GMOD News

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News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the GMOD News Archives. See also the GMOD Calendar and Events List.

GMOD News is also available as an RSS feed. RSS feed

Adding a News Item

Note: If you don't want to do this yourself, please send the item to the GMOD Help Desk and we will post it for you.

GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the GMOD News and GMOD News Archives pages, and in the news tracker on the home page.

Short Instructions

Please follow these guidelines when adding a news item.

  1. Create a new page named "News/News Item Title".
    • Please make News Item Title be as short as possible, and no more 35 characters at most.
  2. Enter the text of your news item.
    • The first link in the news item should point to the page/URL you want the RSS feed to link to.
  3. Preview / save your changes. Edit and save the page until the news item looks like you want.
  4. Once you are happy with how the item looks, insert this line at the end of it:
{{NewsItem|yyyy/mm/dd}}

Longer Instructions

Please follow these guidelines when adding a news item.

  1. Create a new page named "News/News Item Title".
    • Please make News Item Title be as short as possible, and no more 35 characters at most.
    • The page must start with News/, otherwise it won't be picked by the RSS news feed.
  2. Enter the text of your news item.
    • Make the news item succinct.
    • Do not start the item with a MediaWiki header ("== Header ==").
      • It won't render very well. You should be able to avoid headers altogether.
    • The first link in the news item should point to the page/URL you want the RSS feed to link to.
      • For example, the first link in a news item about Chado could point to the Chado page.
    • You can include images in your news item. See preexisting news items for what markup to use to do this.
  3. Preview / save your changes. Edit and save the page until the news item looks like you want.
  4. Once you are happy with how the item looks, insert this line at the end of it:
    {{NewsItem|yyyy/mm/dd}}
    Where yyyy/mm/dd is the current date. This line will cause it to be added to the GMOD News RSS feed. The item will show up in the feed within an hour.
  5. Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.
    • Every edit results in the news item being reposted to the RSS feed. If you do need to update an item later on, you may do so, but please also update the NewsItem line:
    {{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}

Recent News

Applications Open for GMOD Online Training

GMOD will be holding its first online training course for those interested in the set up and use of GMOD components.

The course will be held from Monday 19th May to Friday 23rd May 2014, and will cover core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database.

If you are interested in attending, please see GMOD Online Training 2014 for more information and to submit your application.


Posted to the GMOD News on 2014-03-31

Canto Workshop at Biocuration 2014

CantoTextLogo.png
ISBLogo.jpg

GMOD will be running a workshop at Biocuration 2014 to demonstrate the use of Canto, on Wednesday 9th April in the afternoon. Canto is a literature curation tool that allows users to create functional annotations for genes and gene products using OBO (ontology) terms. Canto will soon be added to GMOD in the Cloud, and this workshop will show participants how to get a GMOD in the Cloud instance up and running--it takes less than ten minutes!--and how to use Canto for literature curation.

We will have more information closer to the time.


Posted to the GMOD News on 2014/03/25

Tripal 2.0a released

The Tripal Development Team is pleased to announce an alpha release of Tripal 2.0 for Drupal 7. This release is expected to have bugs and there is some functionality still under development. However, this release is made to help early adopters of Tripal for Drupal 7. Reports of bugs or other issues are highly welcomed. Below are available resources for Tripal 2.0a

   Download Instructions
   New Functionality
   Installation and Tutorial
   Tripal 2.0 API site
   Tripal Mailing List
   Tripal Developer's Mailing List

The Installation tutorial is still under development but should have enough information for complete installation of Tripal v2.0a as well as loading of organisms and features.


Posted to the GMOD News on 2014/02/27

Precompiled Ontologies in Chado

Eric Rasche and the Center for Phage Technology at Texas A&M University are making Chado database dumps of precompiled ontologies publicly available to save other Chado users the time and hassle of downloading and compiling the ontologies themselves.

Go to the download site.

The ontologies currently available are:

  • Chado Feature Properties
  • Gene Ontology
  • Plant Ontology
  • Relationship Ontology
  • Sequence Ontology

These are updated weekly; the workflow is as follows:

  • clone Chado from SVN
  • build
  • load ontologies
  • dump database as SQL
  • upload to a publicly accessible webserver

Please contact Eric if you are interested in having other ontologies added to the dumps, other builds with different (sub)sets of ontologies, or archived copies of schemas over time.

Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem.


Posted to the GMOD News on 2014/02/20

GCC2014 Registration is Open

2014  Galaxy Community Conference (GCC2014)
GCC2014 Training Day

We are pleased to announce that Early Registration and Talk and Poster Abstract Submission are now open for the 2014 Galaxy Community Conference (GCC2014).

GCC2014 will be held at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States, from June 30 through July 2, 2014. GCC2014 starts with a Training Day featuring five parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!

Early registration is now open. Register early and avoid paying 70% more for regular registration costs.  Early registration is very affordable, with combined registration (Training Day + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, and we expect to hit that limit. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend.

You can also book affordable conference housing at the same time you register. See the conference Logistics page for details on this and other housing options.

Abstract submission for both oral presentations and posters is also open.  Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2.  Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.

GigaScience Journal

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers, and is continuing to take submissions for this year's meeting and beyond. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update.

Thanks, and hope to see you in Baltimore!

The http:GCC2014 Organizing Committee


Posted to the GMOD News on 2014/02/14

GMOD Paper Cuts, Feb 10th, 2014

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


Finding the missing honey bee genes: lessons learned from a genome upgrade [1]

The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.

Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.

Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Interesting findings from the new assembly of the honey bee genome, including many more genes than were found in the initial assembly. The Hymenoptera Genome Database uses numerous GMOD resources, including MAKER for automated genome annotation, JBrowse and GBrowse for sequence browsing, and WebApollo for community genome annotation.


Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila [2]

We and others recently demonstrated that the readily programmable CRISPR/Cas9 system can be used to edit the Drosophila genome. However, most applications to date have relied on aberrant DNA repair to stochastically generate frame-shifting indels and adoption has been limited by a lack of tools for efficient identification of targeted events. Here we report optimized tools and techniques for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome engineering through the precise incorporation of large DNA sequences including screenable markers. Using these donors, we demonstrate the replacement of a gene with exogenous sequences and the generation of a conditional allele. To optimize efficiency and specificity, we generated transgenic flies that express Cas9 in the germline, and directly compared HDR and off-target cleavage rates of different approaches for delivering CRISPR components. We also investigated HDR efficiency in a mutant background previously demonstrated to bias DNA repair towards HDR. Finally, we developed a web-based tool that identifies CRISPR target sites and evaluates their potential for off-target cleavage using empirically rooted rules. Overall, we have found that injection of a dsDNA donor and guide RNA-encoding plasmids into vasa-Cas9 flies yields the highest efficiency HDR, and that target sites can be selected to avoid off-target mutations. Efficient and specific CRISPR/Cas9-mediated HDR opens the door to a broad array of complex genome modifications and greatly expands the utility of CRISPR technology for Drosophila research.

CRISPR is one of the most exciting recent technological advancements of the past couple of years. This paper reports new techniques and tools for using the CRISPR/Cas9 system for complex genome engineering. For more information, see the flyCRISPR website.


Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress [3]

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Check out the JBrowse-powered Brachypodium web genome browser and other resources on the new Brachypodium website!


Analyses of Hypomethylated Oil Palm Gene Space[4]

Demand for palm oil has been increasing by an average of ~8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.

The newly-sequenced oil palm genome used the MAKER automated annotation pipeline. The oil palm is one of a number of genomics projects taking off in Malaysia at the moment. Perfect timing for a GMOD workshop!


Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian [5]

The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies.

[...]

The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”

Information and resources for the newly-sequenced cnidarian E. lineata; all genomic data is publicly available at EdwardsiellaBase, and can be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-86
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1534.2Fgenetics.113.160713
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0087499
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086728
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-71
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2014/02/10

Galaxy Australasia Workshop 2014

1st Galaxy Australasia Workshop 2014 (GAW 2014)

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

The Galaxy Australasia Workshop is a great opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne.

GAW 2014 will also include poster session, keynote speakers.

You should attend to:

  • Present your work!
  • Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets.
  • Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them.
  • Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction.
  • Learn
    • how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics)
    • how to share, publish, and reuse your analyses with Galaxy
    • how to perform and enable your users to perform common, yet complex, analyses using Galaxy
    • when and how to use Galaxy on the Cloud

Topics will potentially include:

  • Image analysis and processing using Galaxy.
  • RNAseq/ChIPseq/Variant Calling/RNA Quality Control.
  • Galaxy on the Research Cloud.
  • CSIRO galaxy service - partnership between science and IT.
  • Identifying proteins from mass spec data with Galaxy.

Registration

Registration is open. Registration is also free, but space is limited.

Call For Abstracts

Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit an abstract and brief one-paragraph bio by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.

Looking forward to seeing you all in Melbourne!

Committee GAW 2014 Organising Committee


Posted to the GMOD News on yyyy/mm/dd

GMOD Paper Cuts, Jan 24th, 2014

After a break for the festive season, PAG XXII, and the GMOD community meeting in San Diego, GMOD Paper Cuts is back with a selection of scholarly publications for your reading pleasure.

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips [1]

Corynebacteria are used for a wide variety of industrial purposes but some species are associated with human diseases. With increasing number of corynebacterial genomes having been sequenced, comparative analysis of these strains may provide better understanding of their biology, phylogeny, virulence and taxonomy that may lead to the discoveries of beneficial industrial strains or contribute to better management of diseases. [...] CoryneBase offers the access of a range of Corynebacterium genomic resources as well as analysis tools for comparative genomics and pathogenomics.

A new bacterial resource that uses JBrowse for genome visualization. The justification for using JBrowse is interesting:

We chose JBrowse for CoryneBase for the following main reasons: (1) most of the traditional genome browsers, e.g., GBrowse, are implemented using the Common Gateway Interface (CGI) protocol—the use of CGI-based genome browsers will inadvertently incurs unnecessary delays since the whole-genome browser page need to be reloaded when users change how the data are displayed; and (2) with the advances in next-generation sequencing technologies and bioinformatic tools, we would expect more corynebacterial genomes will be sequenced and annotated. Therefore a user-friendly genome browser that allows rapid and seamless browsing of the huge genomic data will be a major advantage to the research communities.


The Genome Sequence of the Fungal Pathogen Fusarium virguliforme That Causes Sudden Death Syndrome in Soybean [2]

Fusarium virguliforme causes sudden death syndrome (SDS) of soybean, a disease of serious concern throughout most of the soybean producing regions of the world. Despite the global importance, little is known about the pathogenesis mechanisms of F. virguliforme. Thus, we applied Next-Generation DNA Sequencing to reveal the draft F. virguliforme genome sequence and identified putative pathogenicity genes to facilitate discovering the mechanisms used by the pathogen to cause this disease.

A new draft sequence of the fungal disease Fusarium virguliforme. The genome sequence can be browsed online using GBrowse.


Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode

Georgios Koutsovoulos, Benjamin Makepeace, Vincent N. Tanya, Mark Blaxter; published on arxiv.org

Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes, the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia

DNA to the host genome is common. We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. The fragments were unlikely to derive from a live Wolbachia infection: most were short, and the genes were disabled through inactivating mutations. Many fragments were co-assembled with definitively nematode-derived sequence. We found limited evidence of expression of the Wolbachia-derived genes. The D. viviparus Wolbachia genes were most similar to filarial strains, and strains from the host-promiscuous clade F. We conclude that D. viviparus was infected by Wolbachia in the past. Genome sequence based surveys are a powerful tool for revealing the genome archaeology of infection and symbiosis.

A fascinating study that uses genetic techniques to dig into the history of a host-parasite relationship. The D. viviparus genome was annotated using the MAKER pipeline.


Genome of the human hookworm Necator americanus [3]

The hookworm Necator americanus is the predominant soil-transmitted human parasite. Adult worms feed on blood in the small intestine, causing iron-deficiency anemia, malnutrition, growth and development stunting in children, and severe morbidity and mortality during pregnancy in women. We report sequencing and assembly of the N. americanus genome (244 Mb, 19,151 genes). Characterization of this first hookworm genome sequence identified genes orchestrating the hookworm's invasion of the human host, genes involved in blood feeding and development, and genes encoding proteins that represent new potential drug targets against hookworms. N. americanus has undergone a considerable and unique expansion of immunomodulator proteins, some of which we highlight as potential treatments against inflammatory diseases. We also used a protein microarray to demonstrate a postgenomic application of the hookworm genome sequence. This genome provides an invaluable resource to boost ongoing efforts toward fundamental and applied postgenomic research, including the development of new methods to control hookworm and human immunological diseases.

Another somewhat gruesome parasite, the human hookworm, which is responsible for causing more disease than any other soil-based helminth. The genome was annotated using MAKER and can be viewed online at Nematode.net and Wormbase.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086318
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0081832
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1038.2Fng.2875
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2014/01/24

Postdoc Position in Computational and Plant Evolutionary Biology

The project involves construction and analysis of plant gene families and phylogenies, particularly focusing on the large legume family, and development of a corresponding database and on-line tools for accessing and exploring gene families and associated annotations. Analysis of gene families and genes with known functions for better understanding of key events in evolution of selected plants and agronomic traits.

The primary research groups are located at Iowa State University (Ames, IA) and at National Center for Genome Resources (Santa Fe, NM). Remote work may be considered. This is a two-year position, with possibility for extension. Salary will be at competitive federal rates (>$50k). U.S. citizenship will not be a requirement for the position.

Applicants must have received Ph.D. in computational biology, bioinformatics, computer science, plant biology, genetics, or related discipline involving significant computational experience, statistics, and genetics.

If interested, please contact Steven Cannon.


Posted to the GMOD News on 2014/1/24

Prospecting for Proposals for GSoC 2014

Landing-page-gsoc2014.png

GMOD is participating in Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email help@gmod.org for advice!


Posted to the GMOD News on 2014/01/22

Biocuration 2014

7th International Biocuration Conference

April 6-9, 2014 -- Toronto, Canada

Abstracts Due: February 10, 2014

Biocuration 2014 will provide a forum for trainees, biocurators, investigators, clinicians and developers of biological databases to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research. Participants from academia, government and industry interested in the methods and tools employed in curation of biological and medical data are encouraged to attend. While a number of speakers have been invited, please note that the majority of oral presentations will be drawn from openly submitted abstracts.

SCOPE:

The proposed 2014 conference sessions and workshops will address the following challenges in biocuration:

  • Automated Function Prediction (workshop)
  • Big Data Curation: Dealing with supplementary data (workshop)
  • Biocreative Text Mining (workshop)
  • Biological and Clinical Ontologies (session)
  • Clinical Annotations (session)
  • Data Integration and Data Sharing (session)
  • Functional Annotations (session)
  • Microbial Informatics (session)
  • Phenotype (workshop)
  • Social Tools for publishing and curation (workshop)

INVITED SPEAKERS:

  • Dr. Tim Hubbard, Wellcome Trust Sanger Institute
  • Dr. Suzanna Lewis, Lawrence Berkeley National Laboratory
  • Dr. Patricia Babbitt, California Institute for Quantitative Biosciences (QB3)
  • Dr. Lincoln Stein, Ontario Institute for Cancer Research

WEBSITE:

7th International Biocuration Conference


REGISTRATION:

Online registration is now open


ABSTRACT SUBMISSION:

Submit your abstract for presentation (poster or talks only)


Posted to the GMOD News on 2014/01/17

GMOD At PAG 2014

Pagxxii.png

For those of you attending PAG XXII, we have made up a "cheatsheet" of GMOD-related content to check out.

If you haven't yet signed up for the Jan 2014 GMOD Meeting, please do so ASAP!

Posted to the GMOD News on 2014-01-08

Announcing GMOD Malaysia 2014

We are pleased to announce that GMOD will be running a three day training course in Kuala Lumpur, Malaysia, on 26-28 February 2014. The course will be run by experienced GMOD developers and tutors, and will cover the following tools:

Date: February 26-28, 2014

Venue: Kuala Lumpur, Malaysia.

Please check the GMOD Malaysia 2014 wiki page for updates, or email the GMOD help desk for more information.


Posted to the GMOD News on 2013/12/28

MAKER-P: an annotation pipeline for plants

The popular MAKER annotation pipeline has been extended and optimised to allow the annotation of plant species:

Sequencing diverse plant species of evolutionary, agricultural, and medicinal interest is becoming routine for even small groups; genome annotation and analysis is much less so. The MAKER-P pipeline is designed to make the annotation of novel plant genomes tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources. The MAKER-P pipeline generates species-specific repeat libraries, as well as structural annotations of protein coding genes, non-coding RNAs, and pseudogenes.

—Michael Campbell, MAKER development team


Posted to the GMOD News on 2013/12/16

GMOD Paper Cuts, Dec 6th, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system [1]

Snakes are limbless predators, and many species use venom to help overpower relatively large, agile prey. Snake venoms are complex protein mixtures encoded by several multilocus gene families that function synergistically to cause incapacitation. To examine venom evolution, we sequenced and interrogated the genome of a venomous snake, the king cobra (Ophiophagus hannah), and compared it, together with our unique transcriptome, microRNA, and proteome datasets from this species, with data from other vertebrates.

A fascinating insight into the biology and genome of the king cobra; the Burmese python has also been recently been sequenced [2], with both projects using MAKER for automated annotation.


PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools [3]

PortEco aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a 'virtual' model organism database that provides a single unified interface to the user, while integrating information from a variety of sources.

PortEco integrates E. coli data from numerous sources and uses a wiki-based system to enable collaborative knowledge management. PortEco is currently testing a JBrowse installation with the view to migrating over to JBrowse from their current GBrowse sequence browser.


The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse [4]

The Mouse Genome Database (MGD) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to human biology and disease. MGD maintains a comprehensive catalog of genes, functional RNAs and other genome features as well as heritable phenotypes and quantitative trait loci.

An update on the resources available at Mouse Genome Database (MGD), one of the groups involved in GMOD since the very beginning of the project.


NECTAR: a database of codon-centric missense variant annotations [5]

NECTAR (Non-synonymous Enriched Coding muTation ARchive) is a database and web application to annotate disease-related and functionally important amino acids in human proteins.

This stylishly-designed website draws data on disease mutations from numerous sources, including Ensembl, HGMD-PUBLIC, UniProt, COSMIC, and ClinVar, and includes GBrowse-able disease variants, function annotations, and paralogue annotations and a DAS server. Sweet!


Identification of a 31-bp Deletion in the RELN Gene Causing Lissencephaly with Cerebellar Hypoplasia in Sheep [6]

Lissencephaly is an inherited developmental disorder in which neuronal migration is impaired. A type of lissencephaly associated with cerebellar hypoplasia (LCH) was diagnosed in a commercial flock of Spanish Churra sheep. The genotyping of 7 affected animals and 33 controls with the OvineSNP50 BeadChip enabled the localization of the causative mutation for ovine LCH to a 4.8-Mb interval on sheep chromosome 4 using genome-wide association and homozygosity mapping.

Tracking down a sequence variation that causes developmental problems in sheep: a nice combination of classical genetics (studying families trees and examining phenotypes) and modern techniques, using resources provided at CSIRO's Livestock Genomics website.


Happy reading!


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Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/12/06

Canto, a GMOD tool for functional annotation

CantoTextLogo.png

We are pleased to announce that Canto, the PomBase community curation tool, is now a GMOD component.

Canto is an online tool that supports functional gene annotation by community researchers as well as by professional curators. It provides a simple interface to gather genetic and molecular data from publications for inclusion in public biological databases.

Curation in Canto uses OBO ontologies, and the specific set of ontologies is configurable upon setup. The PomBase Canto instance currently uses GO, PSI-MOD and FYPO.

Genetic and physical interaction annotation is also supported. Canto captures all necessary information about each interaction for submission to BioGRID.

Canto currently supports annotation export in JSON format, either by individual paper or in bulk (see some example data from PomBase Chado loading tests).

The JSON data from Canto can be loaded into a relational database using the Chado schema (as at PomBase) or alternative schemas.

Basic gene association file (GAF) export is also supported for GO annotations.

More information about Canto:


Posted to the GMOD News on 2013/12/02

New WebApollo Release (2013/11/22)

There is a new release of WebApollo available from the WebApollo release website. The updated server setup instructions are available on the WebApollo Installation page, and the WebApollo user guide has been updated accordingly.

If you currently have WebApollo instances up, please make sure to read the updated server setup instructions as some of the configuration files have changed. Since we now support multiple annotation types, you might want to upgrade your existing data stores to change transcripts to mRNAs (the only supported transcript type in previous versions). See the instructions on upgrading your data store.

You can try the public demo at http://genomearchitect.org/WebApolloDemo.

Summary of changes:

  • using JBrowse 1.10.9 release
  • new hybrid store (memory/disk) should use much less memory than the pure memory store (with a small degrade in performance) - useful for genomes with many annotations (you can configure which one to use as best fits your needs)
  • viewing of annotation info editor for users without write privilege (cannot modify the data)
  • FASTA data adapter
  • different annotation info editor configurations for different annotation types
  • database/history merger tool (command line)
  • data adapters now use iterators when exporting data (improves memory footprint)
  • add a configurable option for dumping owner and other meta-data to the GFF3 adapter
  • undoing an "add_feature/add_transcript" operation will now warn the user that proceed will delete the feature
  • data adapter grouping (see FASTA adapter)
  • adding/updating PubMed ID will now show the publication title for confirmation
  • improved add_transcripts_from_gff3_to_annotations.pl
  • adding of different annotation types (gene, pseudogene, tRNA, snRNA, snoRNA, ncRNA, rRNA, miRNA, repeat_region, transposable_element)
  • adding GO terms now supports searching/autocompletion
  • annotation info editor now requests data from the server in batch mode (should improve speed)

Fixes:

  • Chado featureprop writeback for generic attributes
  • add_transcripts_from_gff3_to_annotations.pl now properly loads status attributes
  • attributes being lost after undo/redo
  • redo of a merge_transcript operation after deleting one of the transcripts *should* work now
  • properly handle dragged transcripts that contain UTR elements
  • compressed data sent to the client no longer causes the client to hang when there are too many annotations
  • rewrote much of the split_transcript operation to better handle gene splitting

(via Ed Lee on the WebApollo mailing list)


Posted to the GMOD News on 2013/11/22

GMOD Paper Cuts, Nov 22nd, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The Genome Database for Rosaceae (GDR): year 10 update [1]

The Genome Database for Rosaceae (GDR), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality.

Lots of GMOD goodness in the Genome Database for Rosaceae, which is built using Tripal, includes Pathway Tools data, and has integrated GBrowse and GBrowse syn instances for sequence and synteny viewing respectively.


FlyBase 102—advanced approaches to interrogating FlyBase [2]

FlyBase is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for.

A followup to the FlyBase 101 paper [3] with updates on new features and functionality at FlyBase. FlyBase use the Chado database schema and users can query the database directly.


PATRIC, the bacterial bioinformatics database and analysis resource [4]

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC). [...] PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata.

PATRIC provides an immense data bank on bacteria: over 10,000 bacterial genomes as of Sept. 2013, projections of 15,000 by 2014. This paper details the resources provided, including their JBrowse-based genome browser, and Disease View, which integrates data on pathogens, genes, diseases, and geolocation of disease reports. Very cool!


Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells [5]

The discovery of gene body methylation, which refers to DNA methylation within gene coding region, suggests an as yet unknown role of DNA methylation at actively transcribed genes. In invertebrates, gene bodies are the primary targets of DNA methylation, and only a subset of expressed genes is modified.

Some interesting results from studies of gene body methylation in the sea squirt Ciona intestinalis during development.


Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources [6]

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. [...] The [RIKEN Brachypodium FL cDNA] database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.

TriFLDB, or the Triticeae full-length CDS database, is a new resource of Brachypodium full length cDNA clones and other resources; it includes GBrowse for exploring the B. distachyon genome and its annotations further.


Happy reading!


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Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/11/22

GMOD Paper Cuts, Nov 15th, 2013

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


The Aspergillus genome database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations [1]

The Aspergillus Genome Database (AspGD) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community.

A redesigned website and expanded resources for AspGD, which is now using JBrowse as primary genome browser.


CottonGen: a genomics, genetics and breeding database for cotton research [2]

CottonGen is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton.

An update on the CottonGen database, which uses the Tripal framework to make available data from a Chado database, and to integrate the GMOD tools GBrowse and CMap.


WormBase 2014: new views of curated biology [3]

WormBase is a highly curated resource dedicated to supporting research using the model organism Caenorhabditis elegans.

Updates and expansions on the WormBase website, which is notable not only for developing and using a number of GMOD tools, including GBrowse and Textpresso, but also for being hosted entirely in the cloud.


Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. [4]

The yeast Saccharomyces boulardii is used worldwide as a probiotic to alleviate the effects of several gastrointestinal diseases and control antibiotics-associated diarrhea. While many studies report the probiotic effects of S. boulardii, no genome information for this yeast is currently available in the public domain. We report the 11.4 Mbp draft genome of this probiotic yeast.

The newly-sequenced Saccharomyces boulardii genome, which was annotated with using MAKER.


DOOR 2.0: presenting operons and their functions through dynamic and integrated views [5]

We have recently developed a new version of the DOOR operon database, DOOR 2.0, which is available online at http://csbl.bmb.uga.edu/DOOR/ and will be updated on a regular basis. DOOR 2.0 contains genome-scale operons for 2072 prokaryotes with complete genomes, three times the number of genomes covered in the previous version published in 2009.

A bright, lively update to the Database of prokaryotic operons, which uses JBrowse for sequence visualization.


And finally, if you have access to the Wiley Online Library through your institution, you may like to check out [http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0915s43/abstract Cloud Computing with iPlant Atmosphere], from Current Protocols in Bioinformatics, which details the resources available on the [www.iplantcollaborative.org/‎ iPlant website] and how to get started with tools such as GBrowse.


Happy reading!


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Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2013/11/15

GMOD Job At QMUL

There is a position as a sysadmin/computing officer open at the School of Biological & Chemical Sciences at Queen Mary University of London (QMUL), with duties including setting up Galaxy and GMOD servers. The closing date for applications is 21st November 2013; for more details, see the job description.


Posted to the GMOD News on 2013/11/12


News Archives

The GMOD News Archives lists all news items since autumn 2007.