Friday, April 17, 2009

Genome sequences are not enough

For those interested in either ciliates like Tetrahymena species or how to make sure that a genome sequence is broadly useful to a community of researchers, this email I just got might be of interest.  Basically, in a nutshell, a consortium (of which I led in the past - see our main genome paper in PLoS Biology here and a follow up paper in BMC Genomics here) has been sequencing the genome of Tetrahymena thermophila a really cool ciliate (one clade of eukaryotes) that has been a model organism for much molecular and cellular work.  As part of the NIH portion of funding for sequencing the genome we subcontracted Mike Cherry at Stanford to create the Tetrahymena Genome Database (TGD) based upon his highly successful Saccharomyces Genome Database (SGD).  Now that the grant is over, there is no support for TGD anymore and it is going to at some point become obsolete.  Fortunately, there is support (see email) for a Tetrahymena Stock Center to provide resources to the community like strains and now it looks like this stock center will also take on the task of helping maintain the TGD (with Nick Stover, who used to work at TGD).  Great news and might give some people something to think about in terms of building and maintaining resources for other genome sequencing projects. 

Dear Tetrahymena Community members,

We are delighted to announce that the Tetrahymena Stock Center has been awarded funding by NIH and the National Center for Research Resources (NCRR).

We are very grateful to NIH for continued funding, and to all the members of the Tetrahymena community who have supported our efforts to establish a functional stock center at Cornell University. We are excited that this new funding will allow us to expand the purview of the Stock Center and pursue several goals that will benefit the Tetrahymena community as a whole.

First, we will continue to maintain a large variety of genetic stocks in our secure facilities at Cornell University and make them available to the scientific and educational community. We are constantly seeking to expand the diversity of the strains in the Stock Center as a resource for the community at-large. We are currently are working to complete the acquisition and documentation of several large strain collections, including the critical collections developed by Dr. Eduardo Orias, Dr. Martin Gorovsky, and Dr. Joseph Frankel. In addition, we are now accepting strains from other laboratories to provide a secure site for strains they wish to share with the community. We are also actively providing strains to researchers and educators around the world. We encourage everyone to visit our updated website at http://tetrahymena.vet.cornell.edu/ . We have new expediated online ordering and have streamlined the process for depositing cells. We welcome any comments, suggestions, ideas for other things that you would like to see on this site.

Second, as part of our continuing efforts to make the Tetrahymena Stock Center as useful as possible to the entire Tetrahymena community, we have expanded the purview of the Stock Center to include support for the Tetrahymena Genome Database (TGD). TGD is no longer actively maintained at Stanford and is fast becoming outdated. We believe that making TGD operational under the auspices of the Stock Center and linking support efforts to community annotation strongly complements the overall mission of the Stock Center to facilitate the use of Tetrahymena as a research and teaching organism. We look forward to working with Dr. Nick Stover at Bradley University, who will supervise the development of a genome Wiki and further annotation of the database. Revising the TGD format will be an exciting and challenging task that we hope will involve many members of the Tetrahymena community. We will send out a more detailed explanation of the new TGD format soon. For now, we thank Dr. Mike Cherry for his continued support and help in working with Dr. Stover to make the transition to the Wiki format as easy as possible.

Finally, please continue to use the Stock Center for all of your strain needs, and don't forget to include the costs for strain ordering in your respective grant applications. Contact us with any questions, suggestions, ideas at tetrahymenastockcenter-mailbox@cornell.edu . We look forward to working with the community to enhance the scope and function of the Tetrahymena Stock Center over the next 5 years.

Sincerely,

Ted Clark

Donna Cassidy-Hanley 

2 comments:

  1. That explains why TGD looked a bit abandoned when I poked around there. I expected something to rival TAIR (arabidopsis.org) (which seems to be sufficient to make its users illiterate in using NCBI...) but was promptly reminded about the vast difference in size of community, and funding. Hope this project kicks off though; it's about time more mouse/drosophila/arabidopsis-like stuff is done on the cooler organisms, and a good database is really central to that!


    Any mention of ciliates makes my inner cell biologist drool...

    -Psi-

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  2. Thanks for the plug for Tetrahymena. It's good that TGD will once again have some support. I'm probably one of the biggest users of TGD and I've found it to be indispensable for my work.

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