Saturday, June 14, 2008

Zebrafish Genome Wiki > Vision

I had blogged about the Zebrafish GenomeWiki a couple of days back and people had been asking what is the vision or blueprint for the system.

I had put up a schematic representation on what would the system be for the Zebrafish Genome Community. I am replicating it with this post.

So I thought I would compile them for you.

What we WOULD be doing

Create a portal for community annotation of the Zebrafish Genome.o
Create a Wiki based solution and see how it works for community annotation of genomics data (nobody has created one so far !)
Create a vibrant community that would help understand the Biology of this unique model organism better
Create a system for giving credits to participants in Community Annotation
Make available the entire data for bulk download and data mining
Work towards standards for data definitions and free and collaborative annotation
Work towards open standards for content syndication across databases and tools.

What we WOULD NOT BE trying to do

Compete with existing databases (We think what is already there is really good !)

We are currently working on a system to assign credits to individuals or groups of individuals (for eg: a Lab) for community annotation of data. We have different models in place and I do not know of many people working on the topic other than the Nature team.

We would highly appreciate your ideas and views on the topic. Post them as a comment or e-mail me at vinods[at]

Thursday, June 12, 2008

The Zebrafish GenomeWiki

After creating FishMap, we are rather busy giving the final finishing touches to one of the major systems in our blueprint for Zebrafish Genomics.

We had earlier petnamed it FishWiki, and now we have decided to call it Zebrafish GenomeWiki.

Much has been written on the possibility of using Wiki style software for Genome re-annotation, but nobody has actually created a wiki-based system for genome reannotation (see the recent paper in genome Biology by Steven Salzberg). GenomeWiki would be one of the many Wiki re-annotation servers that

The last few days have been quite busy for us giving the finishing touches to the website and we have unveiled our logo.

You should be getting more details on the project at the Madison Meeting.
Watch the website for more updates.

Wednesday, June 4, 2008

Meet us at Madison

See website for more details
See list of participants here

FishMap team designs the ZEBRAFISH cover

The June issue of Zebrafish featuring FishMap would come up with a brand new cover designed by Vaibhav Jadhav.

Thanks to all who hacked into their image collections and handed him over hundreds of images.