Team:Freiburg software

From 2009.igem.org

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=Project Summary=
=Project Summary=
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==SynBioWave==
==SynBioWave==
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Synthetic Biology aims at constructing whole new genomes. Such an effort is pushed forward by many users and relies on modular combination of genetic elements. The genetic elements represent an increasing complexity by assembling parts to devices and then systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We propose to build a user environment able to analyze and construct genetic parts and ultimately genomes.
Synthetic Biology aims at constructing whole new genomes. Such an effort is pushed forward by many users and relies on modular combination of genetic elements. The genetic elements represent an increasing complexity by assembling parts to devices and then systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We propose to build a user environment able to analyze and construct genetic parts and ultimately genomes.
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We will build the software suite on the Google-Wave format, which is currently in beta testing, and add molecular biology tools mainly from the BioJava library. The first goal is to provide basic molecular biology cloning functionality which appeals to the wet bench scientist. On top of that, we would like to add specific synthetic biology functionality such as biobrick database access and part annotation. The software for the Jamboree will not be feature complete, but demonstrate the principle use, with some molecular biology standard tasks, as well as the power of the wave approach for a distributed collaborative synthetic biology effort. Many wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico.
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Our concept is to create a collaborative web application called SynBioWave for synthetic biology purpose. Based on Google Wave and extended with molecular biology tools from the BioJava library, SynBioWave gives synthetic biological research access to the collaborative and interactive web 2.0.
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SynBioWave makes use of Wave's powerful communication and collaboration functionality and is designed to be be easily extended with new synthetic biology functionality. Mashing up the reinvention of the email with a major library for processing synthetic biology data, raises science collaboration to a new level.
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Our small team of three developers is not be able to create a feature complete software by iGEM Jamboree 2009. Our goal is to lay the foundation for a robust software suite and to implement some basic synthetic biological functionality to demonstrate the the principle use, with some molecular biology standard tasks, as well as the power of the wave approach for a distributed collaborative synthetic biology effort.
The first developments of 'SynBioWave' will lay the ground for a useful grouping of functionality for wave-robots, how the calling of robots and their functions is managed, how robots act on DNA or protein sequences, how intermediate results are stored, etc... The process should be open and clear so that users can add and share robots useful for synthetic biology.
The first developments of 'SynBioWave' will lay the ground for a useful grouping of functionality for wave-robots, how the calling of robots and their functions is managed, how robots act on DNA or protein sequences, how intermediate results are stored, etc... The process should be open and clear so that users can add and share robots useful for synthetic biology.

Revision as of 18:37, 18 October 2009

Project Summary

SynBioWave

Freiburg software SynBioWave-look-and-feel.png

Synthetic Biology aims at constructing whole new genomes. Such an effort is pushed forward by many users and relies on modular combination of genetic elements. The genetic elements represent an increasing complexity by assembling parts to devices and then systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We propose to build a user environment able to analyze and construct genetic parts and ultimately genomes.

Our concept is to create a collaborative web application called SynBioWave for synthetic biology purpose. Based on Google Wave and extended with molecular biology tools from the BioJava library, SynBioWave gives synthetic biological research access to the collaborative and interactive web 2.0.

SynBioWave makes use of Wave's powerful communication and collaboration functionality and is designed to be be easily extended with new synthetic biology functionality. Mashing up the reinvention of the email with a major library for processing synthetic biology data, raises science collaboration to a new level.

Our small team of three developers is not be able to create a feature complete software by iGEM Jamboree 2009. Our goal is to lay the foundation for a robust software suite and to implement some basic synthetic biological functionality to demonstrate the the principle use, with some molecular biology standard tasks, as well as the power of the wave approach for a distributed collaborative synthetic biology effort.

The first developments of 'SynBioWave' will lay the ground for a useful grouping of functionality for wave-robots, how the calling of robots and their functions is managed, how robots act on DNA or protein sequences, how intermediate results are stored, etc... The process should be open and clear so that users can add and share robots useful for synthetic biology.