New version of the Alliance of Genome Resources

A new release (4.1.0) of the Alliance of Genome Resources (Alliance) is now available. Search for your favorite gene and find harmonized data such as gene function, disease models, phenotypes, expression and many more across orthologous model organisms and human. Read about the new data and features in the release notes.

SimpleMine Update: Biotype, GO term, RNAi clone and more

We have added new data fields to SimpleMine, a batch download tool for essential gene information. Users can now access biotype, GO term, and RNAi clones through this simple web interface.

We also added more information to previously existing data fields. All references, including books, reviews, meeting abstracts, and primary research articles, are now listed in the Reference field. For genetic map position, we display error rates of the genetic mapping data. In addition to all “live” gene objects, users can now search for pseudogene or “suppressed” gene objects. 

Changes to the web interface include: improved performance, species-specific or mixed-species searches and a search button for all genes in one species. There are 32 data fields in SimpleMine, organized into five categories so that users can quickly select them. 

Note that WormBase SimpleMine provides essential information for genes in nine nematode species. There is a prototype of the SimpleMine tool for the Alliance of Genome Resources with data related to human, mouse, rat, zebrafish, fly, yeast, and worm (C. elegans only):  https://www.alliancegenome.org/prototypes

Accessing the WormBase FTP site

You may have noticed that many browsers such as Chrome, Firefox, etc., no longer support the File Transfer Protocol (FTP) to access files on remote servers. However, programs such as FileZilla offer free support of FTP. Please stay tuned as we are currently exploring solutions to make access to the WormBase FTP site easier for our users.

WormBase is hiring at OICR: Software Developer 1

WormBase is hiring a Software Developer 1 to be located at the Ontario Institute for Research in vibrant downtown Toronto!

Join a small and flexible team pushing the limits of a ground breaking online resource that supports a global biomedical research community. In addition, you’ll have the chance to work on the Alliance of Genome Resources — a new project building the next generation of Model Organism Databases from the ground up! If things like killer UI/UX, AWS everything, and coding all in an Agile environment makes your heart race, consider submitting your resume!

Read the full job description and apply here.

Introducing the Alliance Community Forum

Dear WormBase and Worm Community Forum Users —

As previously discussed, the Worm Community Forum is moving.

Today, along with the Alliance of Genome Resources, we are pleased to introduce a new online discussion forum, the Alliance Community Forum.

Alliance Community Forum

In keeping with the spirit of the Alliance of Genome Resources, we’ve chosen to organize topics by organism and not by Model Organism Database. Rest assured that it’s easy to only follow specific areas that you may be interested in. Worm related discussions, for example, can be found here, subdivided in a variety of topics. You can choose a variety of notifications for topics of interest.

The Alliance Community Forum represents the first place for discussions across six model organism communities — flies, mice, yeast, rats, worms, and zebrafish (from the participating MODs of FlyBase, MGI, SGD, RGD, WormBase, ZFIN, respectively).

We hope that this Forum provides an opportunity for stimulating discussions, finding new collaborations, raising awareness about techniques from other fields, as well as providing a convenient place for posting notes of interest to the broader community of biomedical researchers (meeting details, job postings, funding announcements, etc).

If you are an existing member of the Worm Community Forum

We have migrated most existing accounts. Please reclaim your account on the Alliance Community Forum by requesting a password reset on the new forum. You will be sent a link to reset your password. If you have trouble logging in, please contact todd@wormbase.org.

Note that due to a technical issue, if you created an account in the last several months, you will need to create a new account in the Alliance Community Forum.

If you are not an existing member of the Worm Community Forum

You can log in with a new account on the forum, or a Google or Github account if you so choose.

Preserving the Worm Community Forum history

We have migrated [b]most[/b] posts from the nearly 20 year history of the forum. Some posts could not be migrated, nor have posts created in the last few months. Feel free to recreate these topics in the new forum.

Interested in working as a moderator on the Alliance Community Forum?

Please contact todd@wormbase.org.

Migration Timeline

July 6, 2021: New registrations disabled on the Worm Community Forum.
July 9, 2021: The “Discussion” panel of the WormBase home page will start displaying entries from the Alliance Community Forum; posting on the Worm Community Forum will be disabled.
August 30, 2021: The Worm Community Forum will be retired.

Questions?
Please either post here, on the new forum, or email either the WormBase (help@wormbase.org) or the Alliance (help@alliancegenome.org) Help Desks.


Technical Details

The Alliance Community Forum is using Discourse, a widely used and full-featured online discussion platform.
User guide and FAQ on using Discourse