Tag Archives: eupathdb

Outreach position for FungiDB/EuPathDB

Dear Colleague – 

The Eukaryotic Pathogen Genomics Resource (EuPathDB.org) is searching for suitable candidates for a full-time outreach staff position. EuPathDB has long provided support for protozoan parasite researchers, but the recent integration of FungiDB brings many new communities on board.  The EuPathDB outreach team is therefore looking to grow, with particular interest in fungal biology expertise.

The ideal candidate would be a recent molecular genetics / genomics post-doc with expertise in one or more experimental systems, and excellent communications skills.  EuPathDB databases including FungiDB provide users with the ability to integrate and explore diverse data types: not just genome sequences, but also polymorphisms, transcriptomics & proteomics data, chromatin marks, metabolic pathways, comparative genomics datasets etc … and the outreach team is responsible for ensuring that bench scientists around the world can make effective use of these data, through workshops, meeting presentations, webinars, on-line tutorials, publications, etc.  Responsibilities also include keeping up with the relevant research literature, and working closely with supported communities to define targeted areas for curatorial effort, and high priority datasets for inclusion in the database.

This job is an exciting opportunity for the right person, with good pay and long-term career prospects.  The successful candidate could be based in Philadelphia PA, Athens GA or Liverpool UK, and will work closely with a dynamic and collaborative team of ~30, including curators & annotators, data loaders, systems & database administrators, software developers, web site designers, data analysis specialists, and other outreach staff members.  Applications may be submitted to http://tinyurl.com/EuPathDBoutreach-Penn or http://tinyurl.com/EuPathDBoutreach-UGA (the Liverpool application has not yet been posted, but will be soon).  Questions may also be directed to EuPathDB Director of Scientific Outreach Omar Harb, at oharb@upenn.edu.

 

Apply for EuPathDB workshop

Dear Colleague,

We are pleased to announce the 10th annual EuPathDB workshop to be held in Athens, Georgia, USA from May 31 – June 3rd, 2015.

Learn how to effectively use EuPathDB resources and mine available data to help guide your research.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

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Databases covered: EuPathDBAmoebaDB, CryptoDB, FungiDB, GiardiaDB, HostDB, MicrosporidiaDB, OrthoMCL, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, TriTrypDB

Costs and Fees: The course is free. Housing, all training materials and lunches are covered. Attendees are expected to provide their own transportation to the course and pay for a few of their meals. Letters of acceptance will be mailed early to facilitate the solicitation of outside travel funds.

When: 6:30pm on Sunday, May 31 to 5:00pm on Wednesday, June 3, 2015

Where: University of Georgia, Athens, GA, USA
Davison Life Sciences Building, room C128.

Application deadline: February 1, 2015. Click here to apply. NOTE: Deadline extended apply before Feb 20!

If you have any questions or concerns please email help@eupathdb.org

Announcing FungiDB 2.1 release

On behalf of the FungiDB development team I am pleased to announce the release of FungiDB 2.1 which includes 39 Fungal genomes from Ascomycota, Basidiomycota, and Mucormycotina (Zygomycota) and 6 genomes of Oomycetes.  This release builds on the 2.0 release from August to include 6 additional species, RNA-Seq from a population of Neurospora strains, growth time points in 3 fungi Coprinopsis, Neurospora, and Rhizopus, and Phytophthora species. The 6 new genomes include Batrachochytrium dendrobatidisCoprinopsis cinereusHistoplasma capsulatumCoccidioides posadasii, Rhizopus delemar (formerly oryzae), and Ustilago maydis.

While the Oomycetes are not true Fungi, as phylogenetically they are in a very distinctly different clade, however we have included them in the database as part of collaboration with Brett Tyler. It may be that some aspects of the convergent evolutionary patterns among these groups can be revealed by having the data in a common system and use of the same tools.

Several human pathogenic and opportunistic fungi are now available in the system including 2 strains of Histoplasma capsulatum and 2 species of Coccidioides, Candida albicans, 2 Cryptococcus gattii strains, C. neoformans var grubii, and 2 C. neoformans var neoformans strains, Fusarium oxysporumAspergillus fumigatus and A. terreus. With the homolog tools available in the FungiDB system, one can map functional data from onto genes in these fungi from related models in the filamentous or yeast species.

Plant pathogens Magnaporthe grisea, Ustilago maydis, Puccinia graminis, and several Fusarium species, and the collection of 6 Oomycetes also provide a platform for comparative genomics among plant pathogens.

Functional annotation data have been imported from model system databases for Aspergillus nidulans, Saccharomyces cerevisiae, and C. albicans.  We also generate predicted GO annotations from InterPro based analyses.

The development team at UC Riverside including Raghu Ramamurthy, past member Daniel Borcherding, and new member Edward Liaw; our collaborators on Oomycete data at Oregon State Brett Tyler and Sucheta Tripathy; and the EuPathDB developers and systems teams that have been essential partners in everything from assisting in data development and software debugging to database administration and web and systems administration.

Future work

Work is likely to begin in the next quarter to curate and support further literature based annotation of gene function in the Cryptococcus species. In addition we plan to expand the supported phenotypic data for Neurospora to support work from the Program Project grant and the phenotyping of the systematic gene deletion collection.

Additional support will be rolled out for more functional and evolutionary genomics data including expanded RNA-Seq datasets, population genetic data sets for several species with cohorts of sequencing of strain populations. We plan to continue to add additional species, with priorities focused on pathogens and model systems, but are interested in the community feedback of specific species that are must include targets in future releases. Please email help[AT]fungidb.org with your suggestions or fill out feedback on the “Contact Us” link on the FungiDB page.

Support
The work in this release was supported by grants from the Burroughs Wellcome Fund and the Alfred P. Sloan Foundation.The Oregon State team is supported by grants from the Agricultural and Food Research Initiative of the  USDA National Institute for Food and Agriculture.  The EuPathDB team is supported by grants from the NIH, Gates Foundation, and Wellcome Trust. Without the direct and indirect support of these funders none of this would have been possible.  All web and computational resources for FungiDB are currently housed at the Univ of Pennsylvania or the University of Georgia, thanks to the many system administrators who keep these services running that have allowed us to make this release.