Team:Berkeley Software

From 2009.igem.org

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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

@@ Line 46: / Line 46: @@
 <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:
+<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:
 *<font size="4">[[Team:Berkeley_Software/Eugene|Eugene]]</font> - A domain specific language for the specification of biological constructs.
@@ Line 54: / Line 54: @@
 *<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.
+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!