Team:BU Wellesley Software/G-nomeSurferPro

From 2011.igem.org

(Difference between revisions)
 
(39 intermediate revisions not shown)
Line 23: Line 23:
/*actual content styles*/
/*actual content styles*/
-
body {width: 860px; margin:auto;}
+
body {width: 800px; margin:auto;}
#bu-wellesley_wiki_content {height:auto; line-height:100%;}
#bu-wellesley_wiki_content {height:auto; line-height:100%;}
-
#bu-wellesley_wiki_content a {color:#69d01d;}
+
/*#bu-wellesley_wiki_content a {color:#69d01d;}*/
-
#bu-wellesley_wiki_content a:hover {text-decoration:none; color:#bababa;}
+
#bu-wellesley_wiki_content a:hover {text-decoration:none; color:#3d3f3c;}
-
</style>
+
.navbar li {color: #ffffff;}
-
<link rel="stylesheet" type="text/css" href="http://cs.wellesley.edu/~hcilab/iGEM_wiki/css/ProjectSpecific.css">
+
.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>
</head>
<body class="basiclayout">
<body class="basiclayout">
-
 
<div id="bu-wellesley_wiki_content">
<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>
<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>
-
<!-- "previous page" action -->
+
 
-
<a class="prev browse left"></a>
+
<ul id="nav">  
-
<!-- root element for scrollable -->
+
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Team">Team</a></li>  
-
<div class="scrollable" width="800px">  
+
<li><a href="#">Project</a>
-
  <div class="items">
+
<ul>
-
  <div id="comp">
+
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Project_Overview">Overview</a></li>
-
<h1>Computational Team</h1>
+
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Clotho">Clotho</a></li>
-
<!-- Comp people's content here-->
+
<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>
-
G-nome Surfer Pro is written in C# for the Microsoft Surface using the Surface SDK. State is managed using the ViewModel system and time consuming processes, like retrieving publications and running BLAST, are run in threads behind the main UI thread.
+
<li><a href="https://2011.igem.org/Team:BU_Wellesley_Software/Trumpet">Trumpet</a></li>
-
<br><br>
+
<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>G-nome Surfer Pro</h6>
 +
 
 +
<div id="tracking_nav">
 +
JUMP TO...<br>
 +
<a href="#bu-wellesley_wiki_content">Top</a><br>
 +
<a href="#overview">Tool Overview</a><br>
 +
<a href="#demo">Demo</a><br>
 +
<a href="#results">Results</a><br>
 +
<a href="#futurework">Future Work</a>
 +
</div>
 +
 
 +
 
 +
<div id="overview">
 +
<h1>Tool Overview</h1>  
 +
<p>
 +
G-nome Surfer Pro is an integrated environment for viewing prokaryotic genomic data and literature. Users can find genes on the chromosome wheel or search for a gene name or Genbank number, access Genbank notes and publications from Pubmed and view alignment and translation from the chromosome bar.  The extended desktop provides distraction free workspace for information processing and hypothesis formation. The Microsoft Surface allows users to collaborate in pairs and teams on design and research tasks.
 +
<p>
 +
<img style="width:800px" src="http://cs.wellesley.edu/~hcilab/iGEM_wiki/images/System/GSPro.jpg"/>
 +
G-nome Surfer Pro is written in C# for the <a href="http://www.microsoft.com/surface/en/us/default.aspx">Microsoft Surface</a> using the <a href="http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=15532">Surface SDK</a>. State is managed using the <a href="http://msdn.microsoft.com/en-us/magazine/dd419663.aspx">MVVM Architecture</a> and time consuming processes, like retrieving publications and running BLAST, are run in threads behind the main UI thread.
 +
<p>
After selecting a genome from the tree menu the chromosome bar is populated with genes from the GenBank file. Another genome can be selected at anytime from the pull down search menu.  
After selecting a genome from the tree menu the chromosome bar is populated with genes from the GenBank file. Another genome can be selected at anytime from the pull down search menu.  
-
<br><br>
+
<p>
-
The chromosome bar is infinitely scrolling and position on the chromosome bar is tied into the orientation of the chromosome wheel through the view-model system allowing manipulation of one to affect change of the other. GenBank files are parsed for sequence, translation and any notes, all of which are available as information objects, which are accessible from any gene on the bar.
+
The chromosome bar is infinitely scrolling and position on the chromosome bar is tied into the orientation of the chromosome wheel through the MVVM architecture allowing manipulation of one to affect change of the other. GenBank files are parsed for sequence, translation and any notes, all of which are available as information objects, which are accessible from any gene on the bar. Users can take genes on the bar directly into the <a href="https://2011.igem.org/Team:BU_Wellesley_Software/OptimusPrimer">Optimus Primer </a> surface application for primer design.
-
<br><br>
+
<p>
-
Information from any gene’s GenBank file are viewable as “ScatterViewItem” objects which can be moved and re-sized on the main “ScatterView” workspace. Users can view and annotate sequence/translation information by dragging and overlaying one over the other. All information objects can be moved to and from the extended desktop by dragging or tossing or erased by tossing them off the sides of the workspace. By moving objects between ScatterViews, users can view and organize data in a distraction free environment which can be pulled up over the main workspace or hidden from view.
+
Information from any gene’s GenBank file are viewable as “ScatterViewItem” objects which can be moved and re-sized on the main “ScatterView” workspace. Users can view and annotate sequence/translation information by dragging and overlaying one over the other. All information objects can be moved to and from the extended desktop by dragging or tossing or erased by tossing them off the sides of the workspace. <p>
-
<br><br>
+
Publications are populated in a scrollable list and can be dragged and dropped from the listBox to the main workspace or extended desktop through manipulation of the objects template.  The PubMed search results for the gene are fetched and parsed for abstracts, authors, and publication data.
 +
<p>
 +
By moving objects between ScatterViews, users can view and organize data in a distraction free environment which can be pulled up over the main workspace or hidden from view.
 +
<p>
Publications are populated in a scrollable list and can be dragged and dropped from the listBox to the main workspace or extended desktop through manipulation of the objects template.  The PubMed search results for the gene are fetched and parsed for abstracts, authors, and publication data.  
Publications are populated in a scrollable list and can be dragged and dropped from the listBox to the main workspace or extended desktop through manipulation of the objects template.  The PubMed search results for the gene are fetched and parsed for abstracts, authors, and publication data.  
-
<br><br>
 
-
In the Primer Genie workspace, alignment results are generated using java algorithm written by the software team, and BLAST results are generated using the NCBI BLAST software. Both are accessed from the command line, with BLAST results being written to file and parsed out for display and alignment results being pulled from common output for further calculation for hetero-dimer and self-dimer tests.
 
-
<img style="float:right; width:280px; height:200px" src="http://cs.wellesley.edu/~hcilab/iGEM_wiki/images/temp_placeholder.png"/>Integer at
 
-
 
-
<br><br>
 
-
 
-
<br><br><br>
 
-
<h5>Results:</h5>
 
-
 
-
<br><br>
 
-
<h5>Ethical User Study practices:</h5>
 
-
</div>
 
-
<div id="overview">
 
-
<h1>Overview: G-nome Surfer Pro</h1>
 
-
<h5>Hypothesis Forming</h5>
 
-
<br><br>
 
-
G-nome Surfer Pro is an integrated environment for viewing prokaryotic genomic data and literature. Users can find genes on the chromosome wheel or search for a gene name or Genbank number(?), access Genbank notes and publications from Pubmed and view alignment and translation from the chromosome bar.  The extended desktop provides distraction free workspace for information processing and hypothesis formation. The Microsoft Surface allows users to collaborate in pairs and teams on design and research tasks
 
-
<br><br>
 
-
Genes can be taken directly into the Primer Genie designer for primer design. In the Primer Genie workspace users can perform alignment related tests, BLAST and save designs as BioBricks. The system is designed for integration with the Clotho database.
 
-
 
-
<br><br>
 
-
<a href="#"><img id="download_button" src="http://cs.wellesley.edu/~hcilab/iGEM_wiki/images/temp_download_button.jpg"/></a>
 
-
<br><br><br><br><br><br><br>
 
-
<h5>Demo Video</h5>
 
</div>
</div>
-
<div id="wetlab">
+
 
-
<h1>Wetlab</h1>
+
<div id="demo">
-
Lorem ipsum dolor sit amet, consectetur adipiscing elit. In et dictum
+
<h1>Demo Video</h1>
-
leo. Maecenas porttitor augue nec arcu lacinia ultricies. Maecenas at
+
<p><a href="https://github.com/igemsoftware/BU_Wellesley_Software_2011/tree/master/G-nome-Surfer-Pro"><img id="download_button" src="http://cs.wellesley.edu/~hcilab/iGEM_wiki/images/temp_download_button.jpg" width="100px"/></a>
-
dictum augue. Proin eget odio ac mi tristique scelerisque.
+
<center><iframe width="560" height="345" src="http://www.youtube.com/embed/URUkqrdFV0k" frameborder="0" allowfullscreen></iframe></center>
-
<img style="width:400px; height:300px" src="http://cs.wellesley.edu/~hcilab/iGEM_wiki/images/temp_placeholder.png"/>Integer at
+
 
-
nisl nec purus laoreet condimentum sed semper dui. Duis feugiat, ligula
+
-
eu vehicula vulputate, sem nisl ornare neque, eu dictum lacus sapien
+
-
eu neque.
+
-
<br><br>
+
-
Vestibulum gravida, turpis tempus suscipit euismod, ipsum mi
+
-
tristique nibh, sed sagittis ante felis at urna. Suspendisse eu neque
+
-
vitae lorem elementum elementum sit amet ac ligula. Mauris vestibulum
+
-
Donec ac sapien erat. Proin id enim sed
+
-
dolor suscipit laoreet vitae sit amet ligula. Nam ultricies orci vitae
+
-
mauris egestas tincidunt. Vestibulum sit amet est dolor.
+
-
<br><br><br>
+
-
<h5>Results:</h5>
+
-
Ut eu nunc eget ante egestas egestas at eu metus. Integer quam justo,
+
-
vehicula non sodales id, consequat vitae eros.<br>
+
-
  Aenean egestas, ipsum sed fringilla porta, erat mi facilisis lectus, quis elementum quam felis nec elit.
+
-
+
-
  <br><br>
+
-
  <h5>Safety practices:</h5>
+
-
  Aliquam in felis sit amet eros pharetra volutpat.
+
</div>
</div>
-
 
 
-
  </div>
 
-
 
 
-
</div>
 
-
<!-- "next page" action -->
 
-
<a class="next browse right"></a>
 
-
 
-
<script>
 
-
// execute your scripts when the DOM is ready. this is mostly a good habit
 
-
$(function() {
 
-
// initialize scrollable
 
-
$(".scrollable").scrollable();
 
-
//move the scrollable content to show the middle section
+
<div id="results">
-
                        var api = $(".scrollable").data("scrollable");
+
<h1>Results</h1>
-
                        api.seekTo(1, 500);
+
<p>
-
});
+
We used G-nome Surfer Pro on the Microsoft surface to easily visualize the plasmid of TB myobacterium and choose the transcription factors we would like to use in our basic device. It also is linked to GenBank files to tell us the sequence of the gene of interest and the amino acids it codes for. In addition, we looked up more information about the transcription factors such as finding it in publications from the PubMed database.  This information was crucial to learn more about the transcription factors we were going to handle in the lab.
-
</script>
+
</div>
 +
 
 +
 
 +
<div id="futurework">
 +
<h1>Future Work</h1>
 +
<ul>
 +
<li> Integrate with the Clotho database.
 +
<li> Expand annotations to include GenBank notes and publications.  
 +
<li> Create save functionality for sessions and workspaces.
 +
<li> Allow users to export publications and annotations.</ul>
 +
</div>

Latest revision as of 20:01, 28 September 2011

BU-Wellesley iGEM Team: G-nome Surfer Pro


G-nome Surfer Pro

Tool Overview

G-nome Surfer Pro is an integrated environment for viewing prokaryotic genomic data and literature. Users can find genes on the chromosome wheel or search for a gene name or Genbank number, access Genbank notes and publications from Pubmed and view alignment and translation from the chromosome bar. The extended desktop provides distraction free workspace for information processing and hypothesis formation. The Microsoft Surface allows users to collaborate in pairs and teams on design and research tasks.

G-nome Surfer Pro is written in C# for the Microsoft Surface using the Surface SDK. State is managed using the MVVM Architecture and time consuming processes, like retrieving publications and running BLAST, are run in threads behind the main UI thread.

After selecting a genome from the tree menu the chromosome bar is populated with genes from the GenBank file. Another genome can be selected at anytime from the pull down search menu.

The chromosome bar is infinitely scrolling and position on the chromosome bar is tied into the orientation of the chromosome wheel through the MVVM architecture allowing manipulation of one to affect change of the other. GenBank files are parsed for sequence, translation and any notes, all of which are available as information objects, which are accessible from any gene on the bar. Users can take genes on the bar directly into the Optimus Primer surface application for primer design.

Information from any gene’s GenBank file are viewable as “ScatterViewItem” objects which can be moved and re-sized on the main “ScatterView” workspace. Users can view and annotate sequence/translation information by dragging and overlaying one over the other. All information objects can be moved to and from the extended desktop by dragging or tossing or erased by tossing them off the sides of the workspace.

Publications are populated in a scrollable list and can be dragged and dropped from the listBox to the main workspace or extended desktop through manipulation of the objects template. The PubMed search results for the gene are fetched and parsed for abstracts, authors, and publication data.

By moving objects between ScatterViews, users can view and organize data in a distraction free environment which can be pulled up over the main workspace or hidden from view.

Publications are populated in a scrollable list and can be dragged and dropped from the listBox to the main workspace or extended desktop through manipulation of the objects template. The PubMed search results for the gene are fetched and parsed for abstracts, authors, and publication data.

Demo Video

Results

We used G-nome Surfer Pro on the Microsoft surface to easily visualize the plasmid of TB myobacterium and choose the transcription factors we would like to use in our basic device. It also is linked to GenBank files to tell us the sequence of the gene of interest and the amino acids it codes for. In addition, we looked up more information about the transcription factors such as finding it in publications from the PubMed database. This information was crucial to learn more about the transcription factors we were going to handle in the lab.

Future Work

  • Integrate with the Clotho database.
  • Expand annotations to include GenBank notes and publications.
  • Create save functionality for sessions and workspaces.
  • Allow users to export publications and annotations.

Retrieved from "http://2011.igem.org/Team:BU_Wellesley_Software/G-nomeSurferPro"