WormBase updated to WS276

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A new release of WormBase, WS276 is live on the website. Please see the release notes which contain complete information about this release.

Data changes: note that C. elegans gene descriptions in the “Overview” section of gene pages have improved orthology statements to human genes. WormBase uses the DIOPT orthology data from the Alliance of Genome Resources and has increased stringency by displaying only those human orthologs that have been determined by three or more methods. This should significantly improve the orthology data in WormBase which is also reflected in the gene descriptions. 

Known Issues: the circRNAs failed mapping so sequence and genomic position are not available for this release, but will be in the WS277 release.

Check out Venn diagrams for interaction data in WormBase

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WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. Check out the micropublication which describes the Vennter tool. This tool is integrated into the interactions widget on WormBase gene pages and allows the visualization and analyses of interaction data.

Open Publishing Fest

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microPublication will participate in the Open Publishing Fest organized by  the Collaborative Knowledge Foundation. We will host four events or ‘tents’ which will focus on different aspects of microPublication and its role in scholarly communication. Mark your calendar for the following events and keep an eye on the  festival website for conference channels details!

Tent 1: microPublication: A Welcome Alternative in Scholarly Communication – May 20th, 10am Pacific

Join us for an hour packed of fun to learn how microPublication is shaping the future of scholarly communication! microPublication is a deliberately brief, peer-reviewed and indexed publication. We publish brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. We will hear from Editor in Chief Paul Sternberg, Editorial board members, Authors, and Reviewers  to learn how microPublication  is changing how they think about publishing.    

Tent 2: Knowledgebases, Repositories, Archives: Curation, Curation, Curation – May 26th, 10am Pacific

Where should your data go? What are the roles of Repositories, Knowledgebases, and Library Archives in Scholarly Communication? How are published data preserved for long term access and how are they made available to the scientific community? We will highlight similarities and differences in a panel discussion with representatives from Dryad, University Libraries, and Knowledgebase curators. 

Tent 3: The microPublication Open Access platform – May 27th, 10am Pacific

microPublication.org offered new software development and workflow challenges in  the publishing landscape. Join us to learn how our submission platform was designed and to savor the final product!  Developers Yannis Barlas from Coko and Nick Stiffler from microPublication will guide you through the submission portal and will be there to answer all your questions.

Tent 4: microPublication Inspires New Communities and Promotes Undergraduate Research – May  27th, 12pm Pacific

Started by serving the C. elegans research community, microPublication Biology has expanded to many model organism communities and beyond. Besides being beneficial to researchers at all career levels, microPublication has proven to be a wonderful tool to showcase undergraduate research and foster education. We will hear from different groups that have been inspired by microPublication and learn how they are using it to make a difference.