Zebrafish GenomeWiki Beta Preview

The Zebrafish GenomeWiki Beta preview is available at http://fishwiki.igib.in
we are still working on the system and there are many more bugs to find than we can fix :)

The system is a bit too slow at the moment, but sure, it will hopefully get faster when we will move to our new production server.

Trip to Sultanpur

Here is a link to view pictures of FishMap Team's Day Out.

Well FishMap team do post ur comments:)..

http://picasaweb.google.com/meenakshish/FishMapTeamOnAHolidayToSultanpur

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]igib.in

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.

Meet us at Madison

See website http://www.union.wisc.edu/zebrafish/index.html 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.

FishMap accepted in Zebrafish

We had a wonderful time yesterday after the FishMap manuscript was accepted. And we plan to enjoy this weekend together with our entire team that made this happen.

We had a nice time with comments and suggestions from the members of the community and the anonymous reviewers of our paper which significantly enriched the resource.

Thank you all for your support!

For all of you who would use this tool, please go ahead and cite us as:

Meli R, Prasad A, Patowary A, Lalwani MK, Maini MK, Sharma M, Singh AR, Kumar G,
Jadhav V, Scaria V, Sivasubbu S.
FishMap: A community resource for Zebrafish genomics. 
Zebrafish 2008  (In press)

We would be back soon with more updates on datasets.

VS

FishMap has new URL

FishMap has a new URL. The resource can now me accessed at
URL: http://fishmap.igib.res.in

The old URL http://miracle.igib.res.in/fishmap would also be accessible for quite some time.

BLAST server added to tool kit

FishMap has a BLAST server for sequence homology search and a gene ID converter added to its tool kit.

50 and more

FishMap today uploaded its 50th track. The data has been pouring from all over, and the FishMap team @ IGIB has been working hard to put it online. We have been currently working on the insertion datasets from various labs. Within a few weeks, you should be updated with these tracks.

TRACKS READY FOR UPLOAD [05/12/2008]

• Becker Lab Insertions
• Ekker Lab Insertions
• Hopkins Lab Insertions
• Kawakami Lab Insertions
• Korzh Lab Insertions
• Parinov Lab Insertions
• Johnson Lab Insertions

FishMap updates-

FishMap currently hosts over 40 datasets (tracks) pertaining to genome-scale data on Zebrafish.
You can now suggest your favorite genomic track for inclusion in FishMap!!

SSB

Welcome to FishMap -a community resource for annotation of the zebrafish genome.

FishMap incorporates a number of tools and resources such as

FishMap Gbrowse - Genome Browser for Zebrafish Genomics datasets.
FishMap BLAT - A public BLAT server has been incorporated to FishMap to aid researchers map their sequence of interest to the Zebrafish Genome.
FishMap ID converter -Converts Zebrafish GeneIDs commonly used for Zebrafish.

FishMap is currently accepting submissions of genome-scale data to be incorporated in the database. Genome-scale predictions are also welcome if the tool/algorithm is published in a peer-reviewed journal. For more information and submissions, please send mail to Dr. Vinod Scaria (vinods@igib.res.in) or Dr. Sridhar Sivasubbu (s.sivasubbu@igib.res.in).

The website is currently under construction and will be functional shortly.

Good luck
Sridhar