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Prospecting for Proposals for GSoC 2024

;

The Open Genome Informatics group and GMOD has submitted an application for 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 different sizes participate 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, don't hesitate to get in touch with us at robin.haw@oicr.on.ca 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 rhaw@oicr.on.ca and help@gmod.org for advice!

Posted to the GMOD News on 2024/02/12

JBrowse2 v1.1.0 Released

1 We're pleased to announce a new release of JBrowse Web!
- 1.1 Changed callbacks language from JavaScript to Jexl
- 1.2 Fetch intron and upstream/downstream sequences
- 1.3 Interactive documentation using Storybook
- 1.4 Enhanced navigation to drawer widget stack
- 1.5 Downloads
- 1.6 1.1.0 (2021-03-29)
  - 1.6.1 🚀 Enhancement
  - 1.6.2 🐛 Bug Fix
  - 1.6.3 📝 Documentation
  - 1.6.4 🏠 Internal
  - 1.6.5 Committers: 6

We're pleased to announce a new release of JBrowse Web!

(Reposted by permission from https://jbrowse.org/jb2/blog/2021/03/29/v1.1.0-release

Changed callbacks language from JavaScript to Jexl

To allow users to safely and seamlessly share advanced configurations in sessions, we now use Jexl to express configuration callbacks. Note that this is a breaking change, function()-style callbacks will no longer work.

For details, see the callbacks section of our configuration guide.

Fetch intron and upstream/downstream sequences

We also have several other improvements including the ability to get intron and upstream/downstream sequence in the feature details

Interactive documentation using Storybook

Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. The docs contain live examples of how the LGV component can be used, along with source-code examples. The site can be found here.

We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web.

See below for demos of the new navigation UI.

Demo of using the minimize button in the drawer

Downloads

v1.1.0

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.1.0 (2021-03-29)

🚀 Enhancement

core

1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
1816 Remove some animation effects (@cmdcolin)
1778 Adds dropdown to show drawer widget stack (@teresam856)
1685 Change callbacks language from JavaScript to Jexl (@peterkxie)

Other

1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)

🐛 Bug Fix

core

1811 Check for existence of window more robustly to allow in SSR or node applications (@elliothershberg)
1793 Fix dotplot rendering outside it's allowed bounds (@cmdcolin)
1783 Add hic aborting and fix remoteAbort signal propagation (@cmdcolin)
1723 A few bugfixes (@garrettjstevens)

Other

1815 Clear tracks when using "Return to import form" (@cmdcolin)
1819 Standardized sentence casing on drawer widget titles (@cmdcolin)
1796 Bump generic-filehandle for fixing CORS errors from Chrome cache pollution (@cmdcolin)

📝 Documentation

1824 Add storybook docs page for nextjs usage (@elliothershberg)
1770 1469 storybook deploy (@elliothershberg)
1807 Update developer guide to cover displays, and highlight working external plugins (@cmdcolin)
1779 Collaborative release announcement editing (@rbuels)
1791 Add a couple more demos for our live version with MDX (@cmdcolin)

🏠 Internal

Other

1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)

core

1834 Change jbrowse-components monorepo default branch from 'master' to 'main' (@rbuels)

Committers: 6

Colin Diesh (@cmdcolin)
Elliot Hershberg (@elliothershberg)
Garrett Stevens (@garrettjstevens)
Peter Xie (@peterkxie)
Robert Buels (@rbuels)
Teresa Martinez (@teresam856)

Posted to the GMOD News on 2021/03/30

Prospecting for Proposals for GSoC 2021

The Genome Informatics group and GMOD will be submitting an application for 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 robin.haw@oicr.on.ca 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 robin.haw@oicr.on.ca and help@gmod.org for advice!

Posted to the GMOD News on 2021/02/16

Codefest 2020

Handlery Hotel in the Balboa room
(down the street from the Town and Country Hotel)
San Diego, California
January 9-10, 2020 </strong>

Immediately before Plant and Animal Genome XXVIII (PAG 2020)

</center>

Participant list now available

There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to

We already know that there will be Tripal, Chado, Apollo and JBrowse developers present.

Agenda

Thursday:

9:00-10:00	Introduction and working group organization
10:00-12:00	Working groups
12:00-1:30	Lunch (on your own)
1:30-4:00	Working groups
4:00-5:00	Report on progress

Friday:

9:00-12:00	Working groups
12:00-1:30	Lunch (on your own)
1:30-3:00	Working groups
3:00-3:45	Report on progress

Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery.

Posted to the GMOD News on 2020/01/08

Tripal 3.5 Released

This Tripal release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedures to update. Changes in this version:

Performance improvements to the Cross References, Relationships, and References.
A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
Updates to the online documentation
Bug fixes in web services
Bug fixes in the OBO loader for ontologies that won't import.

Posted to the GMOD News on 2021/02/08

JBrowse 2 release

We are pleased to announce the first public release of JBrowse 2!

JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

New types of views, including circular, synteny, and dotplot views
Graphical configuration editing
Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action here. To get started using JBrowse 2, visit our quickstart guide here.

We'd love to hear what you think! You can find information about how to contact us here.

The JBrowse Team

Posted to the GMOD News on 2020/11/09

Prospecting for Proposals for GSoC 2020

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.

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

Posted to the GMOD News on 2020/02/03

Call for PAG Abstracts

Time is short!

If you want to attend PAG and would like to present on a topic that would be of interest to the GMOD community, please send an abstract or at least a descriptive title to help@gmod.org. Types of talks typically include updates on GMOD software projects, usage stories for successful sites, proposals for new GMOD projects and descriptions of plugins for existing GMOD software projects like Tripal, JBrowse and Galaxy.

Please consider giving a talk and sharing your experience and ideas!

Posted to the GMOD News on 2016/11/04

New GMOD Server

GMOD.org has a new home

Due to a old server being retired, gmod.org has a new home. In the course of migrating the server, we also had to update the version of MediaWiki that is powering the site. If you notice any problems with gmod.org, please send an email to help at gmod dot org to let us know what's going on.

Posted to the GMOD News on 2016/09/29

GMOD-JBrowse 2016 Survey

Hello Genome Informaticians,

The following survey is aimed at users (and potential users) of GMOD genome databases, especially the JBrowse genome browser. It will directly inform the priorities for renewal of the R01 that funds JBrowse software development and the GMOD helpdesk.

We know surveys are thankless and dull. Your time in filling out this one is GREATLY appreciated.

https://goo.gl/forms/1bKIuAMjGKrS0hUi1

Thanks & best wishes,

The JBrowse team

Posted to the GMOD News on 2016/09/23

GCC2016

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington. Galaxy is a GMOD Component which interacts with many other GMOD Components, including:

Tripal: A web front end for Chado databases. Galaxy is working with the Tripal project to make Galaxy be Tripal's analysis engine.
JBrowse: A client-side genome browser and successor to the venerable GBrowse. JBrowse as a Galaxy Tool was presented by Eric Rasche at GCC2015. Ian Holmes, the JBrowse PI, has put JBrowse-Galaxy integration at "top of the list" for JBrowse's infrastructure upcoming infrastructure work.
MAKER: A genome annotation pipeline that integrates several gene annotation engines, and combines them to produce annotation that is better than any individual tool produces. A MAKER-Galaxy by Agriculture and Agri-Food Canada was presented at ISMB 2014.
InterMine and BioMart: These are both popular data sources that are integrated with Galaxy.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.

Oral presentation abstract submission closes April 8; poster and demo abstract submission close May 20; and scholarship applications close May 1.

Posted to the GMOD News on 2016/04/04

2016 GMOD Meeting

The next GMOD Community Meeting will be held at Indiana University in Bloomington, Indiana, United States, June 30-July 1, directly after the 2016 Galaxy Community Conference (GCC2016). GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.

Please register online at Eventbrite by June 20th 2016. Early bird registration ends May 21.

For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract.

If you have any suggestions or requests for the meeting, please contact the GMOD help desk.

Posted to the GMOD News on 2016/04/04

Please Support EcoCyc

EcoCyc, the E. coli information resource and one of the resources offered by the Pathway Tools group, is in need of letters of support from the community after receiving a poor grant review, which could result in a complete loss of funding on July 1st, 2014. If you are a user of EcoCyc, please consider writing a short letter in support of this vital resource. The deadline for letters is May 26th, 2014.

From the Pathway Tools website

ECOCYC FUNDING CRISIS -- DEADLINE MAY 26

EcoCyc received a very unfavorable grant review in February 2014. We are in discussions with the NIH to resolve this situation.

EcoCyc's usage has steadily increased. We made very strong progress on our challenging aims from the current grant period, and the project has produced many publications. EcoCyc received excellent reviews on previous grant applications. Furthermore, the needs of the prokaryotic research community for the content and software tools offered by EcoCyc have never been higher.

In the worst case, we will lose all funding on July 1, 2014 and be forced to re-apply. Even in the best case, we may receive a crippling funding cut that causes us to fall behind in its manual literature curation effort, and requires us to lay off experienced curation staff until funding can be obtained.

These events could seriously undermine EcoCyc, end the project altogether, or force us to begin charging usage fees.

To maintain EcoCyc as the free, up to date, and high-quality resource that you depend on, please tell the NIH what EcoCyc means to your research. Please click the button below to submit a PDF letter of support on institutional letterhead, or a short support statement, explaining the importance of EcoCyc.

We ask all regular users to submit; a short statement will take less than two minutes of your time. Students and post-docs, please ask your lab head to submit in addition to your submission.

More information on what to write and where to submit letters is available at the Pathway Tools website.

Posted to the GMOD News on 2014/05/21

June 2014 WebApollo Hackathon

Berkeley Bioinformatics Open-Source Projects (BBOP) invites you to join us this summer for a WebApollo Hackathon at Lawrence Berkeley National Laboratory, California.

When: Monday, June 2 - 6, 2014

Where: Lawrence Berkeley National Laboratory. Building 74 (B74), Room 104. 1 Cyclotron Rd, Berkeley, CA 94720

What: five days of intensive, collaborative WebApollo development!

For five days developers will work on new features of interest to their research communities, improve existing features, and collaborate on developing features of interest to other colleagues.

Participants should:

be able to set up their own WebApollo server before arriving in Berkeley, including Postgres, Tomcat, etc.
code comfortably in JavaScript (client) and Java (server).

What will we do while we are there? You tell us! Send your suggestions for feature development, your questions, and any additional comments to apollo [dash] dev [at] lists [dot] lbl [dot] gov

Registration is free of charge, but tickets are required. Register online!

Participants are responsible for arranging travel and accommodation on their own.

More details: WebApollo Hackathon information

via Monica Munoz-Torres

Posted to the GMOD News on 2014-04-22

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

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

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.

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!

↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-86
↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1534.2Fgenetics.113.160713
↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0087499
↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086728
↑ 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

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!

↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086318
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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

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.

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

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:

Chado database schema
GBrowse genome browser
Galaxy workflow generator
Intermine data warehouse
JBrowse genome browser
MAKER and MAKER-P genome annotation pipeline
Tripal website/database interface

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

Read the publication on MAKER-P: MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations

Download and install MAKER and MAKER-P.

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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Posted to the GMOD News on 2013/12/06

Canto, a GMOD tool for functional annotation

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:

GMOD wiki page on Canto -- includes downloads and mailing list
Canto website at PomBase
Canto source code on GitHub

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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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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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

GMOD Paper Cuts, Nov 8th, 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.

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host-parasite interaction ^[1]: The first characterization of the Ruditapes decussatus transcriptome; the team responsible have also set up Rdecusdb, the Ruditapes decussatus database, built with Tripal

The database of genomic variants: a curated collection of structural variation in the human genome ^[2]: An update on the Database of Genomic Variants (DGV), which provides a publicly accessible, comprehensive curated catalogue of structural variation (SV) found in the genomes of control individuals from worldwide populations. The core visualization tool, GBrowse, has been upgraded with additional functions to facilitate data analysis and comparison.

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease ^[3]: A genome-wide association study on humans of European ancestry that identifies new loci associated with Alzheimer's disease.

Crossover Heterogeneity in the Absence of Hotspots in Caenorhabditis elegans ^[4]

Computational framework to support integration of biomolecular and clinical data within a translational approach ^[5]: This article was published earlier this year, and is a good example of extending the Chado schema to fit the needs of the project.

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Posted to the GMOD News on 2013/11/08

Open Position At dictyBase

dictyBase is hiring. We have an open position for a Bioinformatics Software Engineer at dictyBase.
See the official posting for full details.

Posted to the GMOD News on 2013/11/04

Tripal 1.1 Publication

The Tripal team have put out a publication on the 1.1 version of the software. Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. can be read for free at PubMedCentral or at the Database journal.

Here is the abstract:

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include

a new bulk loader that allows a site curator to import data stored in a custom tab delimited format;

full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages);

new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules.

Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info.

Posted to the GMOD News on 2013/10/31

San Diego 2014 Registration Open

Registration is now open for the upcoming GMOD community meeting, to be held at the Best Western Seven Seas, San Diego, CA, on January 16th and 17th 2014.

Register online at Eventbrite now!

Early birds can catch the $50 registration worm, which is available until mid-December; after this, the registration fee will rise to $70.

If you would like to give a presentation at the meeting, please submit your abstract with your meeting registration form.

A block of rooms is being held for attendees of the GMOD meeting at a very good rate; to make reservations in this block, you must call (800) 328-1618 and ask for the GMOD rate. The GMOD rate is not available through online bookings.

If you have any questions or comments, please feel free to contact the GMOD helpdesk on help@gmod.org!

Posted to the GMOD News on 2013/10/25

GCC2014: June 30 - July 2

The 2014 Galaxy Community Conference (GCC2013) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University], in Baltimore, Maryland, United States.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference will also includes a Training Day offering in-depth topic coverage, across several concurrent sessions. See the GCC2013 web site for an idea of what happens at a Galaxy Community Conference. The GCC2013 site includes links to slides and videos for all accepted talks.

Posted to the GMOD News on 2014/10/02

Get the Full ImpactStory

<img alt="ImpactstoryLogo.png" src="http://gmod.ohttps://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/thumb/7/7a/ImpactstoryLogo.png/250px-ImpactstoryLogo.png" width="250" height="46" srcsethttps://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/thumb/7/7a/ImpactstoryLogo.png/375px-ImpactstoryLogo.png 1.5xhttps://raw.githubusercontent.com/GMOD/gmod.github.io/main/mediawiki/images/7/7a/ImpactstoryLogo.png 2x" /> The GMOD wiki now includes ImpactStory altmetrics for publications cited in the page text. See the Publications page for an example of ImpactStory altmetrics.

For those unfamiliar with the term altmetrics, these are measures beyond simple paper citations. The Altmetrics Manifesto provides the following clarification:

Altmetrics expand our view of what impact looks like, but also of what’s making the impact. This matters because expressions of scholarship are becoming more diverse. Articles are increasingly joined by:

The sharing of “raw science” like datasets, code, and experimental designs

Semantic publishing or “nanopublication,” where the citeable unit is an argument or passage rather than entire article.

Widespread self-publishing via blogging, microblogging, and comments or annotations on existing work.

ImpactStory collates metrics from numerous online sources to give a more complete picture of how an article, data set, piece of software, or other research product is being used and discussed. More information is available on the ImpactStory website.

We hope to add impact metrics for GMOD software soon.

GMOD 2014 San Diego: Save the Date

The next GMOD Community Meeting will be held in San Diego, CA, on January 16-17, directly after PAG XXII. In addition to the usual talks and updates, we plan to have a poster session, and a workshop on migrating from GBrowse to JBrowse. If you have items or ideas for the agenda, please feel free to contact the GMOD helpdesk.

GMOD will also have a big presence at PAG, with a day-long workshop covering many of the actively-developed GMOD components.

More details on both the GMOD community meeting and GMOD at PAG will be posted on the wiki closer to the time.

Posted to the GMOD News on 2013-09-10

Statistical Genomics PostDoc at PSU

Are you interested in genomics and do you have skills in Bioinformatics, Computational Biology and Statistics? The Makova lab in the Department of Biology at The Pennsylvania State University is looking to hire a postdoctoral researcher for an NSF-funded project examining regional variation in mutation rates (see our recent publication in PNAS: Kuruppumullage Don, Ananda, Chiaromonte, Makova 2013). With new sequencing technologies, multiple human genomes and their detailed annotations (e.g., ENCODE) are suddenly accessible to us. This gives us a terrific opportunity to explore previously inaccessible evolutionary processes (e.g., mutation) and other biological associations (location of genes in certain mutation states, as identified by HMMs). Such knowledge is vital in a clinical setting where disease mutations need to be evaluated. Our resources and links with medical researchers at Hershey Medical School and computational biologists from the Galaxy team put us in a great position to address these questions.

Candidates should have experience in bioinformatics, working knowledge of statistics and should have a broad understanding of molecular biology and genetics. Familiarity with next-generation sequencing data analysis is desirable. A PhD is required. You will be joining an established dynamic group. We are part of the Center for Medical Genomics and of the Center for Comparative Genomics and Bioinformatics. Penn State is a vibrant scientific community with particular strengths in genomics, bioinformatics and molecular evolution. Our location, in State College, Pennsylvania, is known for excellent schools and numerous opportunities for outdoor activities.

The starting date is flexible, with an earlier date preferred. This position is funded for one year from date of hire, with good possibility of refunding. Interested applicants should send a pdf with a CV, a statement of research interests, and contact information for three referees to Kateryna Makova, indicating postdoc in the subject line. Employment will require successful completion of background check(s) in accordance with University policies. Penn State is committed to affirmative action, equal opportunity, and the diversity of its workforce.

Posted to the GMOD News on 2013/09/09

Support Your Friendly Local GMOD

The Generic Model Organism Database project is applying for a community resources for genomics grant from the NIH to continue the work that GMOD does, with a focus on JBrowse and Chado development, and GMOD coordination (standards, meetings, and courses).

We need to demonstrate that we support the community and have the support of the community, and we would like to demonstrate that by submitting many letters of support from users. We would be very grateful if you could take a couple of minutes to write such a letter; it should include information about how you use or plan to use GMOD software. There are some template paragraphs provided for inspiration.

The letters should be on institutional letterhead, signed, and then scanned to a PDF, or you could mail the original to Scott Cain and he will scan them.

The deadline for getting the letters of support is September 3. Please contact the GMOD helpdesk or email Scott directly if you're willing to write a letter or if you need any help.

This grant would help to secure the future of important parts of the GMOD project, so we would be very grateful for your help!

Via Scott Cain

Posted to the GMOD News on 2013/08/20

2013 Summer School Tutorials Available

The tutorials for the material taught at this year's GMOD summer school are now all available on the GMOD website. There are updated tutorials for several components, particularly those where new software releases have occurred since the last summer school; these include:

The full set of GMOD tutorials, featuring all the material from this year's summer school and more, is available from the Tutorials section of the wiki.

Posted to the GMOD News on 2013-08-02

JBrowse 1.10.0 released

I am very pleased to announce the release of JBrowse 1.10.0, a major new JBrowse release with some big new features, and a *huge* number of smaller improvements!

It can be downloaded from http://jbrowse.org/jbrowse-1-10-0/.

As always, see the updated

JBrowse Configuration Guide for documentation on how to use the new features.

RobertBuels (talk)

Posted to the GMOD News on 2013/07/30

OpenID Account Creation Fixed

Update on July 11:

Account creation using OpenID is currently disabled due to problems with the OpenID plugin. New wiki users wishing to create accounts should use the 'Log in / create account' link and request an account; your request should be dealt with within 24-48 hours. Unfortunately, due to spammers and others creating bogus accounts, we have to had to put protective measures in place.

Please email the GMOD helpdesk if you have any problems or want to expedite the creation of your account!

Posted to the GMOD News on 2013/07/10

GMOD's GSoC Going Great Guns!

GMOD is lucky enough to have a Google Summer of Code student working with us through the summer. Flavien Bossiaux is a computer science student from the University of Nice, France, and he is working on a number of improvements to the GMOD website user experience. He has already created two Mediawiki extensions to allow the embedding of external content into the GMOD wiki; visit the GMOD calendar to see one of them, the iAnn calendar plugin, in action.

Flavien is recording his thoughts and progress on his website through the summer; please check it out! You can also follow Flavien on Twitter, and check out his his Github repo.

If you have any thoughts or suggestions on the GSoC project, please send them along to the GMOD helpdesk.

Posted to the GMOD News on 2013/07/09

GMOD in the Cloud 2.0 Released

from Scott Cain:

I am pleased to announce that GMOD in the Cloud 2.0 has finally been released to the public. This Amazon Web Services (AWS) Amazon Machine Image (AMI) is public and can be cloned by anybody with an AWS account. A demo of GMOD in the Cloud is running (though it may take a day or two for DNS to update fully).

This AMI has several GMOD software packages installed and configured, including:

Chado 1.23
Tripal 1.0 (plus a few bug fixes from dev)
GBrowse 2.54 (with samtools, BigWig and fastCGI support)
JBrowse 1.9.5
WebApollo (most recent release from May, 2013)

For more information about GMOD in the Cloud, visit the Cloud page on the wiki, and post questions about using GMOD in the Cloud to the GMOD developers mailing list, gmod-devel@lists.sourceforge.net.

Posted to the GMOD News on 2013/06/14

Last Call For Summer School Apps

The deadline to apply for the 2013 GMOD Summer School is rapidly approaching! Please submit your application by June 10th to ensure that you are in consideration for a place.

The GMOD Summer School is the best way to get to grips with key components of the GMOD toolkit, including Chado, GBrowse, Galaxy, JBrowse, WebApollo, MAKER, Tripal, and more. Tool developers will be on hand to answer questions and help with troubleshooting.

Applications received after June 10th will be kept in case there are spare places due to accepted applicants not being able to attend.

Posted to the GMOD News on 2013/06/06

GCC2013 Early Reg closes 24 May

Early registration for the 2013 Galaxy Community Conference (GCC2013) ends this Friday, 24 May. Early registration saves up to 75% off regular registration costs, and is downright affordable, with combined registration (Training Day + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations.

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynote, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks.

An early program is available featuring 25 oral presentations, lightning talks and poster sessions, and the just added Birds-of-a-Feather gatherings.

If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you.

Thanks,

GCC2013 Organizing Committee

PS: And please help get the word out!

Posted to the GMOD News on 2013/05/20

New WebApollo Release

From Ed Lee on the WebApollo mailing list:

We'd like to announce a new WebApollo release.

Get the newest release - ## Navigation menu ### Navigation - [GMOD Home](Main_Page) - [Software](GMOD_Components) - [Categories / Tags](Categories) ### Documentation - [Overview](Overview) - [FAQs](Category%253AFAQ) - [HOWTOs](Category%253AHOWTO) - [Glossary](Glossary) ### Community - [GMOD News](GMOD_News) - [Training / Outreach](Training_and_Outreach) - [Support](Support) - [GMOD Promotion](GMOD_Promotion) - [Meetings](Meetings) - [Calendar](Calendar) ### Tools - Browse properties - Last updated at 11:12 on 22 August 2013. - Content is available under a GNU Free Documentation License unless otherwise noted.

GMOD News Archives

All News Items

Contents

We're pleased to announce a new release of JBrowse Web!

Changed callbacks language from JavaScript to Jexl

Fetch intron and upstream/downstream sequences

Interactive documentation using Storybook

Enhanced navigation to drawer widget stack

Downloads

1.1.0 (2021-03-29)

🚀 Enhancement

🐛 Bug Fix

📝 Documentation

🏠 Internal

Committers: 6

Agenda

Call for PAG Abstracts

GMOD.org has a new home