Team:BU Wellesley Software/Notebook/MeganNotebook

From 2011.igem.org

(Difference between revisions)
(→Primers, Permutations, and Papers)
 
(71 intermediate revisions not shown)
Line 1: Line 1:
-
'''Welcome to my wiki!''' I am a first-year PhD student at [http://www.cs.tufts.edu/ Tufts University] studying Human-Computer Interaction. I recently graduated from [http://web.wellesley.edu/web Wellesley College] in May 2010. My research interests focus on how next-generation interaction techniques can support research through enhanced brainstorming and group collaboration. Previous to this summer, I worked on a multi-touch genome browser, [http://www.youtube.com/user/oshaer#p/u/2/me_Maa8xcGM G-nome Surfer], and a teaching tool for phylogenetics, [http://www.youtube.com/watch?v=zb09DCoXfV4 Phylo-Genie]. This summer I'm back at Wellesley as the student mentor to students on the development and engineering of multi-touch and tangible interaction software and tools, lead by [http://cs.wellesley.edu/~oshaer/ Dr. Orit Shaer] of the Wellesley [http://cs.wellesley.edu/~hcilab/ HCI laboratory] and [http://people.bu.edu/dougd/ Dr. Douglas Densmore] of the SynBio laboratory at [http://www.bu.edu/ Boston University].
+
<html>
 +
<head>
 +
<title>BU-Wellesley iGEM Team: Welcome</title>
 +
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
 +
<script src="http://cdn.jquerytools.org/1.2.5/full/jquery.tools.min.js?foo"></script>
 +
<style type="text/css">
 +
/*hide default igem banner and reformat style into blank slate*/
 +
#globalWrapper {width: 100%;}
 +
#top-section {width: 100%; height:30px; border:none;}
 +
#p-logo {display:none;}
 +
#search-controls {display:none;}
 +
#menubar a {color:#000000;}
 +
#menubar a:hover{text-decoration:none; color:#52749C;}
 +
.left-menu {background-color:#FFFFFF; margin:5px 0px 0px 0px; padding:0;}
 +
.left-menu ul {background-color:#FFFFFF; margin:0; padding:0;}
 +
.right-menu ul li a {background-color:#FFFFFF;}
 +
.printfooter {display:none;}
 +
#footer-box {border:none;}
 +
#catlinks {display:none;}
 +
.firstHeading {display:none;}
 +
#content {width: 100%; border:none;}
 +
#bodyContent {border:none;}
-
For daily updates on my work and lab events, '''find me on Twitter as [http://twitter.com/megankstrait megankstrait]'''.
+
/*actual content styles*/
 +
body {width: 800px; margin:auto;}
-
----
+
#bu-wellesley_wiki_content {height:auto; line-height:100%;}
 +
/*#bu-wellesley_wiki_content a {color:#69d01d;}*/
 +
#bu-wellesley_wiki_content a:hover {text-decoration:none; color:#3d3f3c;}
 +
.navbar li {color: #ffffff;}
 +
.navbar li a {color: #ffffff;}
 +
.navbar li a:hover {background:#69d01d; color: #ffffff;}
 +
/*only use for current page content header (i.e. Team, G-nomeSurferPro, etc)*/
 +
H6 {
 +
      font-family: Helvetica;
 +
      text-transform: uppercase;
 +
      text-decoration: none;
 +
      text-align: left;
 +
      color: #3d3f3c;
 +
      font-size: 32pt;
 +
    }
 +
 +
</style>
 +
 +
<link rel="stylesheet" type="text/css" href="http://cs.wellesley.edu/~hcilab/iGEM_wiki/css/Team.css">
 +
 +
</head>
 +
<body class="basiclayout">
 +
<div id="bu-wellesley_wiki_content">
 +
 +
<p  style="text-align:center;"><a href="https://2011.igem.org/Team:BU_Wellesley_Software"><img src="http://cs.wellesley.edu/~hcilab/iGEM_wiki/images/banner.png" width="800px"></a></p>
 +
 +
<ul id="nav">
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Team">Team</a></li>
 +
<li><a href="#">Project</a>
 +
<ul>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Project_Overview">Overview</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Clotho">Clotho</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/G-nomeSurferPro">G-nome Surfer Pro</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/OptimusPrimer">Optimus Primer</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Trumpet">Trumpet</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Puppetshow">Puppetshow</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/eLabNotebook">eLabNotebook</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Wet_Lab">Wet Lab</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Downloads_and_Tutorials">Downloads and Tutorials</a></li>
 +
</ul>
 +
</li>
 +
<li><a href="#">Process</a>
 +
<ul>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Methodology">Methodology</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Safety">Safety</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Notebook">Notebook</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Outreach">Outreach</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Tips">Tips and Tricks</a></li>
 +
</ul>
 +
</li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Gold">Medal Fulfillment</a></li>
 +
<li><a href="#">Additional Info</a>
 +
<ul>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Acknowledgement">Acknowledgement</a></li>
 +
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Social">Fun</a></li>
 +
</ul>
 +
</li>
 +
</ul>
 +
 +
<br>
 +
<h6>Megan's Notebook</h6>
 +
</body>
 +
</html>
 +
 +
<br />
 +
 +
[[File:Wellesley_Logo.gif|left|110px|caption]]'''Welcome to my wiki!''' I am a first-year PhD student at [http://www.cs.tufts.edu/ Tufts University] studying Human-Computer Interaction. I recently graduated from [http://web.wellesley.edu/web Wellesley College] in May 2010. My research interests focus on how next-generation interaction techniques can support research through enhanced brainstorming and group collaboration. Previous to this summer, I worked on a multi-touch genome browser, [http://www.youtube.com/user/oshaer#p/u/2/me_Maa8xcGM G-nome Surfer], and a teaching tool for phylogenetics, [http://www.youtube.com/watch?v=zb09DCoXfV4 Phylo-Genie]. This summer I'm back at Wellesley as the student mentor to students on the development and engineering of multi-touch and tangible interaction software and tools, lead by [http://cs.wellesley.edu/~oshaer/ Dr. Orit Shaer] of the Wellesley [http://cs.wellesley.edu/~hcilab/ HCI laboratory] and [http://people.bu.edu/dougd/ Dr. Douglas Densmore] of the SynBio laboratory at [http://www.bu.edu/ Boston University]. For daily updates on my work and lab events, '''find me on Twitter at [http://twitter.com/megankstrait megankstrait]'''.
 +
 +
<br />
 +
 +
<html>
 +
<div align="left">
 +
<script src="http://widgets.twimg.com/j/2/widget.js"></script>
 +
<script>
 +
new TWTR.Widget(
 +
{
 +
    version: 2,
 +
    type: 'profile',
 +
    rpp: 3,
 +
    interval: 6000,
 +
    width: 965,
 +
    height: 300,
 +
    footer: "follow me",
 +
    theme:
 +
    {
 +
          shell:
 +
          {
 +
              background: '#60BE1B',
 +
              color: '#ffffff'
 +
          },
 +
          tweets:
 +
          {
 +
              background: '#ffffff',
 +
              color: '#005566',
 +
              links: '#E2D61B'
 +
          }
 +
    },
 +
    features:
 +
    {
 +
          scrollbar: false,
 +
          loop: false,
 +
          live: false,
 +
          hashtags: true,
 +
          timestamp: true,
 +
          avatars: false,
 +
          behavior: 'all'
 +
    }
 +
}
 +
).render().setUser('megankstrait').start();
 +
</script>
 +
</div>
 +
</html>
 +
 +
<br />
 +
----
 +
<br />
== Bootcamp ==
== Bootcamp ==
Line 17: Line 154:
===== Bio Basics =====
===== Bio Basics =====
-
Wednesday began the BU-Wellesley iGEM bootcamp. For the next three days, we received a year's dose of biology basics well organized and delivered by our wet lab leader, Traci Haddock. Primers, permutations, invertase and in vitro - we covered the basics to catch the comp team students (including me) up to speed on the terminology, experiments, and tools (both physical and digital) employed by synthetic biologists.  
+
* Lead by wet lab leader, [https://2011.igem.org/Team:BU_Wellesley_Software/Notebook/TraciNotebook Traci Haddock] we learned the basics to catch everyone up to speed on the terminology, experiments, and tools (both physical and digital) employed by synthetic biologists.
===== CAD, Clotho, and Community =====
===== CAD, Clotho, and Community =====
Line 24: Line 161:
*
*
-
== Device, Spice, and Mice ==
+
== Mices and Devices ==
-
''06.06 - 06.10'' : We focused this week on developing the multi-touch interaction for a prokaryotic genome browser. Check out our [http://www.youtube.com/watch?v=PM8hbKfU5iI prototype]!
+
''06.06 - 06.10'' : Week 2, we focused on developing the multi-touch interaction for a prokaryotic genome browser. [https://2011.igem.org/Team:BU_Wellesley_Software/Notebook/MikeyNotebook Mikey], Kathy, and I brainstormed visualizations and types of touch interactions. Based on Kathy's research into conventional representations and Mikey's exploration of [http://circos.ca/ Circos], [http://mkweb.bcgsc.ca/schemaball/ Schemaball], and several other circular visualization softwares, we came up with a pen and paper [http://www.youtube.com/watch?v=PM8hbKfU5iI prototype]. Our main constraints/advantages is developing for a touch-based computational ''device'' to explore biological ''devices'' of varying scale and properties.
== G-nome Surfer Pro ==
== G-nome Surfer Pro ==
Line 31: Line 168:
===== Prokaryotic Parser =====
===== Prokaryotic Parser =====
 +
*
 +
===== Publications and Plasmids =====
===== Publications and Plasmids =====
===== Sequence and Search =====
===== Sequence and Search =====
Line 47: Line 186:
== Primers, Permutations, and Papers ==
== Primers, Permutations, and Papers ==
''06.27 - 07.01'' : Monday the entire comp. team along with Traci collected at Wellesley for a day of brainstorming and demos.
''06.27 - 07.01'' : Monday the entire comp. team along with Traci collected at Wellesley for a day of brainstorming and demos.
 +
 +
== Development and Analysis ==
 +
''07.05 - 07.08'' : tba
 +
 +
<br /><br /><br />
 +
 +
== Current Work ==
 +
*
 +
*
 +
*

Latest revision as of 18:40, 28 September 2011

BU-Wellesley iGEM Team: Welcome


Megan's Notebook


caption
Welcome to my wiki! I am a first-year PhD student at [http://www.cs.tufts.edu/ Tufts University] studying Human-Computer Interaction. I recently graduated from [http://web.wellesley.edu/web Wellesley College] in May 2010. My research interests focus on how next-generation interaction techniques can support research through enhanced brainstorming and group collaboration. Previous to this summer, I worked on a multi-touch genome browser, [http://www.youtube.com/user/oshaer#p/u/2/me_Maa8xcGM G-nome Surfer], and a teaching tool for phylogenetics, [http://www.youtube.com/watch?v=zb09DCoXfV4 Phylo-Genie]. This summer I'm back at Wellesley as the student mentor to students on the development and engineering of multi-touch and tangible interaction software and tools, lead by [http://cs.wellesley.edu/~oshaer/ Dr. Orit Shaer] of the Wellesley [http://cs.wellesley.edu/~hcilab/ HCI laboratory] and [http://people.bu.edu/dougd/ Dr. Douglas Densmore] of the SynBio laboratory at [http://www.bu.edu/ Boston University]. For daily updates on my work and lab events, find me on Twitter at [http://twitter.com/megankstrait megankstrait].




Contents

Bootcamp

05.31 - 06.03 : This is week 1 of our work towards the International Genetically Engineered Machine competition in synthetic biology. We have a lot of excitement, but a lack of experience. Thus the BU team leaders have put together a bio bootcamp to take everyone bio 101, software support, and outreach opportunities in three days.

Technology Tour
  • Tuesday, we welcomed our three newest members - Kelsey, Casey, and Kathy - to the HCI laboratory with a tour of the technology and tools.
  • New students and current iPhone programmers worked on "Hello World", Microsoft Surface style.
  • Kathy, our resident bio-enthusiast and expert, started a survey of state-of-the-art genomics tools and molecular infographics.
Bio Basics
  • Lead by wet lab leader, Traci Haddock we learned the basics to catch everyone up to speed on the terminology, experiments, and tools (both physical and digital) employed by synthetic biologists.
CAD, Clotho, and Community

Mices and Devices

06.06 - 06.10 : Week 2, we focused on developing the multi-touch interaction for a prokaryotic genome browser. Mikey, Kathy, and I brainstormed visualizations and types of touch interactions. Based on Kathy's research into conventional representations and Mikey's exploration of [http://circos.ca/ Circos], [http://mkweb.bcgsc.ca/schemaball/ Schemaball], and several other circular visualization softwares, we came up with a pen and paper [http://www.youtube.com/watch?v=PM8hbKfU5iI prototype]. Our main constraints/advantages is developing for a touch-based computational device to explore biological devices of varying scale and properties.

G-nome Surfer Pro

06.13 - 06.17 :

Prokaryotic Parser
Publications and Plasmids
Sequence and Search

Birthday BLAST

06.20 - 06.24 : Already week 4, already mid mid 20's! My mentor and lab mates, new and old, surprised me with cake and gifts to celebrate the new week and my old age. The focus this week was to finish the adaption of G-nome Surfer to visualize prokaryotic data and to design Primer BLAST for the Surface. This included

Twitter
Twitter Bomb

Defined as spam tweeting one particular topic to the twittersphere. Especially when making it a trending topic.

Twitter Blast

Defined as having a blast on twitter.

Primers, Permutations, and Papers

06.27 - 07.01 : Monday the entire comp. team along with Traci collected at Wellesley for a day of brainstorming and demos.

Development and Analysis

07.05 - 07.08 : tba




Current Work

Retrieved from "http://2011.igem.org/Team:BU_Wellesley_Software/Notebook/MeganNotebook"