We are excited to announce that the beta version of the new WormBase site that was opened for testing six months ago will go live on March 30th. We understand that it may take some time to adjust to the new interface, but hope that the improved organization, customizability, and speed of the site will ease the transition. Once the new website is released, the current (old) website will be frozen at version WS230 and made available for the foreseeable future. We will continue to refine and expand the new site with exciting new features throughout 2012. As always, we welcome all comments and suggestions at help@wormbase.org.
Public beta period of the new WormBase website now open!
Today, we’re excited to announce the opening of the public beta test period for the next generation WormBase website!
About the Design
The new website has been redesigned from the ground up with the following objectives:
* Easily handle many species and populations;
* Present the full extent of experimental data in C. elegans in customizable displays without presenting overwhelming amounts of unrequested data;
* Engage users with new opportunities for directly adding, commenting on, and correcting annotations;
* Provide support for under-served research communities;
* Be accessible to users from different backgrounds (researchers, educators, students);
* Be rock solid, stable, maintainable, and easy for anyone to extend;
* Be fast and easy to scale as demand warrants and database size increases.
Here’s a short list of some of the site’s features:
* Customizable content: pick what you want to see, ignore the rest;
* Customizable layout: arrange and rearrange as you see fit;
* Create an account and save your favorite items, or use a Google, Facebook, or Twitter account;
* Entirely new, more informative displays that make it faster to get desired information in fewer clicks. See, for example, the allele listing on the Gene Summary;
* History tracking;
* Persistent site preferences from device to device;
* Public comments and issue reporting;
* Direct chat with curators;
* Powerful new global database search option;
* For data miners, a complete RESTful API: every piece of information in WormBase uniquely addressable. More on this in subsequent blog posts.
About the Public Beta period
Although we’re really excited to introduce the site, please do watch your step.
There are many features that we are actively working on and many more that we will be rolling out shortly. We are also gauging real-world performance so that we can make improvements and enhancements to the architecture before the public production release in January. That said, we think that at its current state of development, the site is stable, useable, and useful.
You can report issues and leave comments (eg on the glr-1 page) for WormBase staff and other researchers directly on the site.
And if you have a chance, please take our User Survey.
What’s in store
We have a huge number of new features and enhancements in store for the new website, but we wanted to get the site in your hands now to start collecting feedback on the content and look-and-feel.
Help us out
Be sure to leave comments and report issues! And if you or your lab are interested in participating in focus group testing, please drop me a line (todd@wormbase.org).
Roadmap
September – November: Iterative development and testing; focus groups
January 2011 – Launch new website on www.wormbase.org
April 2012 – Retire original WormBase site
Trichinella spiralis Genome Browser now available
We’ve added a Genome Browser instance for the draft genome sequence of Trichinella spiralis. T. spiralis is an obligate parasite of rats, pigs, bears, and humans that causes the disease trichinosis.
Private instances of WormBase in 10 minutes
Are you interested in running your own private instance of WormBase without having to work through a lengthy and complicated installation procedure? The Amazon Elastic Compute (EC2) Machine Images (AMIs) of WormBase are your answer.
Please see this Worm Breeder’s Gazette post for an overview of the process and this blog post for a detailed walkthrough.
Questions? Please drop me a line by email (todd@wormbase.org) or Twitter (@tharris).
SPELL – A display and clustering tool for large scale gene expression data.
SPELL (Serial Pattern of Expression Levels Locator) is a display and clustering tool for large scale gene expression data, including microarray, tiling array and RNAseq. The software is developed and maintained by Matt Hibbs from the Jackson Laboratory. SPELL can now search for worm microarray and RNAseq data.
The current functionalities of SPELL include:
1. Checking expression levels of individual genes in each dataset
2. Searching for other genes with similar expression profiles
3. Identifying biological processes related to the query genes
4. Users can download individual datasets
SPELL users can enter a list of genes that are expected to have similar expression profiles. SPELL checks the correlation of these genes in each dataset. The dataset with the highest correlation will get the most weight. If users provide only one gene, all datasets will get the same weight. Based on the weight of each dataset, SPELL will identify other genes with similar expression profiles, and display biological process gene ontology terms that are enriched in the results. SPELL provides gene-centric microarray and RNAseq data that are mapped to the current WormBase release. WormSPELL226, released on July 29th, contains 3 RNAseq datasets and 112 microarray datasets, including 1726 microarray experiments and 58 RNAseq analyses.