Revision as of 23:54, 21 October 2009

Project Summary

Team Freiburg Software

As the first German software team we are proud to present our ambitious project, a synthetic biological software suite, based on Google's collaboration and communication tool Wave. Announced as the reinvention of the email, chat and wiki, Wave represents an extensible, modular and real-time collaboration platform. On this basis, we built a suite for collaborative synthetic biology research comprising parts design and documentation. To reflect the symbioses of Wave with synthetic biological tools, our software is called SynBioWave.

Abstract

Synthetic Biology, which aims at constructing whole new genomes, is pushed forward by many users and relies on the assembly of genetic elements to devices and later systems. The construction process needs to be transparent and even at final stages control at the basepair level is required. We are building a software environment enabling multiple distributed users to analyze and construct genetic parts and ultimately genomes with real-time communication. Our current version demonstrates the principle use as well as the power of the underlying Google Wave protocol for collaborative synthetic biology efforts. Many wave-robots with a manageable set of capabilities will divide and conquer the complex task of creating a genome in silico. The initial developments of 'SynBioWave' lay the ground for basic layout, calling and data exchange of wave-robots in a clear and open process, so that future robots can be added and shared easily.

SynBioWave

We have created an open-source, synthetic biological software suite called SynBioWave. Based on Google's communication tool Wave, SynBioWave is made for collaborative synthetic biology research comprising parts design and documentation. Moreover, biologists can record and share the process of creating research data and perform basic tasks using SynBioWave. This gives synthetic biological research access to the collaborative and interactive web 2.0.

To create this collaborative web based software for synthetic biology research, we created a software interface on top of Google Wave. This included the work on displaying biological sequence data, importing and exporting such data from different sources, supporting a large range of sequence formats, such as FASTA, GenBank and EMBL. To realise the implementation, we even invented a communication protocol called qooxWave. We were faced the problem of multi-robot communication and how to extend wave's user interface for our purpose.

The result of four month development is enjoyable! We have extended Wave to handle synthetic biological data. Biologists can not only document research results, but also record and share the process of creating these. Moreover scientists can collaboratively perform basic biosynthetic tasks using SynBioWave.

Our small team of three developers is not able to create a feature complete software for 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 principle use, with some molecular biology standard tasks. Moreover, we want to demonstrate the power of the wave approach for a distributed collaborative synthetic biology effort.

Quickstart

The Project A detailed project description including SynBioWave and the presentation of our work
The Code A repository of important classes plus an archive with all code we wrote
User GuideYou want to try out SynBioWave? Have a look here!

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 [[Image:Freiburg_software_SynBioWave-look-and-feel.png|550px|right]]
-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 but, at the same time, is designed to 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.
+We have created an open-source, '''synthetic biological software suite''' called SynBioWave. Based on Google's communication tool Wave, SynBioWave is made for '''collaborative synthetic biology research''' comprising parts design and documentation. Moreover, biologists can record and share the process of creating research data and perform basic tasks using SynBioWave. This gives synthetic biological research access to the collaborative and interactive web 2.0.
+To create this collaborative web based software for synthetic biology research, we created a software interface on top of Google Wave. This included the work on displaying biological sequence data, importing and exporting such data from different sources, supporting a large range of sequence formats, such as FASTA, GenBank and EMBL. To realise the implementation, we even invented a communication protocol called qooxWave. We were faced the problem of multi-robot communication and how to extend wave's user interface for our purpose.
+The result of four month development is enjoyable! We have extended Wave to handle synthetic biological data. Biologists can not only document research results, but also record and share the process of creating these. Moreover scientists can collaboratively perform basic biosynthetic tasks using SynBioWave.
 Our small team of three developers is not able to create a feature complete software for 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 principle use, with some molecular biology standard tasks. Moreover, we want to demonstrate the power of the wave approach for a distributed collaborative synthetic biology effort.

Team:Freiburg software

From 2009.igem.org