SynBioWave: Google Wave extension for synthetic biology

Project SynBioWave, the Google Wave extension for synthetic biology developed by a team of students from Albert Ludwigs University Freiburg. I must accept that team has done excellent job with wave and it is one of the best wave extensions for scientists out there (see a list of wave applications for the scientist at the end of the article). Concept is to develop a Google wave based collaborative environment for synthetic biology which will enable multiple distributed users to analyze and construct genetic parts in real time. Apart from Google Wave environment SynBioWave is using two other technologies: BioJava andQooxdoo. In following image you can see the whole architecture of the SynBioWave.

SynBioWave Conceptual Architecture Flowchart

In order to create a basic wave functionality for the different molecular biology tasks such as cloning, team is using BioJava library. BioJava enables the processing of biological data such as sequences and 3D structures, while Qooxdoo is used to to extend Wave's graphical user interfaces (GUI) with custom tool bars, buttons, forms, context-menus for SynBioWave application. Team has also introduced a qooxWave protocol for creating custom client side GUI inside a wave from a server side robot.

SynBioWave's qooxWave protocol

Sequence manipulation from Google Wave
So what type things you can do with SynBioWave? Development of SynBioWave is currently in early stage, but still you can to several things such as visualizing your sequence data, compare your sequence data or multiple sequence alignment. SynBioWave supports multiple views for visualize the sequence information in a intuitive way, not to mention the automated sequence coloring feature.

Three Sequence Views: Simple, Gadget and Circular

There is a simple view for short sequences typed or copied directly to the wave and a embedded gadget view for longer sequences and sequence comparisons like for example in multiple sequence alignments. Both views providing a clearly represented scaling and increase readability by automatically colorizing the sequences according to the sequence type. And in the end there is a circular view for displaying fully featured circular dna as needed for example in displaying vectors and plasmids.

BLAST from Google Wave
Further there is a BLAST robot which can BLAST the biological sequence information against available resources and further process the received Blast-hits.

So where will this lead us? Google Wave development for life scientists is now moving into next level. SynBioWave and other extensions (listed in the end) are making their way for the next generation of scientific engagement and collaboration.

List of wave applications for the scientists