Announcing the Alliance of Genome Resources

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An Alliance of Genome Resources has been formed to provide better support for the biological sciences via an integration of shared data, standardization of data models and interfaces, and unified outreach to researchers, educators and the public. The initial members of the Alliance are the Gene Ontology Consortium and six model organism databases: Saccharomyces Genome Database, WormBase, FlyBase, Zebrafish Model Organism Database, Mouse Genome Database and Rat Genome Database. The integration of these projects will not decrease the types of data, tools and community support that are currently provided by these resources but rather will provide the best displays and tools currently in use and allow us to efficiently develop new tools in a collaborative manner. As we move toward deeper integration of our content and software we will provide easy-to-use cross-organism queries of the extensive data available in the component resources. Also, future integration of other resources will benefit all biologists.

The Alliance of Genome Resources will continue the tradition of these community resources by enabling researchers to leverage the published results and datasets from well-studied organisms for their daily research. By integrating high-quality expertly curated information, the Alliance will continue to provide researchers access to data, information and knowledge found in published and publicly available sources that would require many lifetimes to assemble.

The modular architecture of modern websites will allow the Alliance to maintain the uniqueness of each research community – and each user – through customization. We will present a common view of information whenever possible. A common website will have distinct entry points for the different communities and tools that will maintain the community-building features of our current resources. By joining the Alliance of Genome Resources, the member organizations pledge mutual support, as well as support of research communities having interests in common with those of the Alliance, with the goal of delivering facile information retrieval for all biologists. We will definitely need your support in obtaining sufficient funding for these efforts.

Please support Model Organism Databases (MODs)

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Model Organisms such as yeast, worm, fly, fish, and mouse are key drivers of biological research, providing experimental systems that yield insights into human biology and health. Model Organism Databases (MODs) and other genome resources like Gene Ontology (GO) Consortium enable researchers all over the world to uncover basic, conserved biological mechanisms relevant to new medical therapies.

NHGRI/NIH has recently advanced a plan to reduce MOD funding while encouraging these resources to share as much infrastructure as possible.  While there are a number of advantages of more integration such as consistent user interfaces and vocabularies, unless other sources of funding are found to offset the planned cuts, core functions at WormBase such as extraction of information from papers and genome annotation will be affected. The Worm Board, worm community leaders and other model organism community leaders have come together to write a Statement of Support for the MODs and the GO. We ask all scientists who value the community-specific nature of the MODs to sign this ‘open letter’. We urge you to add your name, and to spread the word to all researchers who value these resources.

Please sign this letter!

Gene Transfer Format (GTF) files now available

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WormBase now provides the canonical gene set for each species in Gene Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html). These files can be used directly by a number of popular sequence analyses tools (e.g. Cufflinks).

The GTF files are available from the WormBase FTP site, for example, the GTF file for C. elegans, c_elegans.PRJNA13758.WS253.canonical_geneset.gtf.gz, is available here.

 

Great new chapter of WormBook in GENETICS!

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There’s a great new chapter of WormBook in GENETICS by Meera V. Sundaram and Matthew Buechner: The Caenorhabditis elegans Excretory System: A Model for Tubulogenesis, Cell Fate Specification, and Plasticity.

Abstract
The excretory system of the nematode Caenorhabditis elegans is a superb model of tubular organogenesis involving a minimum of cells. The system consists of just three unicellular tubes (canal, duct, and pore), a secretory gland, and two associated neurons. Just as in more complex organs, cells of the excretory system must first adopt specific identities and then coordinate diverse processes to form tubes of appropriate topology, shape, connectivity, and physiological function. The unicellular topology of excretory tubes, their varied and sometimes complex shapes, and the dynamic reprogramming of cell identity and remodeling of tube connectivity that occur during larval development are particularly fascinating features of this organ. The physiological roles of the excretory system in osmoregulation and other aspects of the animal’s life cycle are only beginning to be explored. The cellular mechanisms and molecular pathways used to build and shape excretory tubes appear similar to those used in both unicellular and multicellular tubes in more complex organs, such as the vertebrate vascular system and kidney, making this simple organ system a useful model for understanding disease processes.

New version of Worm Breeder’s Gazette!

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Dear Worm Breeders —

We are pleased to announce the next iteration of the Worm Breeder’s Gazette with some exciting new changes.

Starting today, the Gazette will publish articles on a rolling basis with only a brief editorial period to review formatting. We’ve also made the submission process simpler and more robust. For example, you can start a submission online, saving your progress at any time to complete later.

By accelerating the availability of Gazette articles, we seek to preserve the original spirit of the Gazette: publication of breaking results and new methods of general interest to the community in a brief and digestible format. Submissions will still be restricted to approximately one printed page with notable exceptions for the inclusion of rich media such as images and movies.

We look forward to your contributions!
— The Worm Breeder’s Gazette Editors, Jane Mendel and Todd Harris.

To participate in the new version of the Gazette, first register for an account.

Once registered, you will be able to submit an article online.

If you’ve participated in the past, you will need to reset your password first.

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