Team:Berkeley Software

From 2009.igem.org

(Difference between revisions)
 
(82 intermediate revisions not shown)
Line 1: Line 1:
-
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
+
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert ***  
 +
Keep commented out for now, for reference ~JC
<html>
<html>
Line 15: Line 16:
</html>
</html>
-
<!-- *** End of the alert box *** -->
+
*** End of the alert box *** -->
 +
{{Template:BerkeleySoftwareHeader}}
 +
<!---<H1><center>Welcome to the Berkeley Software team's wiki.  Our wiki is currently under construction.  We apologize for its temporarily disorganized state.</center></H1>-->
 +
<!-- <div id="placeholder" style="width: 700px; height: 500px; margin-left: auto; margin-right: auto; border: 3px solid #000; background-color: #EEEEEE;">
 +
<br /><br /><br /><br /><br /><br />
 +
<center>image placeholder</center>
 +
</div> -->
 +
<div id="placeholder" style="width: 700px; height: 500px; margin-left: auto; margin-right: auto; background-color: #EEEEEE;">
 +
{{imageMap|imap|/wiki/images/0/01/BerkeleySoftware_MainImage.jpg|700|500|
 +
{{imageMapLink|Kepler|291|2|329|430|/wiki/images/2/2e/BerkeleySoftware_KeplerFocus.jpg}}
 +
{{imageMapLink|DataModel|245|337|274|163|/wiki/images/1/15/BerkeleySoftware_DataModelFocus.jpg}}
 +
{{imageMapLink|Clotho|50|97|386|374|/wiki/images/a/ac/BerkeleySoftware_ClothoFocus.jpg}}
 +
{{imageMapLink|Eugene|221|169|113|196|/wiki/images/8/85/BerkeleySoftware_EugeneFocus.jpg}}
 +
{{imageMapLink|Spectacles|178|163|81|93|/wiki/images/b/b5/BerkeleySoftware_SpectaclesFocus.jpg}}
 +
}}<html><center>
 +
<ul id="imap">
 +
<li id="Kepler"></html>[[Team:Berkeley_Software/Kepler|Kepler]]<html></li>
 +
<li id="DataModel"></html>[[Team:Berkeley_Software/Data_Model|Data Model]]<html></li>
 +
<li id="Clotho"></html>[[Team:Berkeley_Software/Project|Project]]<html></li>
 +
<li id="Eugene"></html>[[Team:Berkeley_Software/Eugene|Eugene]]<html></li>
 +
<li id="Spectacles"></html>[[Team:Berkeley_Software/Spectacles|Spectacles]]<html></li>
 +
</ul>
 +
</center></html>
-
{|align="justify"
+
</div>
-
|Welcome to the UC Berkeley computational iGEM team wiki.  
+
 
-
|[[Image:Example_logo.png|200px|right|frame]]
+
<center><b><h2>Welcome to the 2009 iGEM UC Berkeley Software Team Wiki.</h2></b></center>
-
|-
+
 
-
|
+
<font size="4">S</font>ynthetic biology promises to introduce a new paradigm to the biological world. One which is less of a design science and more of an engineering discipline. In order to fulfill this promise, a set of core design activities must be made more amenable to design automation techniques. The first step requires identifying DNA sequences of interest and packaging them as "standard parts". Once these parts have been created, the next step is to construct composite "devices". Finally, devices must be physically created with samples in the lab. Each of these stages has a number of sub-problems and each is equally important in the overall design process. Our project focuses on the latter two processes, ''device creation and physical assembly''. This web page has been designed to introduce you to our project so that you can not only learn more about our activities and use the associated tools but also contribute and collaborate with us! Specifically, our project is organized around the development of three tools:
-
As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well along with making the process easier, more standardized, and powerful. Our project attempts to address three key computational needs of the synthetic biology community:
+
 
-
# Create a robust set of application programming interfaces (APIs) which create a common framework so that individual independent software tools can communicate with each other as well as communicate with data repositories. This is accomplished with a completely revamped [[clothocad.com '''Clotho''']] based framework.
+
*<font size="4">[[Team:Berkeley_Software/Eugene|Eugene]]</font> - A domain specific language for the specification of biological constructs.
-
# Integrate formalized workflow capture programs with synthetic biology assembly protocols. This is accomplished by extending the '''Kepler Workflow Management System'''.
+
 
 +
*<font size="4">[[Team:Berkeley_Software/Spectacles|Spectacles]]</font> - A visual editing framework for the design of composite biological devices and the assignment of physical samples to functional concepts.
 +
 
 +
*<font size="4">[[Team:Berkeley_Software/Kepler|Kepler Integration]]</font> - Development of actors and automated assembly processes for the scientific workflow management system Kepler.
 +
 
 +
While each of these efforts is powerful in its own right, together they form the basis for a complete design framework. To accomplish this integration, the [https://2008.igem.org/Team:UC_Berkeley_Tools Clotho design environment] and its core set of [[Team:Berkeley_Software/Data_Model|APIs have been revamped]] to accommodate these efforts. This not only makes the design process easy for today but paves the way to future designs.
 +
 
 +
We encourage you now to check out the site, play with the tools, and ask questions. Our intention is for this to be a community effort. We have worked with [[Team:Stanford|Stanford University]], the [http://synbioss.sourceforge.net/ University of Minnesota], the [http://www.sys-bio.org University of Washington], the [http://www.jbei.org Joint BioEnergy Institute], and [http://research.microsoft.com/en-us/um/people/thies/iwbda09-slides.pdf Microsoft Research India] to create a truly collaborative environment. You could be next. So think of a tool to create, a suggestion to make, or a problem to solve!
 +
 
 +
 
 +
<center><b>Berkeley iGEM Software Team 2009</b></center>
 +
 
 +
<center><i>Lesia, Joanna, Adam, Richard, Thien, Nina, Bing, and Doug</i></center>
 +
 
 +
 
 +
<!-- Old blurb; kept for reference
 +
 
 +
Welcome to the UC Berkeley computational iGEM team wiki.
 +
 
 +
As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well. If done properly this will make the design process easier, standardized, collaborative, and ultimately much more powerful. Our project attempts to address three key computational needs in the synthetic biology community:
 +
# Create a robust set of application programming interfaces (APIs) which create a common framework so that individual independent software tools can communicate with each other as well as communicate with data repositories. This is accomplished with a completely revamped [http://www.clothocad.com '''Clotho'''] based framework.
 +
# Integrate formalized workflow design programs with synthetic biology assembly protocols. This is accomplished by extending the [https://kepler-project.org '''Kepler Workflow Management System'''].
# Raise the level of abstraction by which designs are specified, shared, and visualized. This is accomplished by the design of a domain specific language called '''Eugene''' and a design tool called '''Spectacles'''.
# Raise the level of abstraction by which designs are specified, shared, and visualized. This is accomplished by the design of a domain specific language called '''Eugene''' and a design tool called '''Spectacles'''.
-
|[[Image:Team.png|right|frame|Your team picture]]
 
-
|-
 
-
|
 
-
|align="center"|[[Team:Berkeley_Software | Team Example]]
 
-
|}
 
-
<!--- The Mission, Experiments --->
+
In addition to these goals our project really attempts to build an inter-university/industry approach by collaborating with researchers at Stanford, the University of Minnesota, Davidson, Washington, and Microsoft Research India.
 +
-->
 +
 
 +
<b><h2>Sponsors</h2></b>
 +
<center><div>
 +
<html>
 +
<a href="http://www.cdc-computing.org/">
 +
<img src="https://static.igem.org/mediawiki/2009/e/ec/BerkeleySoftware_CDCLogo.png" height="85">
 +
</a>
 +
<a href="http://www.nsf.com">
 +
<img src="https://static.igem.org/mediawiki/2009/e/e5/BerkeleySoftware_NSFLogo.png" height="85">
 +
</a>
 +
<a href="http://chess.eecs.berkeley.edu/">
 +
<img src="https://static.igem.org/mediawiki/2009/4/46/BerkeleySoftware_ChessLogo.png" height="85">
 +
</a>
 +
<a href="http://www.synberc.org/">
 +
<img src="https://static.igem.org/mediawiki/2009/e/e2/BerkeleySoftware_SynBERCLogo.png" height="85">
 +
</a>
 +
<a href="http://qb3.org/index.html">
 +
<img src="https://static.igem.org/mediawiki/2009/0/0c/BerkeleySoftware_qb3Logo.png" height="85">
 +
</a>
 +
</html>
 +
</div></center>
-
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
+
<!-- this will eventually be removed -->
-
!align="center"|[[Team:Berkeley_Software|Home]]
+
<!--
-
!align="center"|[[Team:Berkeley_Software/Team|The Team]]
+
Pages:
-
!align="center"|[[Team:Berkeley_Software/Project|The Project]]
+
<ul>
-
!align="center"|[[Team:Berkeley_Software/Parts|Parts Submitted to the Registry]]
+
    <li>[[Team:Berkeley_Software/Project|The Project]]</li>
-
!align="center"|[[Team:Berkeley_Software/Modeling|Modeling]]
+
    <ul>
-
!align="center"|[[Team:Berkeley_Software/Notebook|Notebook]]
+
        <li>[[Team:Berkeley_Software/Data_Model|Data Model]]</li>
-
|}
+
        <li>[[Team:Berkeley_Software/Eugene|Eugene]]</li>
-
(''Or you can choose different headings.  But you must have a team page, a project page, and a notebook page.'')
+
        <li>[[Team:Berkeley_Software/Spectacles|Spectacles]]</li>
 +
        <li>[[Team:Berkeley_Software/Kepler|Kepler]]</li>
 +
    </ul>
 +
    <li>[[Team:Berkeley_Software/Team|The Team]]</li>
 +
    <ul>
 +
        <li>[[Team:Berkeley_Software/Notebook|Notebook]]</li>
 +
    </ul>
 +
    <li>[[Team:Berkeley_Software/Downloads|Downloads]]</li>
 +
    <li>[[Team:Berkeley_Software/Misc|Miscellaneous]]</li>
 +
</ul>
 +
-->

Latest revision as of 17:36, 21 October 2009


Welcome to the 2009 iGEM UC Berkeley Software Team Wiki.

Synthetic biology promises to introduce a new paradigm to the biological world. One which is less of a design science and more of an engineering discipline. In order to fulfill this promise, a set of core design activities must be made more amenable to design automation techniques. The first step requires identifying DNA sequences of interest and packaging them as "standard parts". Once these parts have been created, the next step is to construct composite "devices". Finally, devices must be physically created with samples in the lab. Each of these stages has a number of sub-problems and each is equally important in the overall design process. Our project focuses on the latter two processes, device creation and physical assembly. This web page has been designed to introduce you to our project so that you can not only learn more about our activities and use the associated tools but also contribute and collaborate with us! Specifically, our project is organized around the development of three tools:

  • Eugene - A domain specific language for the specification of biological constructs.
  • Spectacles - A visual editing framework for the design of composite biological devices and the assignment of physical samples to functional concepts.
  • Kepler Integration - Development of actors and automated assembly processes for the scientific workflow management system Kepler.

While each of these efforts is powerful in its own right, together they form the basis for a complete design framework. To accomplish this integration, the Clotho design environment and its core set of APIs have been revamped to accommodate these efforts. This not only makes the design process easy for today but paves the way to future designs.

We encourage you now to check out the site, play with the tools, and ask questions. Our intention is for this to be a community effort. We have worked with Stanford University, the [http://synbioss.sourceforge.net/ University of Minnesota], the [http://www.sys-bio.org University of Washington], the [http://www.jbei.org Joint BioEnergy Institute], and [http://research.microsoft.com/en-us/um/people/thies/iwbda09-slides.pdf Microsoft Research India] to create a truly collaborative environment. You could be next. So think of a tool to create, a suggestion to make, or a problem to solve!


Berkeley iGEM Software Team 2009
Lesia, Joanna, Adam, Richard, Thien, Nina, Bing, and Doug


Sponsors


Retrieved from "http://2009.igem.org/Team:Berkeley_Software"