Team:UCSD Software/Notebook

<!-------------- JUNE/JULY ENDS & AUGUST STARTS HERE!!! --------------------------->

<div id = "w7"><div class = "row text-center"><h3><b>Week of August 1</b></h3></div>

<h3><b>2014 08 01 – Friday </b></h3>

<h3> Updates: </h3>

<ul>

<li> Database normalization complete</li>

<li> Meet with graduate students to update the progress</li>

</ul>

<h3> Updates: </h3>

<ul>

<li>Only 2 months left until the jamboree, we have to collaborate.</li>

</ul>

<h3> Tasks: </h3>

</ul>

<h4>Valeriy</h4>

<ul>

<li> Populated my portion of the database</li>

<li> Worked on a draft of the website homepage for the presentation </li>

<li>Read my research papers as well fernandos paper</li>

</ul>

<h3><b> 2014 08 05 – Tuesday </b></h3>

<h3> Updates: </h3>

</ul>

<h3>Tasks:</h3>

<ul>

<li>Populate the database please. </li>

<li>Fill in powerpoint structure and be ready to present tomorrow.</li>

</ul>

<h3>Personal Status: <h3>

<h4>Huwate (Kwat) </h4>

<ul>

<li>Cleaned the database and commented on everyone's data</li>

<li>Working on the search algorithm</li>

<li>Reading about Petri Nets</li>

<li>The current search algorithm does not follow Petri Nets model, unfortunately. So I am trying to fix this</li>

<li>I made a folder named whiteboard_pictures, where all the pictures of the whiteboard can be found </li>

<li>Wiki model: https://2013.igem.org/Team:USTC-Software </li>

</ul>

<h4> Gary </h4>

<ul>

<li>Continued to clean up the database.</li>

<li>Added NOT gate entries to AND gates involving repressors.</li>

<li>Contributed to Website portion of presentations.</li>

<li>Learning Scale Vector Graphs for possible plotting.</li>

</ul>

<h4> Rohit </h4>

<ul>

<li>Fixing data on database</li>

<li>Working on presentation</li>

</ul>

<h4>Joaquin </h4>

<ul>

<li>Filling in database ppt information</li>

<li>Working with everyone to form a coherent and structured ppt.</li>

<li>Filling Database section.</li>

</ul>

<h4> Lauren </h4>

<ul>

<li>Edit the database</li>

<li> Fix the errors in the traversal: not accepting multiple outputs, returning incorrect outputs when loops are concerned </li>

</ul>

<h4> Valeriy </h4>

<ul>

<li> Looked over the data base </li>

<li>Thinking further about possible website designs</li>

<li>Playing around with json data and having it show up</li>

<li>Still discussing with Joaquin about what we will do to create and pass the json files</li>

<li>Edited more of the database information</li>

</ul>

<h4>Tiffany</h4>

<ul>

<li>Completed database_to_pigeonv2.py (pigeon command generator for plasmids)</li>

</ul>

<h4>Valeriy</h4>

<ul>

<li>Got the rough draft of all the pages ready but still not sure if that will be the final</li>

<li>Reading up on different web style techniques</li>

<li>Talked to Joaquin about the json file and how we will use it.</li>

<li>Further reading about setting up json files</li>

</ul>

<h4> KP </h4>

<li> Worked on the presentation (setting up slides of web dev with Gary). </li>

<li>Reading up on Petri Nets</li>

<li>AngularJS videos for a better understanding (Source YouTube: “Angular JS in 60ish minutes” by Dan Wahlin).</li>

<li>Managed to make CyNetShare run on netbeans with Gary, pushed code for the same on GitHub.</li>

<li>Try to change shapes/sizes of nodes in the CyNetShare network.</li>

</ul>

<h3><b> 2014 08 12 – Tuesday </b></h3>

<h3>Updates: </h3>

<ul>

<li>Presentation make up</li>

<li>When out to eat as a group and got an awesome group photo with the sunset!!!</li>

</ul>

<h3>Tasks: </h3>

<ul>

<li> Incorporate more of a “story” into the presentation to increase cohesiveness. </li>

<li> Had great Indian food at the beach and took an almost complete team picture. </li>

</ul>

<li>Cleaned the database and commented on everyone's data.</li>

<li>Working on the search algorithm.</li>

<li>Reading about Petri Nets.</li>

<li>The current search algorithm does not follow Petri Nets model, unfortunately. So I am trying to fix this.</li>

<li>I made a folder named whiteboard_pictures, where all the pictures of the whiteboard can be found.</li>

<li>Worked on the presentation </li>

</ul>

<h4> Joaquin </h4>

<ul>

<li>Sat down with Gary for 3 hours in Geisel and made up the introduction slides</li>

<li>Came up with a diagram to represent devices</li>

<li>Epiphany at 3am about how ER diagrams are meant to capture table-table relationships via key columns. Will include in next slides.</li>

<li>Worked on the presentation</li>

</ul>

<h4>Gary </h4>

<ul>

<li>Worked with Rohit and Joaquin to build introduction and part of the concluding portions of the presentation.</li>

<li>Continue cleaning up web portion of the slides.</li>

<li>Continued practicing slides.</li>

</ul>

<h4> Lauren</h4>

<ul>

<li>Edited the presentation so the example slides were clearer: enlarged figures, added tags to inputs and outputs</li>

</ul>

<h4> Valeriy </h4>

<ul>

<li>Working on the homepage as well as the app page</li>

<li>Figuring out with Joaquin how to produce the json files for visualization</li>

<li>Trying to see how to get CyNetShare working on netbeans</li>

</ul>

<h3><b> 2014 08 13 – Wednesday </b></h3>

<h3> Updates: </h3>

<ul>

<li>Test run 2 of project presentation</li>

</ul>

<h3> Tasks:</h3>

<ul>

<li>Properly cite your sources</li>

<li>If you need some information from the database just ask</li>

</ul>

<h3> Personal Status: </h3>

<h4> Huwate (Kwat) </h4>

<ul>

<li> Wrote project description.</li>

<li> With JR and Fred, created a petri net model for the sample database. </li>

<li>Thought about the name for the project, SBIDer.</li>

<li>Allocating tasks for people.</li>

<li>Sat with Tiffany and we defined what her slides meant and what types of questions they tried to answer.</li>

<li>Really trying to help everyone tie their parts to the project as a whole.</li>

</ul>

<h4>Gary</h4>

<ul>

<li>Unexpectedly presented the entire web portion of slides.</li>

<li>Aim to continue practicing, being more wary of other parts of the presentation.</li>

<li>Need to learn more about validation.</li>

<li>Added basic code for a simple d3.js plot graph</li>

</ul>

<h4>Lauren</h4>

<ul>

<li>Edited the slides more to include feedback from the meeting: examples and arrows are clearer</li>

<ul>

<li>Finished drawing out the layout of most of the website pages</li>

<li>Reading about possible slider options for the team page</li>

</ul>

<h3><b> 2014 08 14 – Thursday </b></h3>

<h3> Updates: </h3>

<ul>

<li>Sign up for the iGem roster by tomorrow.</li>

<li>With JR and Fred, created a petri net model for the sample database.</li>

<li>Update the slides for the iGEM presentation and add figures explaining the overall traversal algorithm</li>

<li>Write project description</li>

<li>With JR and Fred, created a petri net model for the sample database.</li>

</ul>

<h3><b> 2014 08 15 – Friday </b></h3>

<h3> Updates: </h3>

<ul>

<li>iGem wiki editing had began. Today, the first team description was input. </li>

<li>Team name voting started. Please look at the document.</li>

<ul>

<li>Vote on the project name.</li>

<li>Update this journal.</li>

<li>Communicate better and understand the overall project description better.</li>

<li>Please re-read others’ project description; doing so will help you understand more about the project.</li>

<h3>Personal Status: </h3>

<h4>Huwate (Kwat)</h4>

<ul>

<li>Making a script that can parse a user input, search the graph, and return one or more linear searchable space.</li>

<li>Learning SNAKE and graphviz.</li>

<li>Learning SQL stored function.</li>

</ul>

<h4>Rohit </h4>

<ul>  

<li>Added MST slides to presentation</li>

<li>1am epiphany on how to get CyNetShare running on Netbeans.</li>

<li>2am epiphany on how to fix the tables so that they display node/edge data. properly in CyNetShare. </li>

<li>Continued cleaning database. It’s in poor shape. Considering reading more papers when time allows.</li>

<li>Finalized design for displaying images with KP and Valeriy.</li>

<ul>

<li>Continue working on presentation</li>

<li>Scripting python code to obtain json file information and pass to Rohit</li>

</ul>                

<h4>Valeriy</h4>

<ul>

<li>Working on the slider for the team page, and the contact page</li>

<li>Designing the app page but have to work with gary and kp on it</li>

<li>Trying to prepare some potential slides for the presentation </li>

</ul>

<h3><b> 2014 08 18 – Monday </b></h3>

<h3> Updates: </h3>

<ul>

<li>The project name is voted to be SBIDer!</li>

<li>Search algorithm team need to meet and recap and catch up.</li>

<li>(2am) finalized the database in paper, needs to update it tomorrow.</li>

<li>I need to cooperate with Fred and JR so they start using MySQL instead of SQlte3.</li>

<li>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).</li>

<li>Reading up on this new and amazing Angular UI Bootstrap source: http://angular-ui.github.io/bootstrap/ </li>

<li>Has a nice carousel option to display images.</li>

<li>Will try to use a carouse within CyNetShare to display multiple images when multiple nodes are selected by the end of the week. </li>

</ul>

<h3><b>2014 08 19 – Tuesday</b></h3>

<h3>Updates: </h3>

</ul>

<h3><b>2014 08 20 - Wednesday </b></h3>

<h3> Updates: </h3>

</ul>

<h3> Personal Status: </h3>

<h4> Huwate (Kwat) </h4>

<ul>

<li>Worked with JR on the below things.</li>

</ul>

<h3><b> 2014 08 21 – Thursday </b></h3>

<h3> Updates: </h3>

<ul>

<li>Database structure finished</li>

<ul>

<li>Please take a look at the database structure. It is finished. No more changes.</li>

<li>Fill out 199 form if you want academic credit</li>

</ul>

<h3><b> 2014 08 22 – Friday </b></h3>

<h3><b> 2014 08 26 – Tuesday </b></h3>

<h3> Updates: </h3>

</ul>

<h4> 2014 08 27 – Wednesday </h4>

<h3> Updates: </h3>

<ul>

<li>iGem apparel options are available. Thanks Justin!</li>

<li>Please fill out 199 by tomorrow.</li>

<li>Reviewed presentation.</li>

</ul>

<h3><b> 2014 08 28 – Thursday </b></h3>

<h3><b> 2014 08 29 – Friday </b></h3>

<!--------------- AUGUST ENDS HERE!!!!!!!!!!!------------------->