http://permalink.gmane.org/gmane.science.biology.gmod.announce hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.science.biology.gmod.announce/130 <pre>Learn how to get started with GMOD's toolkit for genetics and genomics, GMOD in the Cloud! July 19-23, 2013; NESCent, Durham, North Carolina http://gmod.org/wiki/2013_GMOD_Summer_School The 2013 GMOD Summer School is the best way to get to grips with GMOD in the Cloud, GMOD's suite of genomic and genetic software. Over five days, attendees will learn how to install, configure, and run popular GMOD software for visualization, storage, and dissemination of genetic and genomic data. The following software is covered: - Chado, a species-independent database schema covering many areas of genetic and genomic data; - GBrowse, the ubiquitous genome browser; - GBrowse syn, a synteny browser built on GBrowse; - Galaxy, analysis and computation pipeline; - JBrowse, genome browsing evolved; - MAKER, automated annotation pipeline; - Tripal, a slick web interface for displaying and editing data from Chado; and - WebApollo, distributed community genome annotation tool (built on JBrowse). There are additional sessions o</pre> Amelia Ireland 2013-05-23T18:51:46 http://permalink.gmane.org/gmane.science.biology.gmod.announce/129 <pre>We are now accepting applications for the 2013 GMOD Summer School, to be held NESCent, Durham, North Carolina from July 19th to 23rd. 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: http://gmod.org/wiki/2013_GMOD_Summer_School Applications are competitive, so we encourage you to apply well before the deadline, June 10th. If you have any questions, please contact help&lt; at &gt;gmod.org and we will be happy to answer them. </pre> Amelia Ireland 2013-04-17T18:15:57 http://permalink.gmane.org/gmane.science.biology.gmod.announce/128 <pre>Dear all, If you would like to attend all or part of this year's GMOD meeting remotely, please send me an email. We will be using Go To Meeting, a browser-based client that allows streaming video and audio. It is free for participants, but does require an invitation to join, so please ensure I know that you want to participate. We will be holding a dry run to ensure everything works well on Thursday April 4th at 4pm BST. More on the meeting: http://gmod.org/wiki/April_2013_GMOD_Meeting Look forward to seeing you there! </pre> Amelia Ireland 2013-04-02T23:08:09 http://permalink.gmane.org/gmane.science.biology.gmod.announce/127 <pre>GMOD is very pleased to announce the keynote speaker for the 2013 GMOD community meeting is Dr. Kentaro Yoshida from the Sainsbury Lab ( http://tsl.ac.uk), talking about the Open Ash Dieback effort. This pioneering bioinformatics project is employing two increasingly important paradigms--open access to data and crowdsourcing--to gather genetic analyses of ash and a fungal pathogen that is threatening tree populations in the UK. Expect an interesting and inspiring talk! Online registration: http://gmod2013.eventbrite.com If you are interested in attending remotely, we will be using Go To Meeting (http://gotomeeting.com) to allow people to attend virtually. Please email me if you would like to join in. Look forward to seeing you all in Cambridge! On Wed, Mar 20, 2013 at 7:28 PM, Scott Cain &lt;scott&lt; at &gt;scottcain.net&gt; wrote: </pre> Amelia Ireland 2013-03-25T23:55:23 http://permalink.gmane.org/gmane.science.biology.gmod.announce/126 <pre>Hi, With several guest speakers, including Jane Lomax from GO, Joseph Rossetto from the EBI, and Manuel Corpas from the Genome Analysis Centre, this GMOD meeting is shaping up to be a very intersting meeting indeed. Today (March 21) is the last day to register with the early registration pricing. To register, go to http://gmod2013.eventbrite.com/ I look forward to seeing you next month (April 5-6) in Cambridge, England. For more information about GMOD 2013, go to http://www.gmod.org/wiki/April_2013_GMOD_Meeting Scott </pre> Scott Cain 2013-03-21T02:28:09 http://permalink.gmane.org/gmane.science.biology.gmod.announce/125 <pre>Hello, The GMOD meeting is in Cambridge, England on April 5-6 (right before the Biocurator meeting) and early registration closes March 21 (in one week). It is shaping up to be a good meeting with several interesting talks scheduled. Please try to make it! For more information on the meeting, see the meeting page: http://www.gmod.org/wiki/April_2013_GMOD_Meeting and to save some money on your registration, go to http://gmod2013.eventbrite.com/ before March 21 to register. If you'd like to give a talk at the meeting please let me know. Scott </pre> Scott Cain 2013-03-14T02:51:55 http://permalink.gmane.org/gmane.science.biology.gmod.announce/124 <pre>Google Summer of Code is a global program that offers student developers stipends to write code for various open source software projects. The Genome Informatics group is coordinating proposals for seven big bioinformatics projects: Galaxy, GBrowse, GMOD, JBrowse, Reactome, and Wormbase. If you have a project idea and/or you are interested in being a mentor, please post on the GSoC page on the GMOD wiki: http://gmod.org/wiki/GSoC. Mentorship proposals should be in by Friday, March 15th. Questions or comments should be directed towards the Genome Informatics GSoC coordinator, Robin Haw, at robin.haw&lt; at &gt;oicr.on.ca. </pre> Amelia Ireland 2013-03-11T21:54:14 http://permalink.gmane.org/gmane.science.biology.gmod.announce/123 <pre>Hello all, Just a quick reminder that the GMOD survey is closing very soon, and with it, your chance to win a personal genome profile from 23andMe.com or a $50 Amazon gift voucher. If you haven't done the survey, please head to http://gmod.org/survey.htmlbefore the end of the week and express your opinions. If you have completed the survey, enjoy the feeling of accomplishment and reflected goodwill. :) Thanks, Amelia. </pre> Amelia Ireland 2013-02-28T00:49:29 http://permalink.gmane.org/gmane.science.biology.gmod.announce/122 <pre>Hello GMODders! Two items: 1. If you haven't yet done so, please do the GMOD Community Survey: http://gmod.org/survey.html It should take about ten minutes maximum, and we want everyone's opinion on what GMOD is doing and how we can do it better. You could win a genome profile from 23andMe! 2. Registration for the April 2013 GMOD meeting in Cambridge, UK, is now open. Meeting details: http://gmod.org/wiki/April_2013_GMOD_Meeting Registration form: http://gmod2013.eventbrite.com/ If you have any questions, I'll be happy to answer them - just email help&lt; at &gt;gmod.org. My apologies if you receive this email more than once. Thanks! </pre> Amelia Ireland 2013-02-19T17:37:51 http://permalink.gmane.org/gmane.science.biology.gmod.announce/121 <pre>Give us your thoughts on the GMOD project and win a personal DNA test from 23andMe! The GMOD project provides tools like GBrowse, Galaxy, MAKER, JBrowse, Tripal, Apollo, Chado, and many more to a huge community of users and developers around the world. To make sure that GMOD is giving you the support you need, we want to know how you use GMOD, which components you find valuable, your opinion on support, training, and GMOD's strengths and weaknesses. Your feedback is vital in helping GMOD to serve its user community more effectively and to suggest future directions for the project. Do the survey: http://gmod.org/survey.html The survey should take between 10 and 15 minutes (including thinking time), and participants can enter a draw to win "A Journey Through Your DNA", the personal DNA test from 23andMe (the winner can pick a $50 Amazon gift voucher if they prefer). The survey will be open until March 1st. Results will be collated and discussed at the April 2013 GMOD Meeting in Cambridge, UK, and posted o</pre> Amelia Ireland 2013-02-04T21:02:05 http://permalink.gmane.org/gmane.science.biology.gmod.announce/120 <pre>Hello all, Want to work in a challenging and cutting-edge environment on one of the fastest growing open source bioinformatics projects around? The Galaxy Project is a successful high throughput data integration and analysis platform for Life Sciences with tens of thousands of worldwide, and we are hiring. See http://wiki.galaxyproject.org/GalaxyIsHiring for details. *Software Engineers * We are seeking ambitious individuals for multiple software engineering openings in the Galaxy Project. If you have expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, or bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics then we want to talk with you. Regardless of area of expertise, we seek talented, self-motivated individuals to join our team. Galaxy is developed in an academic research environment, and members of the Galaxy team work closely wi</pre> Dave Clements 2013-01-25T19:54:53 http://permalink.gmane.org/gmane.science.biology.gmod.announce/119 <pre>In case you missed it, WebApollo was released at the end of last year. Here is the announcement from the Apollo mailing list: We're very excited to announce that we've just released the first version of WebApollo, the next generation Apollo (as you can probably guess from the name, it's now on the web!). You can get the release at: http://icebox.lbl.gov/webapollo/releases/WebApollo-2012-12-21.tgz We also have a public demo available so that you can try the software for yourself: http://icebox.lbl.gov:8080/WebApolloDemo You might want to read the user guide before playing around with the software: http://icebox.lbl.gov/webapollo/docs/webapollo_user_guide.pdf We'll be phasing out support for the old desktop Apollo in the next few months. This is the time to try out WebApollo and (hopefully) consider migrating to it. Please post any questions or issues you may have to the Apollo mailing list: http://gmod.org/wiki/Apollo#Contacts_and_Mailing_Lists Lastly, we'd like to give a huge thanks to Rob Buels f</pre> Amelia Ireland 2013-01-18T18:48:37 http://permalink.gmane.org/gmane.science.biology.gmod.announce/118 <pre>Hello All, I've just released Chado 1.23. This is a bug fix release with no changes to the schema from the 1.22 release. If you are upgrading from Chado 1.2 or later then installing this bug fix release is easy: just do perl Makefile.PL make sudo make install If you're installing from before Chado 1.2, you can add make update which should update the schema (after backing up your database, of course). See http://gmod.org/wiki/Updating_Chado for more information. Chado 1.23 can be obtained from SourceForge at https://sourceforge.net/projects/gmod/files/gmod/chado-1.23/ Here are the changes from the last release: * Added $VERSION to Bio::GMOD::DB::Config so that when installing Bio::DB::Das::Chado it would be happy. * Changed all perl script #! lines to use /usr/bin/env perl instead of the mishmash that was being used in various scripts. * Fixed the GFF3 preprocessor so that if an insert into the sorting table fails, the script will die to avoid losing GFF lines in the resulting file. * Mo</pre> Scott Cain 2012-12-13T20:53:39 http://permalink.gmane.org/gmane.science.biology.gmod.announce/117 <pre>The GMOD project is now on Twitter! We'll be tweeting about all things GMOD--components, papers, projects, people--and other news of note. It's also a quick and easy way to get in touch if you want us to retweet your GMOD-related publication, check out your database, answer a question, or share your news. If you're in the twittersphere, you can find us at &lt; at &gt;gmodproject. See you there, tweeps! </pre> Amelia Ireland 2012-11-15T16:47:24 http://permalink.gmane.org/gmane.science.biology.gmod.announce/116 <pre>Hello all, The GMOD wiki will be undergoing an upgrade this Friday, October 5th, at 5pm EST. Please ensure that you have saved any edits you may be performing well before 5pm to prevent data loss. We should be able to keep the wiki online during the upgrade, but it will be in read-only mode. Please feel free to contact me or the GMOD helpdesk if you have any questions. Thanks! </pre> Amelia Ireland 2012-10-04T15:25:07 http://permalink.gmane.org/gmane.science.biology.gmod.announce/115 <pre>2nd Call for Papers - Submission Deadline in 3 Weeks 5th International Workshop on Semantic Web Applications and Tools for the Life Sciences (SWAT4LS 2012) http://www.swat4ls.org/workshops/paris2012 **** NEWS **** Submission system has been opened - submission deadline in 3 weeks! http://www.easychair.org/conferences/?conf=swat4ls2012 First program structure, keynotes &amp; tutorials announced http://www.swat4ls.org/workshops/paris2012/scientific-programme/ Overview Since 2008, SWAT4LS is a workshop that has provided a platform for the presentation and discussion of the benefits and limits of applying web-based information systems and semantic technologies in the domains of health care and life sciences. SWAT4LS has been in Edinburgh (2008), Amsterdam (2009), Berlin (2010) and London (2011). Growing steadily each year as Semantic Web applications have become more widespread, the program of SWAT4LS has grown to include associated events. The next edition of SWAT4LS will be held in Paris, on November 30th </pre> Adrian Paschke 2012-09-04T10:54:35 http://permalink.gmane.org/gmane.science.biology.gmod.announce/114 <pre>Hello, The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats, initially in Systems Biology and related fields. The Annual COMBINE (Computational Modeling in Biology Network) meeting is a workshop-style event with oral presentations, posters and breakout sessions. The meeting provides an opportunity for those involved in many related standardization and software efforts in systems biology to meet and discuss their efforts, with the aim of working more closely together to ensure smooth interoperability between systems. http://co.mbine.org/events/COMBINE_2012 COMBINE 2012 will take place at The Donnelly Centre building at the University of Toronto from Wednesday August 15 to Sunday Aug. 19, 2012, immediately preceding the 13th International Conference on Systems Biology (http://icsb2012toronto.com/). The COMBINE conference location is a short walk from ICSB events and COMBINE 2012 is an official satellite meet</pre> Robin Haw 2012-07-24T01:32:35 http://permalink.gmane.org/gmane.science.biology.gmod.announce/113 <pre>Hello GMODders, I'm writing to introduce myself as the new GMOD Community Support Specialist. I'm taking up Dave Clements' old job of providing support, doing outreach, teaching, documenting, surveying, publicising, and generally doing all sorts of GMOD in the community activities; I'll be working with Scott, Hilmar, Todd, Dave, and no doubt many others in the group. I worked on the Gene Ontology [GO] before coming to GMOD, so many of the names are familiar, even if the faces are not (yet). I look forward to meeting everyone and providing plenty of community support! Cheers, Amelia. </pre> Amelia Ireland 2012-07-13T22:36:37 http://permalink.gmane.org/gmane.science.biology.gmod.announce/112 <pre>Hello, The deadline to apply for the GMOD Summer School is in one week, July 9th. The application is available as a Google Form: https://docs.google.com/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ In the GMOD Summer School (August 24-29, 2012) we will cover the installation, configuration and use of a variety of GMOD tools, including Chado, GBrowse, JBrowse and Tripal. For more information on the course, see the course web page at http://gmod.org/wiki/2012_GMOD_Summer_School The course will make heavy use of the Amazon Web Service (aka, the Cloud) via a grant from Amazon. Enrollment is limited to 24 students, and the application process is competitive: the last few years we've received over 75 applications for those 24 spots. I look forward to seeing you in North Carolina in August! Scott </pre> Scott Cain 2012-07-02T18:50:45 http://permalink.gmane.org/gmane.science.biology.gmod.announce/112 <pre>Hello, The deadline to apply for the GMOD Summer School is in one week, July 9th. The application is available as a Google Form: https://docs.google.com/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ In the GMOD Summer School (August 24-29, 2012) we will cover the installation, configuration and use of a variety of GMOD tools, including Chado, GBrowse, JBrowse and Tripal. For more information on the course, see the course web page at http://gmod.org/wiki/2012_GMOD_Summer_School The course will make heavy use of the Amazon Web Service (aka, the Cloud) via a grant from Amazon. Enrollment is limited to 24 students, and the application process is competitive: the last few years we've received over 75 applications for those 24 spots. I look forward to seeing you in North Carolina in August! Scott </pre> Scott Cain 2012-07-02T18:50:45 http://permalink.gmane.org/gmane.science.biology.gmod.announce/111 <pre>Applications are now being accepted for the 2012 GMOD Summer School course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD Components. The course will be held August 25-29 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. https://docs.google.com/a/scottcain.net/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ These components will be covered at the school: Apollo or WebApollo - genome annotation editor Chado - biological database schema Galaxy - workflow system GBrowse - genome viewer GBrowse_syn - synteny viewer GFF3 - genome annotation file format and tools InterMine - biological data mining system JBrowse - next generation genome browser MAKER - genome annotation pipeline Tripal - web front end to Chado databases The deadline for applying is the end of July 9, 2012. Admission is competitive and is based on the strength of the appli</pre> Scott Cain 2012-06-15T02:17:54 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.gmod.announce