Tag Archives: fungidb

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.

 

An open letter to the fungal research community regarding genome database resources

An open letter to the fungal research community regarding genome database resources (from the Broad Institute & FungiDB/EuPathDB):

As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.

The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.

MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.

For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to help@FungiDB.org

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

FungiDB 2.3 released with 52 genomes

The latest release of FungiDB (2.3) is now live and includes 52 genomes, 11 of which are new for this release. This was a longer than expected release cycle due to reintegration with the EuPathDB software team. Programmers Raghu Ramamurthy and Edward Liaw at UC Riverside did nearly all the Fungal specific work, collaborating closely with the EuPathDB team who provided many site-specific corrections and assistance in running the workflow. This is a joint collaborative project between the UCR,Oregon State (FungiDB) and U Penn, Univ of Georgia (EuPathDB) and the work in this release was funded through grants from the Burroughs Welcome Fund, the Alfred P. Sloan Foundation, and the USDA-NIFA.

An announcement for FungiDB 2.3 is here and included below.

New genomes included in this release include

Botrytis cinerea
Sclerotinia sclerotiorum
Aspergillus carbonarius
Neosartorya fischeri
Trichoderma reesei
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
Phanerochaete chrysosporium
Sporisorium reilianum
Malassezia globosum
Mucor circinelloides f. lusitanicus
Mitochondrial genomes were added for the following organisms

Aspergillus fumigatus
Neurospora crassa
Saccharomyces cerevisiae
Schizosaccharomyces japonicus
Schizosaccharomyces octosporus
New genomics data available in this release include additional RNA-Seq experiments for Coprinopsis cinerea. High Throughput SNP (HTS) discovery module have been addded for Aspergillus fumigatus and a population of 23 strains from JCVI.

Data fixes and update

Updated in this release include new versions of annotation for

Aspergillus fumigatus – s03-m02-r18 from AspGD
Aspergillus nidulans – s09-m05-r03 from AspGD
Fusarium oxysporum f. sp. lycopersici – correcting some annotation problems in Broad v2
Neurospora discreta – correcting some annotation problems from JGI
Saccharomyces cerevisiae version from 2012-11-20
The current annotation for N. crassa is still v10 release and does not reflect the V12 release made March 2013. The updated version will be available in the 3.0 release of FungiDB.

Corrections

The Coccidioides RNA-Seq data in the previous release had flipped the labels of the spherule and mycelium results, this has been corrected.

Errors in previous loading of gene product information for P. sojae had left many genes without sufficient product information and description. This has been corrected.

Synteny results between several species were not properly loaded in the previous release. This has been corrected.

Data summary tables of genomes and gene metrics have been updated to reflect the current state of the database.

Known errors

Alternative splicing and starting/ending non-coding exons may not be properly represented in GBrowse and in the GFF files available for download.

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.

Annotating genes in FungiDB

As part of our newly launched FungiDB I wanted to demonstrate the capabilities of attaching additional annotation to gene records.  This is an important feature that allows the community to contribute to the knowledge base about an organism’s genes and gene functions.  This can be done by anyone in the community who has registered an account. Once the information is entered is also searchable so that added gene names are immediately part of the searchable text across the entire database.

We encourage you to register for an account (which allows you to also save your strategies and queries) and also to provide feedback about the look and feel (interface), the datasets that are provided, the need for additional species, and the capabilities and tools in the system.

Linking to a gene page
Here is a record for the C. neoformans var. grubii gene SXI1.  If you look at that URL you can see I am using one of the built-in shortcut URLs for EuPathDB/FungiDB which is http://fungidb.org/gene/GENENAME. Since we need names to be unique across the whole database we have chosen to prefix names with the species and strain prefix separated by two underscores.  So the link is  http://fungidb.org/gene/CneoH99__CNAG_06814 which gets expanded into a full accessible record which is much longer as you’ll see when you click on it.  This redirection gives us some flexibility to indicates that we’re talking to the beta release version of the database at this time.  This full (and long URL) has some flexibility so that in the future we can still have a beta and production server or even frozen release servers.

SXI1 top
Screen shot of SXI1 page on FungiDB

Comment pages
Comment pages provide a way to add additional information from the community to a page. This can be as simple as the gene name assigned, a link to a publication, GenBank Accession of the sequence, or descriptive text about a mutant phenotype. The comments can also describe corrections or additions to the gene model which can be noted. Currently the EuPathDB system does not allow direct manipulation of the gene model from the page as these types of updates need vetting and technical work to re-analyze the updated protein sequence in the downstream analyses (e.g. Pfam, InterPro, homology assignments, etc). For SXI1 there is a comment which links the gene to several publications and submitted accession numbers.  Since multiple strains have been studied for this gene, but not all are part of FungiDB, it may be useful to have direct links to the sequence variants for someone wanting to do followup work on the gene and the key residues.

SXI1 comment
How a comment looks on a gene page when it is entered
SXI1 comment
A comment page showing the linked pubmed records and genbank accessions

Postdoc for Fungal genome data integration

There is an open position in my lab to support development of FungiDB, a database for fungal genome data integration.

Postdoctoral fellow supporting fungal genome database development

Position Description

A postdoc position is available in the laboratory of Dr. Jason Stajich to support the development of FungiDB, a database for fungal genomic and functional data.   Strong candidates will be proficient in the Perl programming language; modern biology in general and bioinformatics in particular; show a demonstrated ability to quickly pick up new biology and computer science concepts; be comfortable using relational databases; and possess core Unix skills to do these tasks efficiently.  Experience using Perl for genome sequence data processing a plus.

You’ll also have a relentless attention to detail, the ability to work independently on challenging problems with no direct easy solution.  You will use these skills to help organize, analyze, and display a vast amount of disparate biological data and interact with the fungal community. There will be opportunities for self-directed research utilizing this collection of genomics and comparative database and tools.

Application evaluation will begin Feb 1, 2011 until the position is filled. Salary and benefits will be commensurate with experience and University of California Postdoctoral Union agreement.

Qualifications

Minimum qualifications include a Ph.D. in Biological Sciences, Computer Science, Statistics, or a related field. Demonstrated experience in bioinformatics and high proficiency in Perl programming is required.  Demonstrated experience in web or bioinformatics software development is a plus. The ability to work with a small, distributed team is essential including exceptional written and verbal communication skills.

To Apply

Contact Jason Stajich jason.stajich@ucr.edu with a CV and the names of three references letter writers.

Information available on UC Riverside and the Stajich lab.

Information about UCR
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