GMOD News
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. 
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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.
- 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.
- 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.
- Preview / save your changes. Edit and save the page until the news item looks like you want.
- Once you are happy with how the item looks, insert this line at the end of it:
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{{NewsItem|yyyy/mm/dd}}
Longer Instructions
Please follow these guidelines when adding a news item.
- 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.
- 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.
- You can include images in your news item. See preexisting news items for what markup to use to do this.
- Preview / save your changes. Edit and save the page until the news item looks like you want.
- Once you are happy with how the item looks, insert this line at the end of it:
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{{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.
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- 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:
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{{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}
Recent News
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.
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.
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,
PS: And please help get the word out!
New WebApollo Release
From Ed Lee on the WebApollo mailing list:
We'd like to announce a new WebApollo release.
Get the newest release -- Public demo -- Server setup instructions -- Updated user guide
Summary of changes:
- Fully revamped genomic sequence selection screen
- sorting by name and length (uses customizable JavaScript function)
- filtering of genomic sequence names
- Annotation info editor
- allows editing of symbols, comments, and dbxrefs
- Script for bulk loading gene/transcript/exons to annotation track
- Improved login system
- allows logging in from either genomic region selection screen or editor
- Configuration for using computed CDS (if available) when first creating a transcript (rather that using the longest ORF)
- Improved memory management
- Improved handling of concurrent edits
- HTTPS support
- Deletion of transcripts now warn users
- Accessing editor without logging in hides annotation track
- Using "[" and "]" to navigate through subfeatures when a feature in the annotation track is selected
- Improved interface for adding insertions and deletions
- Option to hide plus and/or minus strand
- Various bugfixes
2013 Meeting Notes Online
For those of you who were unable to attend the April GMOD meeting, slides and archived tweets from the meeting are now online. See the April 2013 GMOD Meeting page for the material.
Apply For GSoC 2013 Now!
The Genome Informatics group is now accepting applications from students to participate in Google Summer of Code 2013.
Please check out the FAQs, timeline, and student manual if you are unfamiliar with the process. You can also read the Melange manual if you need help with Melange. The deadline to apply is 19:00 UTC, 3 May 2013. Late proposals will not be accepted for any reason.
For the GMOD-related project proposals, see the GSoC wiki page, and to ask questions or make suggestions, please join the Genome Informatics GSoC mailing list.
Accepting Applications For GMOD Summer School 2013
Applications are now open for the 2013 GMOD Summer School!
This year's course will be held from July 19th to 23rd at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina.
The GMOD Summer School is the best way to learn how to install, configure, and use popular GMOD tools, including GBrowse, JBrowse, Galaxy, MAKER, Tripal, WebApollo, and Chado; courses are taught by the tool developers, and there will be evening sessions for those who want to work on their own data or troubleshoot issues with the developers.
More information and online application form
Applications are competitive, so we encourage you to apply well before the deadline, June 10th.
If you have any questions, please contact help@gmod.org and we will be happy to answer them.
JBrowse 1.9.0 released
JBrowse 1.9.0 is out today, with some great new features, and lots of smaller improvements and bug fixes.
It can be downloaded from jbrowse.org.
Headline features for this release:
- VCF variants support: we've added a new direct-access data backend for reading VCF files that have been compressed and indexed with bgzip and tabix, along with a new track type (HTMLVariants) optimized for viewing the sometimes-huge amounts of detail (particularly genotypes) associated with VCF variants.
- Wiggle track types now by default choose a y-axis scale dynamically for the region being displayed (set as
"autoscale": "local"in JBrowse configuration JSON). This is a big win for usability! Thanks to Gregor Rot and Raymond Wan for pushing for this feature! - If configured to do so, JBrowse can now display a dropdown dataset selector on the left side of the menu bar (similar to the one in GBrowse) that lets users switch between multiple datasets in the same JBrowse installation.
- The default "Simple" track selector now has a search input at the top that can quickly filter the list of displayed tracks to find the text you type.
- JBrowse now ships with a REST datastore backend that lets developers serve data to JBrowse from custom back-end systems. See JBrowse_Configuration_Guide#JBrowse_REST_Feature_Store_API for details.
Happy browsing!
--RobertBuels (talk) 10:09, 17 April 2013 (EDT)
Pathway Tools 17.0 Released
Version 17.0 of Pathway Tools has been released, and can be downloaded from the Pathway Tools website.
Version 17.0 is a major release that includes updates to the BioCyc Web site, downloadable data files, and downloadable Pathway Tools software/database bundle. Version 17.0 of BioCyc contains 2,920 Pathway/Genome Databases.
Contents |
General Changes
- Groups Enhancements
- A number of enhancements have been made to both Web Groups and Desktop Groups including re-organization of Web Groups menus and addition of new transformations.
- Rate-Limiting Reactions
- A reaction can now be designated as rate limiting with respect to a given metabolic pathway, using the pathway editor. Rate-limiting reactions are identified as such in pathway diagrams using an hourglass icon.
- Web Omics Pop-ups
- When using the Cellular Omics Viewer you can view a graph of omics data (e.g., plotting gene-expression data over time for a given gene). To do so, paint expression data on the Cellular Overview. Then mouse over a reaction (or metabolite) of interest. Click "Omics" in the menu of the resulting pop-up window, which will graph the omics data for that reaction.
- PGDB Registry Speedups
- The PGDB registry is a facility whereby Pathway Tools users can share and download PGDBs via the Internet. As the number of PGDBs in the registry grew, the speed of the registry became far too slow; the registry interface has been re-designed so that finding PGDBs within the registry is much faster.
RouteSearch -- Metabolic Route Search
The new Web-based RouteSearch tool, accessible from command Tools -> Metabolic Route Search, supports two types of searches in metabolic networks. For both types of search, the user specifies a starting and ending metabolite of interest, and the software generates alternative reaction pathways connecting those metabolites.
- Mode 1 -- Within Organism Searches
- In this mode the search makes use of reactions within the selected PGDB only.
- Mode 2 -- Synthetic Pathway Searches
- In this mode the search makes use of reactions within the selected PGDB plus reactions within the MetaCyc DB. The user may specify a higher penalty for introducing reactions from MetaCyc. This mode is not available within public Pathway Tools web servers but may be accessed by installing Pathway Tools locally and running a web server accessible on an intranet.
PathoLogic
- Pathway Abundance Scores for Metagenome Data
- PathoLogic can now compute abundance scores for pathways based on gene abundance values provided in a .PF input file. Gene entries in a .PF file may contain ABUNDANCE fields that specify the number of times that gene was observed in a metagenomics dataset. The abundance scores are present in file pathways-report.txt in the PGDB reports directory. More information on calculation of abundance scores will be provided in a future blog post.
Full details in the Pathway Tools release notes.
SGD and ENCODE DCC Jobs
From Mike Cherry at the Cherry Lab, Stanford, CA:
I have multiple positions open in my group, either with the Saccharomyces Genome Database or the ENCODE Data Coordination Center. The positions include Senior Biocurator, Data Wrangler (Bioinformatic Analyst), and Python Software Engineer for UI construction. Please see the job advertisement (PDF) for more information.
New NGDx Group at Novartis
From Pamela Bailey at Novartis Institutes for BioMedical Research:
Novartis Institutes for BioMedical Research (NIBR) is building a new Next Generation Diagnostics (NGDx) group at its global headquarters in Cambridge, MA. Next generation sequencing and other cutting-edge molecular characterization technologies will be important tools for discovering breakthrough therapeutics and for delivering the right medicines to the right patients. We are hiring scientists at all levels to staff this group and opportunities will exist for genomics scientists, computational biologists, software and systems engineers, and more. To find out more about this new group, please visit http://novartis.avature.net/NGDX.
2013 Meeting: Keynote Announcement
We are extremely pleased to announce that the keynote speaker at the [April 2013 GMOD Meeting] will be Dr. Kentaro Yoshida of The Sainsbury Lab, speaking about the Open Ash Dieback Project.
The Open Ash Dieback project is an exciting and vital effort to gain insight into ash dieback, a chronic fungal disease of ash trees. Ash dieback is caused by a fungus, Hymenoscyphus pseudoalbidus, and is characterised by leaf loss and crown dieback in infected trees. Ash dieback has already caused significant damage to tree populations in northern Europe and was recently discovered in the UK. The Open Ash Dieback project embraces the new paradigms of open science and crowdsourcing by making all its data public and asking scientists to analyse genetic data from ash and the fungus.
More information and media coverage of OADB:
- Paper: Crowdsourcing genomic analyses of ash and ash dieback – power to the people
- Scientists crowdsource to decode genetic code of ash dieback fungus - from The Guardian
- Open Science versus Ash Dieback
2013 Meeting: Last Day For Early Birds
Early bird registration for the April 2013 GMOD Meeting closes today, so if you would like to register at the lower rate, please head over to Eventbrite ASAP!
The meeting agenda is shaping up nicely, with some interesting guest speakers including Dr. Jane Lomax from the Gene Ontology, Dr. Manuel Corpas from The Genome Analysis Centre on BioJS, Joseph Rossetto and Bren Vaughan talking about Drupal at the European Bioinformatics Institute, as well as updates on GMOD components like Galaxy, JBrowse, and Tripal.
If you would like to give a lightning talk or a longer presentation, please email the GMOD help desk and let us know!
We are assessing demand for remote attendance, so if you want to join in from the comfort of your own office (or home, car, etc.), please add your name to the Remote Attendee list or email GMOD help desk.
ISMB 2013: Automated Function Prediction
Those of you attending ISMB may be interested in the Automated Function Prediction special interest group. The following comes from Iddo Friedberg, co-chair, on behalf of the AFP 2013 organizing committee:
The Automated Function Prediction, an ISMB 2013 Special Interest Group meeting.
Key Dates:
- April 20, 2013: Deadline for submitting extended abstracts posters & talks
- May 9, 2013: Notifications for accepted abstracts e-mailed to corresponding authors
- May 16, 2012: Deadline for presenters to confirm acceptance of invitation to speak.
- July 20, 2013: AFP SIG preceding ISMB/ECCB 2013, Berlin
Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered sequences are increasing, and the fraction of genes whose function is known is decreasing. In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the available function prediction software.
For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry.
The Automated Function Prediction Special Interest Group (AFP SIG) has been part of ISMB since 2005. We call upon all researchers involved in gene and protein function prediction and annotation, both computational and experimental, to submit an abstract to the AFP meeting. Authors of select abstracts will be invited to give a talk and/or present a poster.
We will also be discussing the upcoming second Critical Assessment of Function Annotations, or CAFA. CAFA 1 was a highly successful experiment, engaging 30 groups worldwide, and has resulted in 16 peer-reviewed papers in Nature Methods and BMC Bioinformatics:
- http://www.nature.com/nmeth/journal/v10/n3/full/nmeth.2340.html
- http://www.biomedcentral.com/bmcbioinformatics/supplements/14/S3
We are looking forward to a new and expanded CAFA 2 in 2013-2014, which will include a cellular component prediction track, and a human-specific track.
Keynote speakers:
- Patricia Babbitt, University of California, San Francisco
- Alex Bateman, European Bioinformatics Insitute
- Anna Tramontano, "La Sapienza" Universtiy, Rome.
For further instructions on AFP 2013, please see BioFunctionPrediction.org.
Contact: afp.cafa.2013@gmail.com.
GSoC 2013 Mentors Wanted!
GMOD's participation in Google Summer of Code has been confirmed as the Genome Informatics proposal has been accepted by Google. GSoC is a global program that offers student developers stipends to write code for various open source software projects. This year, the Genome Informatics group is coordinating proposals for seven big bioinformatics projects: Galaxy, GBrowse, GMOD, JBrowse, Reactome, and Wormbase. See the GSoC wiki page for more information or visit the Genome Informatics GSoC page.
We are still interested in new project ideas; if you have one, or you are interested in being a mentor, please post on the Google Summer of Code page.
Questions or comments should be directed towards the Genome Informatics GSoC coordinator, Robin Haw.
More information is also available on the Genome Informatics mailing list.
Tripal v1.0 Released
From Stephen Ficklin on the Tripal mailing list:
Dear Tripal Community,
We are happy to announce that Tripal v1.0 is officially released!
Here are some useful links:
- A list of new features and functionality
- Download Instructions
- Upgrade Instructions
- Compatible Extension modules
- The updated v1.0 Tutorial
- Updated API
If you have been using the v1.0 development version you should update your version of Tripal and perform database updates (e.g. 'drush updatedb').
Please feel free to provide any feedback on the Tripal mailing list! Thank you to those who have done so already and have helped make Tripal better.
Last Chance To Be Surveyed
The GMOD community survey will close on March 8th, so please make sure that you have given us your feedback by then!
Results will be discussed at the April 2013 GMOD Meeting in Cambridge, UK.
GCC2013: Register! Present!
We are pleased to announce that early registration and paper and poster abstract submission are now open for the 2013 Galaxy Community Conference (GCC2013). GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo.
GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Day for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics.
If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at:
- Bioinformatics tool developers and data providers
- Workflow developers and power bioinformatics users
- Sequencing and Bioinformatics core staff
- Data archival and analysis reproducibility specialists
Early registration saves up to 75% off regular registration costs, and is very 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. Early registration closes 24 May.
Abstract submission for oral presentations closes 12 April, and for poster submissions on 3 May. Please consider presenting your work. If you are working with big biological data, then this meeting wants to hear about your work.
Thanks, and hope to see you in Oslo!
The GCC2013 Organizing Committee
PS: And please help get the word out!
2013 Meeting Registration Open
Registration for the 2013 GMOD Community Meeting is now open at gmod2013.eventbrite.com.
Standard registration costs $85 and is available until March 21st; after that, the price rises to $100. Registration covers the cost of the venue hire and refreshments; for information on accommodation, please see the April 2013 GMOD Meeting page.
If you do plan on attending the meeting (or even if you don't!), please do the GMOD Community Survey. We will be discussing the survey results at the meeting and making plans for the future.
Using GBrowse 2.0 paper
There is a new GBrowse paper by Lincoln Stein out in Briefings in Bioinformatics, entitled Using GBrowse 2.0 to visualize and share next-generation sequence data, PMID:23376193 [1]
Abstract:
GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data.
- ↑ . Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief. Bioinformatics 2013 14:162-71.
DOI:10.1093/bib/bbt001 PMCID:PMC3603216 PMID:23376193
News Archives
The GMOD News Archives lists all news items since autumn 2007.
