Team:UCSD Software/Project

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<h1>SBiDer: Synthetic Biocircuit Developer</h1>
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<h3>Abstract</h3>
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Genetic circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. SBiDer, a web tool developed by the UCSD Software iGEM team, will leverage existing devices to construct a database with consideration for the function of each device interpreted as boolean logic. The data can be queried by the user through SBiDer's visual interface to explore circuit designs. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. Basic validation of the circuit performance is also provided within in the interface. SBiDer's web of information can be expanded through user-generated additions to the database to improve the efficiency of the application and the accuracy of the models.   
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<h1>Project Description</h1>
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<h3>Problem Statement</h3>
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Synthetic genetic circuits created by synthetic biologists have yielded exciting applications such as biofuels production and cancer killing bacteria. These circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. Although there are many genetic devices that have been built, re-using these devices often requires a time-consuming review of the literature. The UCSD Software iGEM team will address this challenge by creating a web-tool that leverages existing genetic devices to create complex genetic circuits. We will accomplish this by:
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                <h2>Week </h2>
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                        <li><button id = "w1click">Week 1</button></li>
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<div id = "w1"><h3><b>Week 1</b></h3>
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<hl> Huwate (Kwat) </hl>
<ol>
<ol>
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<li>building a comprehensive database that captures the behavior, composition, and interactions of existing genetic devices in the literature</li>
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<li> Generated Pydoc </li>
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<li>constructing and visualizing the network of all synthetic genetic circuits that can interact with one another</li>
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<li> Learnt SQL </li>
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<li>devising algorithms to search this network for the set of genetic devices that can be used to construct a complex genetic circuit.</li>
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<li> Learnt Petri Nets </li>
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<li>Perform some basic validation via kinetic modelling.</li>
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<li> Read about past IGEM teams and projects </li>
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<li> Read emailed papers and also helped others understand their assigned papers </li>
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<li> Read more about synthetic biology theories and concepts </li>
</ol>
</ol>
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<h3>Aim 1 - Building a Database</h3>
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<p>
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<hl> Lauren </hl>
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We will mine the scientific literature for existing genetic devices and then construct a database that captures device characteristics such as:
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</p>
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<li> Did Learn Python the Hard Way </li>
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<li>composition of devices</li>
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<li> Read Python Wiki </li>
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<li>function</li>
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<li>characterization data</li>
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<li>literature reference</li>
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</ol>
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We will design our database by rigorously constructing an entity relationship diagram and then normalizing these relationships to construct tables for a relational database.
 
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<h3>Aim 2 - Constructing Network of Interacting Devices</h3>
 
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<p>
 
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We will connect known genetic devices together via device input and outputs to create a network of devices that can interact. We define a genetic device as a DNA construct transformed into cells that can cause expression of some protein in response to stimuli (or input). We will  develop a web interface to facilitate access to the complex network that we have constructed. Our Web interface makes extensive use of Cytoscape, an open source bioinformatics software package for metabolic network visualization and simulation.  In addition, the interface will generate SBOL Visual Images, a standard language that is easily understood by synthetic biologists all over the world.  Users can also update our database with additional devices through this interface.  Using the Cynetshare framework, users can share their circuit designs</p>
 
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<h3>Aim 3 - Searching the Network</h3>
 
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<p>
 
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This interface will allow researchers to query our database network for a circuit design expressed as logical operators such as “AND”, “OR”, and “NOR”, and retrieve the subnetwork of genetic devices that satisfies the circuit design. To Perform our search  we modified several traditional graph search algorithms to traverse this graph, including but not limited to Prim’s algorithm (minimum spanning tree), Dijkstra’s algorithm and a breadth-first search. Results are visualized graphically in our web interface
 
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<hl> Gary </hl>
-
<table width="70%" align="center">
+
<ol>
 +
<li> Read Cytoscape.js API </li>
 +
</ol>
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li> Learnt Boolean Networks </li>
 +
<li> Continued Petri Nets </li>
 +
<li> Learnt Dynamic Programming and Path Traversal </li>
 +
</ol>
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Learnt Cytoscape </li>
 +
<li> Learnt Python </li>
 +
<li> Learnt Petri Nets </li>
 +
<li> Attempted to develop basic parser for Pigeon commands </li>
 +
<li> Read up on synthetic biology and Pigeon images </li>
 +
</ol>
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Finished command line interface </li>
 +
<li> Acquired snippet of Linh's database </li>
 +
</ol>
-
<!--welcome box -->
 
-
<tr>
 
-
<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
 
-
<h1 >WELCOME TO iGEM 2014! </h1>
 
-
<p>Your team has been approved and you are ready to start the iGEM season!
 
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
 
-
<br>
 
-
<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:UCSD_Software/Project&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
 
-
</td>
 
-
</tr>
 
-
<tr> <td colspan="3"  height="5px"> </td></tr>
+
</div>
-
<!-- end welcome box -->
+
-
<tr>  
+
-
<!--navigation menu -->
+
<div id = "w2"><h3><b>Week 2</b></h3>
-
<td align="center" colspan="3">
+
-
<table  width="100%">
+
<hl> Huwate (Kwat) </hl>
-
<tr heigth="15px"></tr>
+
<ol>
-
<tr heigth="75px">  
+
<li> Learnt boolean networks </li>
 +
<li> Continued learning Petri Nets</li>
 +
<li> Looked for useful Python packages for the project </li>
 +
</ol>
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Learnt Boolean networks</li>
 +
<li> Continued learning Petri nets </li>
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
+
</ol>
-
<a href="https://2014.igem.org/Team:UCSD_Software"style="color:#000000">Home </a> </td>
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<hl> Gary </hl>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Team"style="color:#000000"> Team </a> </td>
+
<ol>
 +
<li> Continued playing with Cytoscape.js add/remove nodes </li>
 +
</ol>
-
<td style="border:1px solid black;" align="center"  height ="45px"  onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<hl> Joaquin </hl>
-
<a href="https://igem.org/Team.cgi?year=2014&team_name=UCSD_Software"style="color:#000000"> Official Team Profile </a></td>
+
<ol>
 +
<li> Learnt Boolean Networks</li>
 +
<li> Learnt reachability treees </li>
 +
<li> Developed Entity Relationship Diagram </li>
 +
</ol>
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Learnt Boolean networks </li>
 +
<li> Found SNAKES- a Python package that utilizes Petri nets </li>
-
<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
</ol>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Project"style="color:#000000"> Project</a></td>
+
<hl> Fernando </hl>
 +
<ol>
 +
<li> Learnt Boolean networks </li>
 +
<li> Disambiguated Linh's device composition</li>
 +
<Div>
 +
</ol>
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
</div>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Parts"style="color:#000000"> Parts</a></td>
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<div id = "w3"><h3><b>Week 3</b></h3>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Modeling"style="color:#000000"> Modeling</a></td>
+
-
<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
+
<hl> Huwate (Kwat) </hl>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Notebook"style="color:#000000"> Notebook</a></td>
+
<ol>
 +
<li> Learnt SQL </li>
 +
<li> Learnt traversal algorithms </li>
 +
<li> Read assigned papers to populate database </li>
 +
<li> Read about past IGEM teams and projects </li>
 +
</ol>
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<hl> Lauren </hl>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Safety"style=" color:#000000"> Safety </a></td>
+
<ol>
 +
<li> Petri net reading</li>
 +
<li> CodeAcademy Python tutorials</li>
 +
<li> BFS/DFS algorithms </li>
 +
<li> Read papers to fill in database </li>
 +
</ol>
-
<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
+
<hl> Gary </hl>
-
<a href="https://2014.igem.org/Team:UCSD_Software/Attributions"style="color:#000000"> Attributions </a></td>
+
<ol>
 +
<li> Learnt basics of Angular.js </li>
 +
<li> Meet with CyNetShare team </li>
 +
<li> Got approval to use CyNetShare code </li>
 +
</ol>
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li> SQl columns modification</li>
 +
<li> Read papers to fill in database </li>
 +
<li> </li>
 +
</ol>
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Learnt SQL </li>
 +
<li> Conceptualized traversal algorithms </li>
 +
<li> Read assigned papers to populate database </li>
 +
</ol>
-
<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
+
<hl> Fernando </hl>
-
</tr>
+
<ol>
-
</table>
+
<li> Found possible approach to weigh our edges using "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements" and its database </li>
 +
</ol>
-
</tr>
+
<hl> Valeriy </hl>
-
</tr>
+
<ol>
-
</td>
+
<li> Started relearning python to work with the traversal as suggested by Jenhan </li>
 +
<li> Read a few chapters from different books about Jquery functions to use for data loading onto the website </li>
 +
</ol>
 +
</div>
-
<tr> <td colspan="3"  height="15px"> </td></tr>
 
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
 
-
<tr> <td colspan="3"  height="5px"> </td></tr>
 
 +
<div id = "w4"><h3><b>Week 4</b></h3>
 +
<hl>Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Learnt HTML </li>
 +
<li> Went over everyone else's codes </li>
 +
<li> SQL cleanup </li>
 +
</ol>
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Wrote code for BFS and DFS </li>
 +
<li> Learn Python the Hard Way </li>
 +
<li> Prepared presentation for expanded BFS on Monday </li>
 +
</ol>
-
<!--Project content  -->
+
<hl> Gary </hl>
-
<tr><td > <h3> Project Description </h3></td>
+
<ol>
-
<td ></td >
+
<li> Continued shifting through CyNetShare code  and annotate functions </li>
-
<td > <h3> Content</h3></td>
+
</ol>
-
</tr>
+
-
<tr>
+
<hl> Joaquin </hl>
-
<td width="45%"  valign="top">  
+
<ol>
-
<p>Tell us more about your project.  Give us background.  Use this as the abstract of your project.  Be descriptive but concise (1-2 paragraphs) </p>
+
<li> Learnt Bioservices for Miriam</li>
-
<br>
+
<li> Read papers to fill in database </li>
-
<h3>References </h3>
+
<li> scheme for UUID </li>
-
<p>
+
<li> add implicit output list to device table </li>
-
iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you. </p>  
+
<li> promoter sequence database (biobrick registry) </li>
-
</td>
+
<li> insert_into_database fix </li>
 +
<li> determine necessary data for device input </li>
 +
</ol>
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Worked on traversal algorithm</li>
 +
</ol>
-
<td></td>
+
<hl> Fernando </hl>
-
<td  width="45%"  valign="top">
+
<ol>
-
<p> You can use these subtopics to further explain your project</p>
+
<li> Continued debugging network</li>
 +
<li> Updated database </li>
 +
</ol>
 +
<hl> Valeriy </hl>
<ol>
<ol>
-
<li>Overall project summary</li>
+
<li> Learnt Angular.js main functions to use for the website </li>
-
<li>Project Details</li>
+
<li> Went over more CyNetShare code </li>
-
<li>Materials and Methods</li>
+
<li> Read a few articles about visualizing data using JSON files and different techniques to do so </li>
-
<li>The Experiments</li>
+
-
<li>Results</li>
+
-
<li>Data analysis</li>
+
-
<li>Conclusions</li>
+
</ol>
</ol>
 +
</div>
 +
 +
<div id = "w5"><h3><b>Week 5</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Created database structure </li>
 +
<li> Normalization complete </li>
 +
<li> Working on algorithm </li>
 +
<li> Reading on petri nets </li>
 +
 +
<li> Learning about designing wiki </li>
 +
<li> Populating new database </li>
 +
<li> Learnt more about Petri Nets </li>
 +
<li> Learnt more about SQL and its functions </li>
 +
<li> Met with Joaquin and Fred to brainstorm the traversal algorithm </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Edited the Petri Net traversal to accept multiple inputs </li>
 +
<li> Formatted integration of Bolean logic and multiple outputs </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Busy with Final Exams </li>
 +
<li> Began outlining Web part of presentation </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Designed a new structure for the database and the traversal</li>
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Improved BFS algorithm </li>
 +
<li> Populated database </li>
 +
<li> Kept journal clean </li>
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Incorporated NetworkX into script</li>
 +
<li> Began Boolean Satisfiability Problem </li>
 +
</ol>
 +
 +
<hl> Valeriy </hl>
 +
<ol>
 +
<li> Worked on designing a specific JSON file to visualize database with CyNetShare </li>
 +
<li> Played around with more JSON data to add more key values and data </li>
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Enabled CyNetShare on his server </li>
 +
<li> Cleaned up web dev part of master branch </li>
 +
</ol>
 +
 +
<hl> Fred </hl>
 +
<ol>
 +
<li> Met with Joaquin and Huwate (Kwat), improved database structure, finished database normalization, prepared for presentation and traversal algorithm </li>
 +
</ol>
 +
</div>
 +
 +
<div id = "w6"><h3><b>Week 6</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Cleaned the database and commented on everyone's data </li>
 +
<li> Worked on search algorithm </li>
 +
<li> Read about Petri nets </li>
 +
<li> Tried to modify traverse algorithm to fit Petri Net model </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Edited the database </li>
 +
<li> Fixed errors in traversal </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Continued to clean up database </li>
 +
<li> Added NOT gate entries to AND gates involving repressors </li>
 +
<li> Contributed to website portion of presentations </li>
 +
<li> Learnt scale vector graphs for possible plotting </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Filled database PowerPoint presentation</li>
 +
<li> Filled database section </li>
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Improved BFS algorithm </li>
 +
<li> Populated database </li>
 +
<li> Kept journal clean </li>
 +
<li> Worked on presentation </li>
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Incorporated NetworkX into script</li>
 +
<li> Began Boolean Satisfiability Problem </li>
 +
</ol>
 +
 +
<hl> Valeriy </hl>
 +
<ol>
 +
<li> Worked on designing a specific JSON file to visualize database with CyNetShare </li>
 +
<li> Looked over database </li>
 +
<li> Thought about possible website designs </li>
 +
<li> Played around with JSON data </li>
 +
<li> Edited more database information </li>
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Enabled CyNetShare on his server </li>
 +
<li> Cleaned up web dev part of master branch </li>
 +
</ol>
 +
</div>
 +
 +
<div id = "w7"><h3><b>Week 7</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Made a script that parses a user input, searches graph and returns one more more linear searchable space </li>
 +
<li> Learned SNAKES </li>
 +
<li> Learned SQL stored function </li>
 +
<li> Provided Fernando data for analysis </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Added traversal algorithm to presentation</li>
 +
<li> Updated slides for iGEM presentation and added figures explaining overall traversal algorithm </li>
 +
<li> Wrote project description </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Continued to clean up database </li>
 +
<li> Got CyNetShare running on NetBeans </li>
 +
<li> Discussed implementing Ryan’s modeling to the application </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Worked on presentation</li>
 +
<li> Started script to get JSON information </li>
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Added minimum spanning tree slides to presentation </li>
 +
<li> Started learning JSON </li>
 +
<li> Wrote project description </li>
 +
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Read Overpowering the Component Problem and Circuit Simulation of Genetic Networks</li>
 +
 +
</ol>
 +
 +
<hl> Valeriy </hl>
 +
<ol>
 +
<li> Designed web app page </li>
 +
<li> Worked on wiki </li>
 +
<li> Added slides to presentation </li>
 +
</ol>
 +
 +
 +
</div>
 +
 +
<div id = "w8"><h3><b>Week 8</b></h3>
 +
<hl>Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Finished parser </li>
 +
<li> Finished database structure</li>
 +
<li> Wrote pseudocode for search algorithm </li>
 +
<li> Learnt SQL stored function </li>
 +
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Changed size/shapes of nodes in CyNetShare</li>
 +
<li> Began learning Angular UI Bootstrap </li>
 +
<li> Began working on carousel within CyNetShare </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Added dynamic labels to graph that enumerates lines as they are added</li>
 +
<li> Got CyNetShare running on NetBeans </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Finished operon, plasmid I.D.s etc. In database</li>
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Worked on JSON</li>
 +
<li> Edited presentation</li>
 +
 +
</ol>
 +
 +
<hl> Tiffany</hl>
 +
<ol>
 +
<li> Modified pigeon command generator for plasmid to generate commands for each individual operon</li>
 +
<li> Modified logo </li>
 +
 +
</ol>
 +
 +
<hl> Valeriy </hl>
 +
<ol>
 +
<li> Designed web app page </li>
 +
<li> Worked on wiki </li>
 +
<li> Added slides to presentation </li>
 +
</ol>
 +
 +
 +
</div>
 +
 +
<div id = "w9"><h3><b>Week 9</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Got inputs on parser working </li>
 +
<li> Began working on outputs and verifying codes</li>
 +
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Finished adding line removal buttons to legend</li>
 +
<li> Cleaned up Web Dev branch </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Populated working data</li>
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Worked on JSON</li>
 +
<li> Began learning NetworkX</li>
 +
<li> Revisited learning Cytoscape </li>
 +
 +
</ol>
 +
 +
</div>
 +
 +
 +
 +
<div id = "w10"><h3><b>Week 10</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Patched codes together </li>
 +
<li> Finished database with Joaquin</li>
 +
<li> Worked on reachability </li>
 +
<li> Worked on convergence </li>
 +
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Validated database</li>
 +
<li> Drafted JSON format </li>
 +
<li> Went remote </li>
 +
<li> Learnt how to use database </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Parsed excel file into database</li>
 +
<li> Prepared for presentation </li>
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Wrote Python script that takes SQL query and outputs JSON</li>
 +
<li> Began learning Cytoscape.js</li>
 +
<li> Began learning igraph </li>
 +
 +
</ol>
 +
</div>
 +
<div id = "w11"><h3><b>Week 11</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Worked on poster </li>
 +
<li> Worked on presentation outline</li>
 +
<li> Updated traverse code </li>
 +
<li> Updated Google Drive </li>
 +
<li> Updated Parser again <li>
 +
<li> Updated reachability analyzer again to not return AND logic </li>
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Designed master Python</li>
 +
<li> Designed device insert page</li>
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Read up on network motif algorithms (mfinder, color-coding, Kavosh)</li>
 +
<li> Decided on Kavosh</li>
 +
<li> Began learning CytoKavosh </li>
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Almost finished JSON graph constructor </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Verified database code compatibility with network traversal </li>
 +
</ol>
 +
 +
</div>
 +
 +
 +
<div id = "w12"><h3><b>Week 12</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Populated and finalized database </li>
 +
<li> Combined visualization property with traverse code</li>
 +
<li> Tested and debugged traversal algorithm </li>
 +
<li> Started working on presentation </li>
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> No longer remote </li>
 +
<li> Met with Ryan and Jenhan to refine modeling development directoin </li>
 +
<li> Decided to use dictionaries of each operon's modeling information </li>
 +
<li> Stored equations locally for reference </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Populated new database structure</li>
 +
<li> Implemented dictionaries necessary for traversal</li>
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Continued network analysis with Kavosh</li>
 +
<li> Began validating database</li>
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Generated DOT file creator to retrieve node coordinates from GraphViz </li>
 +
</ol>
 +
 +
</div>
 +
 +
 +
<div id = "w13"><h3><b>Week 13</b></h3>
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Worked on reachability </li>
 +
<li> Worked on convergence </li>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Rendered full network JSON </li>
 +
<li> Tweaked HTML and laid down function frameworks for search box </li>
 +
<li> Reorganized app HTML for easier styling and positioning </li>
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Fixed operon I.D.s in database creator</li>
 +
<li> Fixed operon to output transition mapping</li>
 +
<li> Connected positions to JSON creator </li>
 +
<li> Worked on Pidgeon </li>
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Rendered full network on CytoScape</li>
 +
<li> Attempted to run Linux VirtualBox on my machine to run CytoKavosh</li>
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Debugged JSON file creator </li>
 +
<li>
 +
</ol>
 +
</div>
 +
 +
<div id = "w14"><h3><b>Week 14</b></h3>
 +
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Worked on update functions </li>
 +
<li> Worked on documentation </li>
 +
<li> Worked on testers for traversal algorithm </li>
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> Remote </li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Connected algorithms and servlet between database and SBIDer</li>
 +
<li> Modified GET requests to accept JSON strings instead of JSON files </li>
 +
<li> Edited color scheme and style of nodes</li>
 +
 +
</ol>
 +
 +
<hl> Joaquin </hl>
 +
<ol>
 +
<li>Connected algorithms to servlet between database and SBIDer</li>
 +
<li>Integrated database into file creator </li>
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> VirtualBox did not work</li>
 +
<li> Ran CytoKavosh on CSE lab Linux machines and found motifs</li>
 +
</ol>
 +
 +
<hl> Fernando </hl>
 +
<ol>
 +
<li> Worked on SBML modeling script </li>
 +
<li> Finished QualitativeSpecies class and Modeling class </li>
 +
</ol>
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> Integrated database into file creator</li>
 +
<li>
 +
</ol>
 +
 +
</div>
 +
<div id = "w15"><h3><b>Week 15</b></h3>
 +
 +
<hl> Huwate (Kwat) </hl>
 +
<ol>
 +
<li> Worked on update functions </li>
 +
<li> Worked on documentation </li>
 +
<li> Worked on testers for traversal algorithm </li>
 +
</ol>
 +
 +
<hl> KP </hl>
 +
<ol>
 +
<li> No longer remote!</li>
 +
</ol>
 +
 +
<hl> Gary </hl>
 +
<ol>
 +
<li> Brought all basic functionality online remotely </li>
 +
 +
</ol>
 +
 +
 +
 +
</ol>
 +
 +
<hl> Rohit </hl>
 +
<ol>
 +
<li> Made wiki notebook for past 15 weeks</li>
 +
<li> Wrote network analysis/Kavosh documentation</li>
 +
<li> Updated slides to include motifs found with Kavosh and sent to Jenhan/Justin/Ben </li>
 +
</ol>
 +
 +
 +
<hl> Lauren </hl>
 +
<ol>
 +
<li> New names for pigeon files</li>
 +
<li> Added colors to each species so that no color repeats within a single operon </li>
 +
</ol>
 +
 +
 +
</div>
 +
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 +
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 +
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Revision as of 11:21, 15 October 2014


Week

Entries

Week 1

Huwate (Kwat)
  1. Generated Pydoc
  2. Learnt SQL
  3. Learnt Petri Nets
  4. Read about past IGEM teams and projects
  5. Read emailed papers and also helped others understand their assigned papers
  6. Read more about synthetic biology theories and concepts
Lauren
  1. Did Learn Python the Hard Way
  2. Read Python Wiki
Gary
  1. Read Cytoscape.js API
Joaquin
  1. Learnt Boolean Networks
  2. Continued Petri Nets
  3. Learnt Dynamic Programming and Path Traversal
Rohit
  1. Learnt Cytoscape
  2. Learnt Python
  3. Learnt Petri Nets
  4. Attempted to develop basic parser for Pigeon commands
  5. Read up on synthetic biology and Pigeon images
Fernando
  1. Finished command line interface
  2. Acquired snippet of Linh's database

Week 2

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

Week 3

Huwate (Kwat)
  1. Learnt SQL
  2. Learnt traversal algorithms
  3. Read assigned papers to populate database
  4. Read about past IGEM teams and projects
Lauren
  1. Petri net reading
  2. CodeAcademy Python tutorials
  3. BFS/DFS algorithms
  4. Read papers to fill in database
Gary
  1. Learnt basics of Angular.js
  2. Meet with CyNetShare team
  3. Got approval to use CyNetShare code
Joaquin
  1. SQl columns modification
  2. Read papers to fill in database
Rohit
  1. Learnt SQL
  2. Conceptualized traversal algorithms
  3. Read assigned papers to populate database
Fernando
  1. Found possible approach to weigh our edges using "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements" and its database
Valeriy
  1. Started relearning python to work with the traversal as suggested by Jenhan
  2. Read a few chapters from different books about Jquery functions to use for data loading onto the website

Week 4

Huwate (Kwat)
  1. Learnt HTML
  2. Went over everyone else's codes
  3. SQL cleanup
Lauren
  1. Wrote code for BFS and DFS
  2. Learn Python the Hard Way
  3. Prepared presentation for expanded BFS on Monday
Gary
  1. Continued shifting through CyNetShare code and annotate functions
Joaquin
  1. Learnt Bioservices for Miriam
  2. Read papers to fill in database
  3. scheme for UUID
  4. add implicit output list to device table
  5. promoter sequence database (biobrick registry)
  6. insert_into_database fix
  7. determine necessary data for device input
Rohit
  1. Worked on traversal algorithm
Fernando
  1. Continued debugging network
  2. Updated database
Valeriy
  1. Learnt Angular.js main functions to use for the website
  2. Went over more CyNetShare code
  3. Read a few articles about visualizing data using JSON files and different techniques to do so

Week 5

Huwate (Kwat)
  1. Created database structure
  2. Normalization complete
  3. Working on algorithm
  4. Reading on petri nets
  5. Learning about designing wiki
  6. Populating new database
  7. Learnt more about Petri Nets
  8. Learnt more about SQL and its functions
  9. Met with Joaquin and Fred to brainstorm the traversal algorithm
Lauren
  1. Edited the Petri Net traversal to accept multiple inputs
  2. Formatted integration of Bolean logic and multiple outputs
Gary
  1. Busy with Final Exams
  2. Began outlining Web part of presentation
Joaquin
  1. Designed a new structure for the database and the traversal
Rohit
  1. Improved BFS algorithm
  2. Populated database
  3. Kept journal clean
Fernando
  1. Incorporated NetworkX into script
  2. Began Boolean Satisfiability Problem
Valeriy
  1. Worked on designing a specific JSON file to visualize database with CyNetShare
  2. Played around with more JSON data to add more key values and data
KP
  1. Enabled CyNetShare on his server
  2. Cleaned up web dev part of master branch
Fred
  1. Met with Joaquin and Huwate (Kwat), improved database structure, finished database normalization, prepared for presentation and traversal algorithm

Week 6

Huwate (Kwat)
  1. Cleaned the database and commented on everyone's data
  2. Worked on search algorithm
  3. Read about Petri nets
  4. Tried to modify traverse algorithm to fit Petri Net model
Lauren
  1. Edited the database
  2. Fixed errors in traversal
Gary
  1. Continued to clean up database
  2. Added NOT gate entries to AND gates involving repressors
  3. Contributed to website portion of presentations
  4. Learnt scale vector graphs for possible plotting
Joaquin
  1. Filled database PowerPoint presentation
  2. Filled database section
Rohit
  1. Improved BFS algorithm
  2. Populated database
  3. Kept journal clean
  4. Worked on presentation
Fernando
  1. Incorporated NetworkX into script
  2. Began Boolean Satisfiability Problem
Valeriy
  1. Worked on designing a specific JSON file to visualize database with CyNetShare
  2. Looked over database
  3. Thought about possible website designs
  4. Played around with JSON data
  5. Edited more database information
KP
  1. Enabled CyNetShare on his server
  2. Cleaned up web dev part of master branch

Week 7

Huwate (Kwat)
  1. Made a script that parses a user input, searches graph and returns one more more linear searchable space
  2. Learned SNAKES
  3. Learned SQL stored function
  4. Provided Fernando data for analysis
Lauren
  1. Added traversal algorithm to presentation
  2. Updated slides for iGEM presentation and added figures explaining overall traversal algorithm
  3. Wrote project description
Gary
  1. Continued to clean up database
  2. Got CyNetShare running on NetBeans
  3. Discussed implementing Ryan’s modeling to the application
Joaquin
  1. Worked on presentation
  2. Started script to get JSON information
Rohit
  1. Added minimum spanning tree slides to presentation
  2. Started learning JSON
  3. Wrote project description
Fernando
  1. Read Overpowering the Component Problem and Circuit Simulation of Genetic Networks
Valeriy
  1. Designed web app page
  2. Worked on wiki
  3. Added slides to presentation

Week 8

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

Week 9

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

Week 10

Huwate (Kwat)
  1. Patched codes together
  2. Finished database with Joaquin
  3. Worked on reachability
  4. Worked on convergence
KP
  1. Remote
Gary
  1. Validated database
  2. Drafted JSON format
  3. Went remote
  4. Learnt how to use database
Joaquin
  1. Parsed excel file into database
  2. Prepared for presentation
Rohit
  1. Wrote Python script that takes SQL query and outputs JSON
  2. Began learning Cytoscape.js
  3. Began learning igraph

Week 11

Huwate (Kwat)
  1. Worked on poster
  2. Worked on presentation outline
  3. Updated traverse code
  4. Updated Google Drive
  5. Updated Parser again
  7. Updated reachability analyzer again to not return AND logic
KP
  1. Remote
Gary
  1. Remote
Joaquin
  1. Designed master Python
  2. Designed device insert page
Rohit
  1. Read up on network motif algorithms (mfinder, color-coding, Kavosh)
  2. Decided on Kavosh
  3. Began learning CytoKavosh
Fernando
  1. Almost finished JSON graph constructor
Lauren
  1. Verified database code compatibility with network traversal

Week 12

Huwate (Kwat)
  1. Populated and finalized database
  2. Combined visualization property with traverse code
  3. Tested and debugged traversal algorithm
  4. Started working on presentation
KP
  1. Remote
Gary
  1. No longer remote
  2. Met with Ryan and Jenhan to refine modeling development directoin
  3. Decided to use dictionaries of each operon's modeling information
  4. Stored equations locally for reference
Joaquin
  1. Populated new database structure
  2. Implemented dictionaries necessary for traversal
Rohit
  1. Continued network analysis with Kavosh
  2. Began validating database
Fernando
  1. Remote
Lauren
  1. Generated DOT file creator to retrieve node coordinates from GraphViz

Week 13

Huwate (Kwat)
  1. Worked on reachability
  2. Worked on convergence
    3. KP
    1. Remote
    Gary
    1. Rendered full network JSON
    2. Tweaked HTML and laid down function frameworks for search box
    3. Reorganized app HTML for easier styling and positioning
    Joaquin
    1. Fixed operon I.D.s in database creator
    2. Fixed operon to output transition mapping
    3. Connected positions to JSON creator
    4. Worked on Pidgeon
    Rohit
    1. Rendered full network on CytoScape
    2. Attempted to run Linux VirtualBox on my machine to run CytoKavosh
    Fernando
    1. Remote
    Lauren
    1. Debugged JSON file creator

Week 14

Huwate (Kwat)
  1. Worked on update functions
  2. Worked on documentation
  3. Worked on testers for traversal algorithm
KP
  1. Remote
Gary
  1. Connected algorithms and servlet between database and SBIDer
  2. Modified GET requests to accept JSON strings instead of JSON files
  3. Edited color scheme and style of nodes
Joaquin
  1. Connected algorithms to servlet between database and SBIDer
  2. Integrated database into file creator
Rohit
  1. VirtualBox did not work
  2. Ran CytoKavosh on CSE lab Linux machines and found motifs
Fernando
  1. Worked on SBML modeling script
  2. Finished QualitativeSpecies class and Modeling class
Lauren
  1. Integrated database into file creator

Week 15

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

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