Updates:

 voting result is posted on google drive

### Tasks:

* 199 paper due
* must have meeting asap to decide who presents at boston

### Personal Status:

#### Huwate (Kwat)

* Decided to implement the whole parse myself. Working on the products now
* Inputs are fully working
* Currently working on outputs and verifying the codes

#### Gary

* Cleaning Web Dev code for KP going remote.
* Began to decide on presenters.

### **Week (12) of September 1**

### **2014 09 01 – Monday**

### Updates:

* Connecting the database and network with the reachability table

![](http://i.imgur.com/z4BBb8c.jpg?1)

Working at Biomedical Research Facility Building 2 (BRF2).

### Tasks:

* Finish reachability
* Finish traversal

![](http://i.imgur.com/o5WQNHB.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* working on reachability with Joaquin
* working on convergence with Joaquin
* patching up traversal algorithms
* working with Lauren on traversal

#### Joaquin

* working on reachability with Huwate (Kwat)

#### Lauren

* working on traversal with Huwate (Kwat)
* returns multiple paths
* explores only necessary transitions

#### Gary

* Finished implementing functions and a button inside the table for selecting images.
* Met with graph traversal team to discuss state of algorithm
* Discussed the format of the JSON required for CytoscapeJs

#### KP

* Worked with Gary on pigeon images to show up inside the CyNetShare table
* Met with graph traversal team to discuss state of algorithm
* Discussed the format of the JSON required for CytoscapeJs with them & Gary

### **2014 09 02 - Tuesday**

### Updates:

* Tiffany voted.

### Tasks

* Update global notebook.

### Personal Status:

#### Huwate (Kwat)

* Patching together codes (user\_input + reachability)
.* Waiting for database to finish in order to query the database.
* patching up traversal algorithms

#### Lauren

* Working on traversal
* ranks the paths
* fixing bugs associated with long paths organizing the list of output transitions to fit specifications from Monday

#### Rohit

* Wrote Python program that takes SQL query and produces json file
* Waiting for database to finish in order to test with real data
* Graphviz is not working, learning igraph
* Learning Cytoscape JS format

#### Gary

* Finished adding buttons to the app image carousel to select next image in the array of selectedNodes id.

### **2014 09 03 – Wednesday**

### Updates:

* Connecting the database and network with the reachability table

### Tasks:

* Update the journal
* Organize git
* Update each other with tasks
* Comment on our codes in pydoc format
* Re-build presentation
* Have a general meeting

### Personal Status:

#### Huwate (Kwat)

* Working on reachability
* Working on convergence
* Patching up traversal algorithms
* Documentation
* Pydoc
* Rebuilding presentation
* Started writing paper
* Awaiting database

#### Joaquin

* Working on database by verifying devices and syntax

#### Gary

* Worked with Joaquin in the evening to validate the entire database spreadsheet.
* Drafted format for the JSON object to be passed along.

### **2014 09 04 – Thursday**

### Updates:

* Connecting the database and network with the reachability table
* Moving out of the Jacobs… Bye bye…
* Return Jacobs’ keys to Justin!!!

### Tasks:

* Organize git
* Update each other with tasks
* Comment on our codes in pydoc format
* Re-build presentation
* Have a general meeting

### Personal Status:

#### Huwate (Kwat)

* Working on reachability
* Working on convergence
* Patching up traversal algorithms
* Documentation
* Pydoc
* Rebuilding presentation
* Started writing paper
* Awaiting database

#### Joaquin

* Parsing excel file into database
* Preparing for demo tomorrow

#### Gary * Learned how to use the database from Joaquin. **2014 09 05 – Friday** Updates: Connecting the database and network with the reachability table Tasks: * Do your part of the work by deadline. * Please document your work. * Please comment on your codes based on pydoc. Personal Status:Huwate (Kwat) * Working on patching codes together * Working on finishing up the database with Joaquin * Waiting for database and Lauren’s codes. Gary * Went remote for family affairs.

### **Week (13) of September 8**

### **2014 09 08 – Monday**

### Updates:

* Database is up and accessible

![](http://i.imgur.com/tAZUPs4.jpg?1)

![](http://i.imgur.com/Y2gVQiG.jpg?1)

### Tasks.

* Presentation Friday

![](http://i.imgur.com/EsZxhuY.jpg?1)

### Personal Status:

#### Huwate (Kwat)

- Worked with Joaquin to finish the database. Now, making documentation for database.
- Waiting for Lauren to finish her portion of the code.
- Started to patch up the entire traverse codes together.

#### Rohit

* Reading Uri Alon papers
* Doing network analysis

#### Gary

* Remote

#### KP

* Remote

### **2014 09 09 – Tuesday**

### Updates:

* Database is up and accessible.

### Tasks.

* Presentation of work on Friday!
* Check out database. Point out anything that could be wrong.

### Personal Status:

#### Huwate (Kwat)

* Patching up traversal codes
* Started to update parser
* Organized google drive

#### Joaquin

* created to\_network() method that currently returns the whole network to Lauren
* Starting the JSON file creator

### **2014 09 10 – Wednesday**

### Updates:

* Servlet has been created and Python scripts can be run.

### Tasks

.* Connecting database to Cytoscape JSON style.

### Personal Status:

#### Huwate (Kwat)

* Updated parser
* Modularized parser, reachability analyzer, and search algorithm
* Updated pydoc
* Updated reachability analyzer
* Organized google drive
* Had a meeting on traverse
* Met with V to discuss communicating with the server

#### Joaquin

* Designing the master python
* Designing the device insertion page

#### Fernando

* Creating and finishing the json converter

#### Lauren

* Verify database code is compatible with network traversal

#### Rohit

* Working on mfinder implementation
* Looking at other algorithms to implement (color-coding?)

### **2014 09 11 – Thursday**

### Updates:

* Server has been created and Python scripts can be run.
* Tasks.
* Finish the traverse module
* Make sure that we all know where to get out inputs from and where to send to
* Make sure to understand the format in which we exchange information between different branches of the project.

### Personal Status:

#### Huwate (Kwat)

* Updated parser again
* Modularized parser, reachability analyzer, and search algorithm - combined them into a single file and checked the flow of information
* Updated reachability analyzer again to not return AND logic for this may be redundant
* Organized google drive
* Had a meeting on traverse and database
* Met with JR to discuss communicating with the database
* Patched together the codes for the traverse

### **2014 09 12 – Friday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

.

* Check the email that Justin has sent
* Update this journal
* Clean git branch
* Ask Huwate (Kwat) about the project; he will tell you about the big picture and may be able to assign you some task
* Ask Huwate (Kwat) about the format in which data is transferred between different parts of the project
* Update the google drive
* Start working on poster
* Start working on the presentation

### Personal Status:

#### Huwate (Kwat)

- - Worked on poster
  - Worked on presentation outline
  - Upgraded traverse code - version 2
  - Debugged many parts of the traverse
  - Renamed variables for the previously used variables caused trouble and vagueness
  - Patching the codes together and building the engine module – sbiderPath(...)
  - Updated google drive
  - Organized google drive
  - Organized git
  - Had meeting with V and JR to understand better the flow of information

  #### Fernando

  * JSON graph constructor is near finished
  * script requires database\_pytools.py and node\_positions.py@database\_pytools.py
  * purpose: access database
  * input: sbider.db
  * output: database elements @node\_positions.py
  * purpose: generate node coordinates
  * input: graph network text file
  * output: dictionary : {key = node ( chemical species,transitions, or device name), value = (x,y)}
  * Script not complete because edges are inaccessible from database (I already message Joaquin). I can develop an ad hoc solution independent of the database however this would defeat the purpose of having a database

  #### Rohit

  * Finished familiarizing myself with NetworkX
  * Writing program to analyze graphs and calculate input/output degree
  * Learning CytoKavosh (will explain Tuesday)
  * CytoKavosh only works on Linux- finding workaround
  * Will be in touch with Fernando/Joaquin regarding traversal/database

### **Week (14) of September 15**

### **2014 09 15 – Monday**

### Updates:

* Servlet has been created and python scripts can be run.

![](http://i.imgur.com/6CX5tiV.jpg?1)

### Tasks.

* Check the email that Justin has sent
* Update this journal
* Clean git branch
* Ask Huwate (Kwat) about the project; he will tell you about the big picture and may be able to assign you some task
* Ask Huwate (Kwat) about the format in which data is transferred between different parts of the project
* Update the google drive
* Start working on poster
* Start working on the presentation

### Personal Status:

### Huwate (Kwat)

* Found many errors in the database structure and the data itself.
* Had to fix the structure
* Now, we have another version of the database structure so the current functions may not work… be careful
* Found errors in our codes, and currently debugging it as I restructure the database
* Repatching the traversal codes
* Organized google drive
* Organized git

#### Gary

* Edited modeling code to allow for a dynamic addition of graphs.
* Implemented a counter for graph ID’s so they can later be referenced/edited.

#### KP

* Remote
* Tried to help Gary classify the nodes using 'classes' (he found a better way to do it though)

### **2014 09 16 – Tuesday**

### Updates:

* Servlet has been created and python scripts can be run.

- Tasks.

* Check the email that Justin has sent
* Update this journal
* Clean git branch
* Ask Huwate (Kwat) about the project; he will tell you about the big picture and may be able to assign you some task
* Ask Huwate (Kwat) about the format in which data is transferred between different parts of the project
* Update the google drive
* Start working on poster
* Start working on the presentation

### Personal Status:

#### Huwate (Kwat)

* Updated database
* Updated master traverse code
* Organized git

#### Joaquin

* Populated new database structure
* Implemented dictionaries needed for the traversal

### Lauren

* Updated JSON file creator

#### Gary

* Wrapped graph creation functions in a larger function for ease of use and reduction of redundant code.

### **2014 09 17 – Wednesday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks.

* Check the email that Justin has sent
* Update this journal
* Clean git branch
* Ask Huwate (Kwat) about the project; he will tell you about the big picture and may be able to assign you some task
* Ask Huwate (Kwat) about the format in which data is transferred between different parts of the project
* Update the google drive
* Start working on poster
* Start working on the presentation

### Personal Status:

#### Huwate (Kwat)

* Structured database
* Updated master traverse code
* Tested and debugged traverse algorithm

#### Gary

* Cleaned up modeling code
* Moved global variable declarations towards the top and used spacing to improve legibility.
* Outlined the code structure in comments.

### **2014 09 18 – Thursday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks.

* Check the email that Justin has sent
* Update this journal
* Clean git branch
* Ask Huwate (Kwat) about the project; he will tell you about the big picture and may be able to assign you some task
* Ask Huwate (Kwat) about the format in which data is transferred between different parts of the project
* Update the google drive
* Start working on poster
* Start working on the presentation
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* RE-Structured database
* Updated master traverse code
* Tested and debugged traverse algorithm
* populated database, which is finalized
* combined visualization property to the traverse code
* tested and debugged traversal algorithm
* started working on presentation

### Rohit

* Continuing network analysis
* Slow progress on database validation. I want to take my time to make sure I have done a good job.

### Gary

* Return flight to San Diego.
* No longer remote.
* Met with Ryan and Jenhan to refine modeling development direction.
* Decided to use dictionaries of each operon’s modeling information.
* Abandoned current approach of parsing large JSON files.
* Storing equations locally for reference.

### **2014 09 19 – Friday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Working on reachability
* Working on convergence
* Working on presentation
* Read more about synthetic biology theories and past accomplishments.
* Relate our project.
* This will give better ideas of how to organize the presentation

#### Lauren

* generated a dot file creator if needed to retrieve coordinates for nodes from graphviz

#### Gary

* Moving to new apartment for the upcoming school year.
* Unavailable.

### **Week (15) of September 22**

### **2014 09 22 – Monday**

### Updates:

* Servlet has been created and python scripts can be run.

![](http://i.imgur.com/nyegpd9.jpg?1)

### Tasks:

* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Still working on reachability
* working on convergence
* Working through presentation
* Brainstorming outline

![](http://i.imgur.com/0JVoCCm.jpg?1)

#### Lauren

* completed first version of the json file creator. Not in the proper format
* started restructuring the creator to be in proper format to work with Cytoscapejs

#### Gary

* Placing heavy emphasis on completing the JSON converter.
* Ran Lauren’s converter which resulted in failure.
* Annotating and correcting structure of produced JSON.
* Laid down structure for selecting paths from the algorithm query.

#### KP

* Remote

### **2014 09 23 – Tuesday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* working on reachability
* Read more about synthetic biology theories.
* Relate our project.
* Making progress with convergence
* Still working on presentation

#### Lauren

* updated the json file creator to fit with Gary’s specifications
* worked with Joaquin on the structure of the inputs to the JFC

#### Gary

* Further refining JSON specifications for Lauren.

### **2014 09 24 – Wednesday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* Making progress with presentation outline
* Working on reachability
* Working on convergence
* Starting to make testers for traverse algorithm

#### Lauren

* Debugged the json file creator with Joaquin and Gary. The following issues still exist:
* miriam ids not present since they correspond to plasmids, not operons
* edge id’s need to be incorporated into the data currently dummy id’s are used based upon the number of edges

#### Gary

* Worked with Joaquin and Lauren to finish JSON Converter.
* Refined and debugged JSON converter.
* Created a viable dummy JSON for SBiDer to render.
* Helped connect database information retrieval with JSON Converter.
* Fully rendered a subnetwork generated from real data.
* Helped implement a temporary system for generating node coordinates.
* Finished path highlighting system.
* Paths can be selected from a dropdown menu dynamically.

#### Rohit

* Got CytoKavosh running on my machine
* Got database from Joaquin and JSON file from Gary
* Writing program to select nodes from database and run CytoKavosh on

### **2014 09 25 – Thursday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* working on reachability
* working on convergence
* Working on making testers for traverse algorithm
* Finalizing presentation outline
* Starting to work on update functions
* Beginning to work on overall project documentation
* Cleaned up google drive

#### Joaquin

* connecting the json to a positions dictionary

### **Week (16) of September 25**

### **2014 09 25 – Thursday**

### Updates:

* Servlet has been created and python scripts can be run.

![](http://i.imgur.com/PqaFAhH.jpg?1)

![](http://i.imgur.com/AGZ7avT.jpg?1)

### Tasks:

* update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

![](http://i.imgur.com/M3M4wft.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* working on reachability
* working on convergence
* Working on making testers for traverse algorithm
* Finalizing presentation outline
* Starting to work on update functions
* Beginning to work on overall project documentation
* Cleaned up google drive

#### Joaquin

* connecting the json to a positions dictionary

### **2014 09 26 – Friday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* Working on making testers for traverse algorithm
* Finalizing presentation outline
* Starting to work on update functions
* Beginning to work on overall project documentation
* Cleaned up google drive

#### Joaquin

* Fix operon ID’s in the database creator
* Traverse subnetwork needs to be reconfigured to build network from input\_transition\_ids only.
* Fix operon to output transition mapping.
* Right now operons have multiple output transitions.
* As part of the above bullet. Need to fix method to reflect the operon to single output transition mapping. Fix is located inside of the method just uncomment the correct part. Delete the incorrect function.
* def get\_output\_transition\_node\_from\_it\_id(cursor, input\_transition\_id):
* Path list of list is still incomplete. Must work on it.
* Positions are connected to the json creator
* Need a x\_factor and y\_factor to scale the positions as necessary. Got a number!!!
* x\_factor = 1376
* y\_factor = 768
* Keep pigeon work going.
* Contact Lauren
* dummy id’s are used based upon the number of edges

#### Gary

* Rendered full network JSON from Joaquin’s code.
* Needs further refinement on systematic attribution of ID’s.
* Tweaking html and laying down function frameworks for search box.
* Reorganized app html for easier styling and positioning.

#### Rohit

* Network is rendered on CytoScape
* Fixing errors in network
* Virtual Machine Linux

#### KP

* Remote

### **Week (17) of September 29**

### **2014 09 29 – Monday**

### Updates:

* Servlet has been created and python scripts can be run.

![](http://i.imgur.com/Jx4c1Qj.jpg?1)

Working late at BRF2!

### Tasks:

* Update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

![](http://i.imgur.com/spTdqMA.jpg?1)

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* Working on general documentation of the project
* researching other igem projects and their public presentation
* Starting to work on update functions
* Working on update functions
* Working on documentation of the project.
* Cleaned google drive again - better organization
* Working on testers for traverse algorithm

#### Gary

* Revisted modeling html and javascript functions.
* Turned archetype functions into dictionaries including entries for input names, inputs, and equation.
* Updated script codes to reference dictionaries entries.

#### Lauren

* Revised the structure of the pigeon file creator with Joaquin

#### Rohit

* Updated Kavosh slides

#### KP

* Remote
* Vacation in India coming to an end
* Started communicating with the team & tried to get on board with the progress that had been made in the past month.

### **2014 09 30 – Tuesday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* Update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

### Personal Status:

#### Huwate (Kwat)

* Improving runtime for the code
* Working on update functions
* Working on documentation of the project
* Cleaned google drive again - better organization
* Working on testers for traverse algorithm

#### Gary

* Updated SBiDer html for further ease of access and editing.
* Updated application, app toolbar, and interface styling and positioning.
* Rendered full network with all nodes and edges.
* Full render of database complete without errors.

#### Lauren

* Finished the code for the pigeon file creator. Takes an input string and separates out the species into pigeon commands. Can also save pigeon command string to file.

#### Rohit

* Fixed errors in network rendered on CytoScape desktop

### **Week (18) of October 1**

### **2014 10 01 – Wednesday**

### Updates:

* Servlet has been created and python scripts can be run.

![](http://i.imgur.com/P5VhhvV.jpg?1)

### Tasks:

* Update this journal
* Complete your tasks as listed on the URGENT TASKS spreadsheet

![](http://i.imgur.com/zYuf20Y.jpg?1)

Votes for presentation

### Personal Status:

#### Huwate (Kwat)

* Working on update functions
* Working on testers for traverse algorithm
* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on organizing pictures, google drive, etc.
* Working on presentation* Working on Posters

![](http://i.imgur.com/bjJstfe.jpg?1)

Kwat's desk

#### Gary

* Worked with Valeriy and Joaquin to connect algorithms to servlet between database and SbiDer.
* Continued modifying GET requests to accept JSON strings instead of JSON files.
* Continued editing color scheme and style of nodes.

#### Lauren

* worked with Joaquin to integrate the database into the file creator

#### Fernando

* Worked on SBML modeling script
* Finished QualitativeSpecies class and Model class
* outputs SBML strings
* also wrote method to convert string outputs into a text file
* Working on Transitions class, will use methods from JSON constructor script

#### Rohit

* Got CytoKavosh running on CSE lab Linux machines!
* Fernando and I found motifs

### **2014 10 04 – Saturday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* Team meeting

### Personal Status:

#### Huwate (Kwat)

* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on complexity analysis
* Working on organizing pictures, google drive, etc.
* Working on presentation
* Working on Posters

### Lauren

* New names for pigeon files
* Added colors to each species. No color repeats within single operon

### Gary

* Continued to work with Valeriy to improve the layout of the SBiDer app page.
* Encountered major error when trying to debug and run GET requests.* * For some reason, parts of the application written on Mac are not compatible with the Windows machines. Causes GET requests to fail.
    * Error also makes git pull’s between affected computers and files non-operational.
    * As of now, I’m working off dummy files made of the real data, meaning that the only difference is that they are not grabbed live from the database.
    * Completely redesigned WIP modeling and validation.
    * The code was not sufficiently modularized and separated into functions to provide the dynamicism needed to handle varying numbers of graphs and equations.
    * Current code is more modularized and partitioned.

### **Week (19) of October 7**

### **2014 10 07 – Tuesday**

### Updates:

* Servlet has been created and python scripts can be run.

![](http://i.imgur.com/WInX9Wk.jpg?1)

### Tasks:

* Team meeting

### Personal Status:

#### Huwate (Kwat)

* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on complexity analysis
* Working on organizing pictures, google drive, etc.
* Working on presentation
* Working on Posters

#### Rohit

* Began Kavosh complexity analysis

#### Gary

* Continued to spot and fix bugs in the application.
* Spotted errors in the syntax of a few lines of code.
* Began complexity analysis on WIP modeling.
* Can’t run complexity analysis on the app page until it is fully assembled and linked up with all parts of the project.

#### KP

* Back at UC San Diego!
* Started getting updates at the meeting
* Took over wiki responsibility from Valeriy.

### **2014 10 08 – Wednesday**

### Updates:

* Servlet has been created and python scripts can be run.

### Tasks:

* Team meeting canceled

### Personal Status:

#### Huwate (Kwat)

* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on complexity analysis
* Working on organizing pictures, google drive, etc.
* Working on presentation
* Working on Posters

### Rohit

* Updated slides to include motifs found with Kavosh and set to Jenhan/Justin/Ben

#### Gary

* Talked with Kwat about updating slides.
* Looking into software to capture a video tutorial for the application.
* Delaying update of slides until the application is finished to avoid redundant or extraneous work.

#### KP

* Continued working on wiki.
* Updated the pages and the CSS

### **2014 10 09 – Thursday**

### Updates:

* Working SBIDer application.

### Tasks:

* Team meeting

### Personal Status:

#### Huwate (Kwat)

* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on complexity analysis
* Working on organizing pictures, google drive, etc.
* Working on presentation
* Working on Posters
* Cleaning codes for Python3 compatibility
* Researching any other possible difference between python 2 and 3.

### Rohit

* Updated slides to include motifs found with Kavosh and set to Jenhan/Justin/Ben

### Gary

* Continued bringing all basic SBiDer functions online.
* Communicated with Joaquin and Valeriy to iron out the syntax issues between the python back-end, the servlet, and the app page.
* Updates were made using Valeriy’s computer b/c the Mac to Windows error persists.

### KP

* Updated team page - looks sleek now!
* Communicated with the team to ask for text/info for various pages on the wiki
* Discussed wiki style/info with the team and the advisors in great detail

### **2014 10 10 – Friday**

### Updates:

* Working SBIDer application.

### Tasks:

* Team meeting Saturday at BRF

### Personal Status:

#### Huwate (Kwat)

* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on complexity analysis
* Working on organizing pictures, google drive, etc.
* Working on presentation
* Working on Posters
* Cleaning codes for Python3 compatibility
* Researching any other possible difference between python 2 and 3.

### Rohit

* Updated slides to include motifs found with Kavosh and set to Jenhan/Justin/Ben
* Wrote CytoKavosh documentation

### KP

* Implemented changes on wiki as discussed
* Kept working hard on the wiki! Trying to put things togeter

### **2014 10 12 – Saturday**

### Updates:

* Working SBIDer application.

### Tasks:

* Team meeting today at BRF

### Personal Status:

#### Huwate (Kwat)

* Complexity analysis
* Error catching for algorithms
* Improving runtime for the code
* Working on update functions for the database
* Working on documentation of the project
* Working on testers for traverse algorithm
* Working on complexity analysis
* Working on organizing pictures, google drive, etc.
* Working on presentation
* Working on Posters
* Cleaning codes for Python3 compatibility
* Researching any other possible difference between python 2 and 3.

### Lauren

* New names for pigeon files
* Added colors to each species. No color repeats within single operon

### Rohit

* Made wiki notebook for the past 15 weeks
* Wrote network analysis/Kavosh documentation
* Updated slides to include motifs found with Kavosh and set to Jenhan/Justin/Ben

### Gary

* Fallen ill again and missed meeting.
* Brought all basic function online remotely.
* I edited the image slider and corrected the pathing to be able to call the SBOL visuals properly and to be able to cycle through them.

### Joaquin

* Worked on database documentation

### KP

* Thanks to all my team members and advisors for providing me with all the information and pictures needed for the team page & the project page
* The wiki is ready & raring to go ! :)
* 'Twas a fun summer working for UCSD @ iGEM!