http://blog.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://comments.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 on setting up a GMOD in the Cloud virtual machine in the Amazon cloud, and common file formats. Courses are taught by members of the software development teams, and there are work sessions in the evenings for participants to talk to the developers or apply what they have been taught to their own data. For more information and to apply, visit http://gmod.org/wiki/2013_GMOD_Summer_School. There are some scholarship funds available for those from underrepresented minorities. All applications should be in by June 10th. If you have any questions, please contact the GMOD help desk at help&lt; at &gt;gmod.org. Hope to see you there! Thanks, Amelia Ireland GMOD Community Support http://gmod.org || &lt; at &gt;gmodproject ------------------------------------------------------------------------------ Try New Relic Now &amp; We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, &amp; servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may</pre> Amelia Ireland 2013-05-23T18:51:46 http://comments.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://comments.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://comments.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://comments.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://comments.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://comments.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://comments.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://comments.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 on the GMOD wiki at http://gmod.org. Please spread the word to other friends and colleagues who use GMOD: the more voices we hear, the better the picture we get of the needs of our users, and the better we can help you! Do the survey: http://gmod.org/survey.html If you have any questions or problems with the survey, please email me -- I will be happy to help out! Thanks, Amelia. </pre> Amelia Ireland 2013-02-04T21:02:05 http://comments.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 from the JBrowse team for his invaluable contribution (and countless hours) in helping migrate WebApollo to the current version of JBrowse. Thanks!!! </pre> Amelia Ireland 2013-01-18T18:48:37 http://comments.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. * Modified Makefile.PL so that if using PREFIX it won't stomp on the GMOD_ROOT environment variable (that is, everything goes in PREFIX, except what goes in GMOD_ROOT). Cheers, Scott </pre> Scott Cain 2012-12-13T20:53:39 http://comments.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://comments.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://comments.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 2012, and it will be preceded by two days of tutorials and hackathons. We are confident that the next edition of SWAT4LS will provide the same open and stimulating environment that brought together researchers, developers, and users, from various fields including biomedical informatics, systems biology, computational biology, drug discovery, bioinformatics and biocomputing, to discuss goals, current limits and real experiences in the use of Semantic Web technologies in Life Sciences. ________________________________________ Rationale The web is a key medium for information publishing, and web-based information systems play a key role in biomedical information exchange and integration. At the same time, the variety and complexity of biomedical information call for the adoption of semantic-based solutions. The Semantic Web provides a set of technologies and standards that are key to support semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the web-based semantic-enabled technologies in the Life Sciences has potential impact on the future of publishing, biological research and medicine. This workshop will provide a venue to present and discuss benefits and limits of the adoption of these technologies and tools in biomedical informatics and computational biology. It will showcase experiences, information resources, tools development and applications. It will bring together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and some real use cases for Semantic Web technologies in Life Sciences. ________________________________________ Topics Topics of interest include, but are not limited to: Standards, Technologies, Tools for the Semantic Web: - Big Metadata - Semantic Web standards and new proposals (e.g.: RDF, OWL, SKOS, SPIN, RuleML, Microformats) - Tools for ontology editing, annotation, versioning and provenance management - RDF stores, NoSQL, reasoners, query and visualization systems - Knowledge representation for biomedical knowledge bases - Query federation systems for distributed knowledge and data discovery - Tools for semantics-enabled web publication Systems for a Semantic Web for Bioinformatics: - Biomedical knowledge bases on the Semantic Web - Semantic biomedical Web Services - Semantics-enabled biomedical information systems and solutions - Linked Data for biomedical research - Semantic Scientific Workflow Systems Existing and prospective applications of the Semantic Web for Bioinformatics: - Semantic Wikis - Semantic collaborative research environments - Semantic crowdsourcing and collective intelligence - Alternative approaches to biomedical metadata generation and management - Methods for data sharing and open data - Approaches to data privacy and security - Case studies, use cases, and scenarios ________________________________________ Type of contributions The following possible contributions are sought: - Research papers - Position papers - Posters - Software demos ________________________________________ Proceedings Proceedings of SWAT4LS will be published in CEUR Workshop proceedings. Please refer to the SWAT4LS website for detailed formatting instructions prior to submission: http://www.swat4ls.org/workshops/paris2012/call/ ________________________________________ Special issue Authors of accepted contributions to the upcoming edition of SWAT4LS will be invited to submit to a special issue of the BMC Journal of Biomedical Semantics. ________________________________________ Deadlines Expression of interest for tutorials: 5th July 2012 Submission opening: 3rd September 2012 Papers submission deadline (abstracts): 28th September 2012 Papers submission deadline (full text):9th October 2012 Early registration deadline: 15th October 2012 Posters and demos submission deadline: 22nd October 2012 Communication of acceptance: 29th October 2012 PDF ready: 23rd November 2011 Hackathon, Tutorials28-29th November 2012 Workshop day:30th November 2012 ________________________________________ Instructions: All papers and posters must be in English and submitted in pdf format. Submissions for papers should report original research, and should be between 8 and 15 pages. Submissions for position papers should report qualified opinions, recommendations or conclusions, and should be between 3 and 6 pages. Submissions for posters should be between 2 and 4 pages. Submissions for software demo proposals should also be between 2 and 4 pages. Please refer to the SWAT4LS website for detailed formatting instructions prior to submission: http://www.swat4ls.org/workshops/paris2012/call/ ________________________________________ Submission All submissions will be handled via the EasyChair submission system http://www.easychair.org/conferences/?conf=swat4ls2012 To ensure high quality, submitted papers will be carefully peer-reviewed by at least three members of the Scientific Committee. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ </pre> Adrian Paschke 2012-09-04T10:54:35 http://comments.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 meeting of ICSB, so you can follow the same travel and accommodation instructions for ICSB and use the same hotel discounts. Registration for COMBINE is $125 (Canadian) to cover costs associated with the meeting, including a workshop dinner and catering. We hope to see you there! ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/</pre> Robin Haw 2012-07-24T01:32:35 http://comments.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://comments.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://comments.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://comments.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 application, especially the statement of interest. The 2011 school had over 70 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $300 (only $60 per day). There will be a limited number of scholarships available. Thanks, Scott Cain </pre> Scott Cain 2012-06-15T02:17:54 http://comments.gmane.org/gmane.science.biology.gmod.announce/110 <pre>Forwarded from Nomi Harris: Register now for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012), a Special Interest Group (SIG) of ISMB 2012! Important Dates: June 1, 2012: Last day for early registration discount (registration is through the ISMB website, http://www.iscb.org/ismb2012-registration </pre> Scott Cain 2012-05-30T20:26:12 http://comments.gmane.org/gmane.science.biology.gmod.announce/109 <pre>Hello, As we are trying to plan for next years GMOD meeting, we would like to decide between two venues as soon as possible. To help us decide, we've put together a simple survey. We are asking your help in deciding between: * San Diego, California in January before or after the Plant and Animal Genomes meeting * Cambridge, England in April before or after the International Society of Biocurators meeting. Each option has its upsides: the Plant and Animal Genomes is a large meeting attended by several members of the GMOD community, so it would likely have a fairly high attendance. On the other hand, having a meeting in Cambridge would make it easier for European members of the GMOD community to attend. Please share your thoughts with us and take this survey. http://www.surveymonkey.com/s/CPC25P5 Thanks, Scott </pre> Scott Cain 2012-05-04T15:28:25 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.gmod.announce