FishBlog | Zebrafish Genomics and Community Annotation

Zebrafish GenomeWiki has gone LIVE

2009-01-21T11:03:00.000-08:00

Zebrafish GenomeWiki has gone live today.

A flyer describing the features of the Zebrafish GenomeWiki and a request for community participation can be downloaded from the home page of the Zebrafish GenomeWiki.

Zebrafish GenomeWiki gets a new address

2009-01-18T05:41:00.000-08:00

The Zebrafish GenomeWiki Beta Preview version is now available at

http://fishwiki.igib.res.in

It can also be viewed at its older address

http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WebHome

Zebrafish GenomeWiki unleashes its WikiPower

2009-01-17T10:09:00.000-08:00

Manually curated gene list

Over the last few days we have manually curated/edited over 200 genes. Manual curation includes information regarding Gene description, Gene Function, Gene Cloning, Gene Structure, Disorders and Mutations, and Related PubMed articles.

These genes are listed separately and can be viewed through the ALL MANUALLY CURATED GENES link on the right hand side banner of the Zebrafish GenomeWiki home page. The link is also available at

http://fishwiki.igib.in/TWiki_4_2_4/bin/view/ZebrafishGenome/WebHome

Watch this space for more manually curated gene in the near future.
Hail to the WikiPower!!

Learn Your Way Around Zebrafish GenomeWiki

2009-01-17T05:20:00.000-08:00

A Short guide entitled Learn Your Way Around Zebrafish GenomeWiki is available for new users. The guide can be viewed at

http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WayAroundFishWiki

The guide provides basic information on why this project was initiated and also provides a brief description of the ultimate goal of the project. In addition it also provides brief information on the following topics such as:

- Browsing and registering at the Zebrafish GenomeWiki
- Finding your favorite gene on the Zebrafish GenomeWiki
- Annotating / Editing the contents of the Zebrafish GenomeWiki
- Who can contribute/ annotate on the Zebrafish GenomeWiki?
- How to annotate/edit your favorite gene?
- A short tutorial on TWiki.

2009-01-17T00:17:00.000-08:00

Zebrafish GenomeWiki Beta Preview

Zebrafish GenomeWiki is a shared genomics resource for community annotation of the Zebrafish genome on the lines of the “Wikipedia”. Members of the Zebrafish community can create new data sets, annotate, comment and edit existing data sets using the Zebrafish GenomeWiki portal. The Zebrafish GenomeWiki will permit community experts and individual investigators to add the latest genomics information and discuss alternative annotations in real time there by speeding up the fine annotation the Zebrafish genome. Currently there are over 3 x 10^5 documents in the Zebrafish GenomeWiki and we are still growing!!

The Zebrafish GenomeWiki Beta Preview version is now available at

http://fishwiki.igib.in/TWiki_4_2_4/bin/view/Main/WebHome

Please Note: We are still working on the portal and many obvious thinks need to be fixed including the Search tool.

Zebrafish GenomeWiki Beta Preview

2009-01-14T21:53:00.000-08:00

Zebrafish GenomeWiki Beta Preview version is now available to the community.

We are still working on the portal and many obvious thinks need to be fixed including the Search tool. We have been trying to crawl the site using swish-e but it seems the site has grown so huge (3*10^5 documents and growing).

Zebrafish GenomeWiki Beta Preview

2008-09-24T04:29:00.000-07:00

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

2008-08-03T22:25:00.000-07:00

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

2008-06-14T05:23:00.000-07:00

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

2008-06-12T01:01:00.001-07:00

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

2008-06-04T01:51:00.001-07:00

See website http://www.union.wisc.edu/zebrafish/index.html for more details
See list of participants here

FishMap team designs the ZEBRAFISH cover

2008-06-04T01:45:00.001-07:00

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

2008-05-28T21:07:00.000-07:00

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

2008-05-25T01:36:00.000-07:00

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

2008-05-24T08:03:00.000-07:00

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

50 and more

2008-05-11T15:32:00.000-07:00

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

2008-04-22T08:15:00.000-07:00

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

2008-04-21T23:10:00.000-07:00

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