SynBioWave: Google Wave extension for synthetic biology

10.21.2009 // iGEM2009, Popular, Synthetic Biology, Technology // abhishektiwari // 13 Comments

As I mentioned in my previous posts that for next few days we are going to cover various interesting activities related to iGEM 2009 and selected student projects will be featured on the Fisheye Perspective blog. Next in our list is 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 and Qooxdoo. 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.
and many more
There is another BioBrick robot which integrates different assembly-algorithms and enables the DAS communication with BioBrick database for genetic part import and upload in compliance with BioBrick standards. Further team is developing an Eclipse-plugin for SynBioWave-developers and several other robots.

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

1. SynBioWave Robot for Synthetic Biology (synbiowave@appspot.com)
2. BLAST Robot (blastrobot@appspot.com)
3. ChemSpidey- A Google Wave Robot for displying chemical structures and molecular weight calculation (chemspidey@appspot.com)
4. CDKitty -A Google Wave robot for CDK functionality (chemdevelkit@appspot.com)
5. Igor – A Google Wave robot to manage your references (helpmeigor@appspot.com )
6. Watexy- A Google wave robot for Latex writing (watexy@appspot.com)
7. A proteomics robot for Google Wave (systems-biology-data@appspot.com)
8. CodeBot – A Coding Robot for Google Wave (codebot-wave@appspot.com)

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13 Responses to “SynBioWave: Google Wave extension for synthetic biology”

1. 

   chris bailey

   10.21.2009

   At my college we use a different tool for working on our projects online.
   Its free and needs no installation since its online, go to http://www.showdocument.com
   pretty useful for me since i usually do my projects on the laptop. -chrisman
2. 

   chris bailey

   10.21.2009

   At my college we use a different tool for working on our projects online.
   Its free and needs no installation since its online, go to http://www.showdocument.com
   pretty useful for me since i usually do my projects on the laptop. -chrisman
3. 

   shahir shamsir

   10.27.2009

   RT @tweetmeme SynBioWave: Google Wave extension for synthetic biology- by Fisheye Perspective http://retwt.me/1epPu
4. 

   Mike Spear

   10.27.2009

   RT@karsten RT @InterfaceSynBio: SynBioWave: Google Wave extension for synthetic biology http://j.mp/4vJ6vc #genomics
5. 

   Ricardo Vidal

   10.28.2009

   I was thinking about this… RT @interfacesynbio: SynBioWave: Google Wave extension for synthetic biology http://j.mp/4vJ6vc
6. 

   Ricardo Vidal

   10.28.2009

   SynBioWave: Google Wave extension for synthetic biology- by Fisheye Perspective http://ff.im/-aCuuK
7. 

   Peter Scott

   10.28.2009

   [GWaveBlogs] SynBioWave: Google Wave extension for synthetic biology- by Fisheye Perspective http://ow.ly/15XKG5
8. 

   Joshua Havumaki

   10.28.2009

   @rvidal RT SynBioWave: Google Wave extension for synthetic biology- by Fisheye Perspective http://ff.im/-aCuuK
9. 

   Abhishek Tiwari

   11.02.2009

   Freiburg iGEM Team got to goldy and final for SynBioWave, I blogger about this earlier http://bit.ly/68ibO
10. 

    Abhishek Tiwari

    11.02.2009

    Freiburg iGEM Team got to goldy and final for SynBioWave, I blogged about this earlier http://bit.ly/68ibO
11. 

    Khurram Chaudhry

    11.08.2009

    RT @tweetmeme SynBioWave: Google Wave extension for synthetic biology- by Fisheye Perspective http://retwt.me/1epPu
12. 

    kimmy

    12.06.2009

    Bioinfomaticsの人たちは、反応が早くいようでBLASTのwave gadgetをつくってました。http://bit.ly/7Ccbim @kitayamatakeshi
13. 

    Eldon Schneider

    01.14.2010

    Fairly discussed the features of google wave in relation to biology applications. Great effort for simplifying the important points. Appreciated this post a lot.