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From: Dave C. <cle...@ga...> - 2017-01-12 23:19:51
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And I accidentally dropped the list from my response. Sorry, I've only been using email since 1983. Give me another year. :-/ Looking forward to seeing a lot of you in San Diego! Dave C On Thu, Jan 12, 2017 at 3:13 PM, Dave Clements <cle...@ga...> wrote: > Hi Maximillian, > > I think a good way to get up and running in a project is with a hackathon, > and there happen to be several coming up: > > Tripal Hackathon > <https://docs.google.com/document/d/1e8g0NfihOzBDO0kp0OTrao1vgn1ODkrm394b5mTwk8w/edit#heading=h.fv5015i6n16h>, > TODAY and TOMORROW, San Diego, California, United States. > Might be too late for that one. > > InterMine Hackathon > <https://intermineorg.wordpress.com/dev-workshop-2017/>, 1-2 April, in > Berkeley, California, United States. > I don't know if they are open to remote participants or not. > > Galaxy Hackathons > The big, in person ones will be in Montpellier, France, 26-27 June this > year. Registration is not open yet. > However, the community/project has many smaller online ones. Watch the events > page <https://new.galaxyproject.org/events/>. > > Hope this helps, > > Dave C > > On Thu, Jan 12, 2017 at 2:22 PM, <max...@we...> wrote: > >> Dear Ladies and Gentleman, >> >> my name is Maximilian Greil and I would like to participate in the GMOD >> project. >> I recently recieved my B.Sc. in Bioinformatics and will soon continue >> with my M.Sc. in Bioinformatics. >> To extend my knowledge and skills in computer science and especially in >> bioinformatics I want to take part in bioinformatic projects. According to >> the forum biostars.org a good way to start and acquire experience is to >> participate in Open Source software development projects. I discovered the >> GMOD project on open-bio.org. >> >> Now my question: is it possible that I can participate in the GMOD >> project? I would like to start sonner rather than later. >> >> Kind regards, >> Maximilian Greil >> >> ------------------------------------------------------------ >> ------------------ >> Developer Access Program for Intel Xeon Phi Processors >> Access to Intel Xeon Phi processor-based developer platforms. >> With one year of Intel Parallel Studio XE. >> Training and support from Colfax. >> Order your platform today. http://sdm.link/xeonphi >> _______________________________________________ >> Gmod-devel mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-devel >> >> > > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ |
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From: <max...@we...> - 2017-01-12 22:22:14
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<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div> <div style="font-family: Verdana;font-size: 12.0px;"> <div>Dear Ladies and Gentleman,</div> <div> </div> <div>my name is Maximilian Greil and I would like to participate in the GMOD project.</div> <div>I recently recieved my B.Sc. in Bioinformatics and will soon continue with my M.Sc. in Bioinformatics.</div> <div>To extend my knowledge and skills in computer science and especially in bioinformatics I want to take part in bioinformatic projects. According to the forum biostars.org a good way to start and acquire experience is to participate in Open Source software development projects. I discovered the GMOD project on open-bio.org.</div> <div> </div> <div>Now my question: is it possible that I can participate in the GMOD project? I would like to start sonner rather than later.</div> <div> </div> <div>Kind regards,</div> <div>Maximilian Greil</div> </div> </div></div></body></html> |
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From: Cannon, E. K [C. S] <ekc...@ia...> - 2017-01-10 02:57:50
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We are still looking for a Drupal/Tripal developer for the Legume Federation project. The position is based at Iowa State University, in Ames, IA. Position announcement closes January 22nd. Description below: The Computer Science Department at Iowa State University is seeking a Software Engineer to extend an open source software package called Tripal (http://tripal.info), which is a set of Drupal modules and database for maintaining genomic, genetic, and breeding data that has national and international impact. The work of the Software Engineer includes developing infrastructure for the Legume Federation, a federation of legume databases, and two websites in the federation, the Legume Information System (LegumeInfo.org) and PeanutBase (PeanutBase.org). Position responsibilities include programming extension modules for Drupal, which requires the use of PHP, JavaScript, and SQL; integration of Unix command-line tools within a web-based analytical workflow system; and development of tutorials and outreach materials. Duties will also include administration of the back-end database, and collaborative work with International crop research communities, other database projects, and the Tripal development community. The successful candidate will possess excellent communication and interpersonal skills; solid coding and code design practices; and the ability to work effectively within a multidisciplinary team. Apply: https://www.iastatejobs.com/postings/23947 |
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From: GRLMC <gr...@gr...> - 2017-01-02 07:10:42
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DeepLearn 2017: early registration January 27*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************ INTERNATIONAL SUMMER SCHOOL ON DEEP LEARNING DeepLearn 2017 Bilbao, Spain July 17-21, 2017 Organized by: University of Deusto Rovira i Virgili University http://grammars.grlmc.com/DeepLearn2017/ ************************************************************ SCOPE: DeepLearn 2017 will be a research training event with a global scope aiming at updating participants about the most recent advances in the critical and fast developing area of deep learning. This is a branch of artificial intelligence covering a spectrum of current exciting machine learning research and industrial innovation that provides more efficient algorithms to deal with large-scale data in neuroscience, computer vision, speech recognition, language processing, drug discovery, biomedical informatics, recommender systems, learning theory, robotics, games, etc. Renowned academics and industry pioneers will lecture and share their views with the audience. Most deep learning subareas will be displayed, and main challenges identified through 4 keynote lectures, 24 six-hour courses, and 1 round table, which will tackle the most active and promising topics. The organizers are convinced that outstanding speakers will attract the brightest and most motivated students. Interaction will be a main component of the event. An open session will give participants the opportunity to present their own work in progress in 5 minutes. ADDRESSED TO: In principle, graduate students, doctoral students and postdocs from around the world will be typical profiles of participants. However, there are no formal pre-requisites for attendance in terms of academic degrees. Since there will be a variety of levels, specific knowledge background may be assumed for some of the courses. DeepLearn 2017 is also appropriate for more senior people who want to keep themselves updated on recent developments and future trends. All will surely find it fruitful to listen and discuss with major researchers, industry leaders and innovators. REGIME: In addition to keynotes, 3 courses will run in parallel during the whole event. Participants will be able to freely choose the courses they wish to attend as well as to move from one to another. VENUE: DeepLearn 2017 will take place in Bilbao, the largest city in the Basque Country, famous for its gastronomy and the seat of the Guggenheim Museum. The venue will be: DeustoTech, School of Engineering University of Deusto Avda. Universidades, 24 48014 Bilbao, Spain KEYNOTE SPEAKERS: tba PROFESSORS AND COURSES: (to be completed) Sven Behnke (University of Bonn), [intermediate] Visual Perception using Deep Convolutional Neural Networks Mohammed Bennamoun (University of Western Australia), tba Hervé Bourlard (Idiap Research Institute), tba George Cybenko (Dartmouth College), tba Rina Dechter (University of California, Irvine), tba Li Deng (Microsoft Research), tba Jianfeng Gao (Microsoft Research), [introductory/intermediate] An Introduction to Deep Learning for Natural Language Processing Yufei Huang (University of Texas, San Antonio), tba Soo-Young Lee (Korea Advanced Institute of Science and Technology), tba Li Erran Li (Columbia University), tba Jose C. Principe (University of Florida), [intermediate/advanced] Cognitive Architectures for Object Recognition in Video Ruslan Salakhutdinov (Carnegie Mellon University), tba Joos Vandewalle (KU Leuven), Data Processing Methods, and Applications of Least Squares Support Vector Machines Georgios N. Yannakakis (University of Malta), Deep Learning for Games - But not for Playing them OPEN SESSION: An open session will collect 5-minute presentations of work in progress by participants. They should submit a half-page abstract containing title, authors, and summary of the research to david.silva409 (at) yahoo.com by July 10, 2017. ORGANIZING COMMITTEE: José Gaviria Carlos Martín (co-chair) Manuel Jesús Parra Iker Pastor Borja Sanz (co-chair) David Silva REGISTRATION: It has to be done at http://grammars.grlmc.com/DeepLearn2017/registration.php The selection of up to 8 courses requested in the registration template is only tentative and non-binding. For the sake of organization, it will be helpful to have an approximation of the respective demand for each course. Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed and the on-line registration facility disabled when the capacity of the venue will be complete. It is much recommended to register prior to the event. FEES: Fees comprise access to all courses and lunches. There are several early registration deadlines. Fees depend on the registration deadline. ACCOMMODATION: Suggestions for accommodation will be available on the website. CERTIFICATE: Participants will be delivered a certificate of attendance including the number of hours of lectures. QUESTIONS AND FURTHER INFORMATION: david.silva409 (at) yahoo.com ACKNOWLEDGMENTS: Universidad de Deusto Universitat Rovira i Virgili |
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From: Sebastian H. <pr...@in...> - 2016-12-22 19:16:38
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Call for Research & Innovation Papers SEMANTiCS 2017 - The Linked Data Conference 13th International Conference on Semantic Systems Amsterdam, Netherlands September 11 -14, 2017 http://2017.semantics.cc The Research & Innovation track at SEMANTiCS welcomes the submission of papers on novel scientific research and/or innovations relevant to the topics of the conference. Submissions must be original and must not have been submitted for publication elsewhere. Papers should follow the ACM ICPS guidelines for formatting (http://www.acm.org/sigs/publications/proceedings-templates) and must not exceed 8 pages in lenght for full papers and 4 pages for short papers, including references and optional appendices. Research & Innovation Papers are published within ACM ICP Series. Important Dates (Research & Innovation) Abstract Submission Deadline: May 17, 2017 (11:59 pm, Hawaii time) Paper Submission Deadline: May 24, 2017 (11:59 pm, Hawaii time) Notification of Acceptance: July 3, 2017 (11:59 pm, Hawaii time) Camera-Ready Paper: August 14, 2017 (11:59 pm, Hawaii time) For details please go to: https://2017.semantics.cc/calls or contact the Research and Innovation Chairs: Catherine Faron Zucker, faron [@] i3s.unice.fr, Université Nice Sophia Antipolis Rinke Hoekstra, rinke.hoekstra [@] vu.nl, Vrije Universiteit Amsterdam/University of Amsterdam As in the previous years, SEMANTiCS’17 proceedings will be published by ACM ICP (pending). SEMANTiCS 2017 will especially welcome submissions for the following hot topics: *Data Science (special track, see below) *Web Semantics, Linked (Open) Data & schema.org *Corporate Knowledge Graphs *Knowledge Integration and Language Technologies *Data Quality Management *Economics of Data, Data Services and Data Ecosystems Following the success of previous years, the ‘horizontals’ (research) and ‘verticals’ (industries) below are of interest for the conference: Horizontals *Enterprise Linked Data & Data Integration *Knowledge Discovery & Intelligent Search *Business Models, Governance & Data Strategies *Semantics in Big Data *Text Analytics *Data Portals & Knowledge Visualization *Semantic Information Management *Document Management & Content Management *Terminology, Thesaurus & Ontology Management *Smart Connectivity, Networking & Interlinking *Smart Data & Semantics in IoT *Semantics for IT Safety & Security *Semantic Rules, Policies & Licensing *Community, Social & Societal Aspects Data Science Special Track Horizontals *arge-Scale Data Processing (stream processing, handling large-scale graphs) *Data Analytics (Machine Learning, Predictive Analytics, Network Analytics) *Communicating Data (Data Visualization, UX & Interaction Design, Crowdsourcing) *Cross-cutting Issues (Ethics, Privacy, Security, Provenance) Verticals *Industry & Engineering *Life Sciences & Health Care *Public Administration *e-Science *Digital Humanities *Galleries, Libraries, Archives & Museums (GLAM) *Education & eLearning *Media & Data Journalism *Publishing, Marketing & Advertising *Tourism & Recreation *Financial & Insurance Industry *Telecommunication & Mobile Services *Sustainable Development: Climate, Water, Air, Ecology *Energy, Smart Homes & Smart Grids *Food, Agriculture & Farming *Safety, Security & Privacy *Transport, Environment & Geospatial For details please go to: https://2017.semantics.cc/calls |
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From: Monica Munoz-T. <mcm...@lb...> - 2016-12-09 18:39:54
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*We are pleased to announce the latest Apollo release* *Apollo 2.0.5 * *Some of the new features include:* - Numerous UI and performance improvements, including easier navigation between annotated elements via the Annotator Panel. - Better server and client-side reporting. - It is now possible to also include metadata on import. - Upgrade to Java 8 / GWT 2.8, and updated JBrowse. - Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 ( #9334e76fd <https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>). Use ./apollo clean-all or install from a formal release download for best performance. *Some important bug fixes:* - Import script were logging preferences unnecessarily. - Improved security for non-public genomes. - Fixed for going between logged-out mode and the Annotator Panel while retaining history. - Improved display of sequence over the annotation after moving the annotation to the opposite strand. - Users will see a warning message when it is not possible to create an intron with canonical splice sites in the selected region. * The *latest release* can be downloaded from GitHub at: https://github.com/GMOD/Apollo/releases/latest * *Detailed, searchable documentation* on pre-requisites, configuration, and installation guides found at: http://genomearchitect.readthedocs.io/ * A more *detailed account of all changes* is available in the Apollo ChangeLog: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md * *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo instances running, you can use your current JBrowse data directories. The quick-start guide is available at: http://genomearchitect.rea dthedocs.io/en/stable/Apollo2Build.html * *Migrating existing annotations:* Please find detailed information about migrating existing installations and their annotations at http://genomearchitect.readthedocs.io/en/latest/Migration.html ** Troubleshooting, GitHub tracker, Mailing List: * - Browse the Troubleshooting guide at http://genomearchitect.readthe docs.io/en/stable/Troubleshooting.html <http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html> - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/ - Post your questions on our mailing list at ap...@li... * *The Apollo User Guide* is available at http://genomearchitect.org/use rs-guide/ ** Public Demo: If you are new to Apollo we encourage you to learn more about our software and its functionality by taking a tour of our Apollo Demo at http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>* * These and more details are available at the Apollo Website <http://genomearchitect.org/> and the Apollo repository <https://github.com/GMOD/Apollo/blob/master/README.md>. We look forward to your questions and suggestions. Sincerely, The Apollo Development Team <http://genomearchitect.org/about/> [image: Inline image 1] It is very likely you will receive this message more than once; we offer our sincere apologies for the redundancy. Bee photograph by www.AlexanderWild.com -- Mentorship Matters! -- Monica Munoz-Torres, PhD. Berkeley Bioinformatics Open-source Projects (BBOP) Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Mailing Address: Lawrence Berkeley National Laboratory 1 Cyclotron Road Mailstop 977 Berkeley, CA 94720 |
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From: Dave C. <cle...@ga...> - 2016-11-23 22:04:23
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Hello all, The 2017 Galaxy Australasia Meeting (GAMe 2017) <http://www.embl-abr.org.au/game2017/> will be held 3-9 February in Melbourne, Australia, and bring together biomedical researchers, bioinformaticians, infrastructure providers, and data producers from across Australia and Asia. GAMe 2017 spans a week and includes a two day conference <http://www.embl-abr.org.au/game2017/conference>, one day of training for researchers <https://www.embl-abr.org.au/game2017/training-day/>, and four days of training for Galaxy administrators <http://www.embl-abr.org.au/game2017/training-for-admin-workshop>. The two day conference <http://www.embl-abr.org.au/game2017/conference> starts 4th February with a BIO day – for Galaxy users (biologists and bioinformaticians) – followed by an INFO day on 5th February, focussing on technical aspects of Galaxy – for bioinformaticians, tool and software developers, and research infrastructure providers. Both days feature keynotes, accepted and sponsored talks, poster and sponsor sessions, birds-of-a-feather gatherings, and lots of opportunities for networking. The conference is preceded by a Researcher Training Day on 3 February for analysis-focussed biologists and biomedical researchers with limited experience of Galaxy. A four day intensive Galaxy Admin Training session for those installing and maintaining Galaxy servers follows the conference. Talk abstracts <http://www.embl-abr.org.au/game2017/submit-your-talkposter/> are due 30 November. Early registration ends 31 December. Register now. Space is limited. *About Galaxy:* Galaxy <https://galaxyproject.org/> is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life. Galaxy enables life science researchers to perform their own data analysis without having to learn command line interfaces or Linux package management. Galaxy transparently records all analysis steps and eases workflow reuse and sharing. Galaxy is also a long standing and active member of GMOD. Please let us know if you have any questions, and we hope to see you in Melbourne! The GAMe 2017 Organising Committee <http://www.embl-abr.org.au/game2017/organisers/> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ |
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From: Scott C. <sc...@sc...> - 2016-11-04 19:25:09
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Time is short! If you want to attend PAG <http://www.intlpag.org/> 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 he...@gm.... 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 <http://gmod.org/wiki/Tripal>, JBrowse <http://gmod.org/wiki/JBrowse> and Galaxy <http://gmod.org/wiki/Galaxy>. Please consider giving a talk and sharing your experience and ideas! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Chris M. <cjm...@lb...> - 2016-10-28 22:01:40
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A number of GMOD related groups are exploring the idea of building GMOD components on top of graph databases, or layering Chado on top of a graph or RDF back end. I know SANBI talked briefly about this at the last GMOD meeting. I started on a google doc trying to weave these threads together, but it's still a very messy early draft: https://docs.google.com/document/d/1iZbtUurhUuqsM2oxnfklXa18yGlNZwEYI8npWRukGyY/edit#heading=h.ne5osa106xyc I got some great comments from some of you, but have not yet done a good job of integrating these. If there is interest, perhaps we could coordinate a few short talks at the GMOD workshop at PAG? |
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From: Scott C. <sc...@sc...> - 2016-10-28 20:57:14
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Hi, I am pleased to announce a call for talks to be given at the Plant and Animal Genomes conference this January in the GMOD workshop on Wednesday, January 18th. Any talks that involve the development or use of GMOD software are welcome. In particular this year, I'd really like to highlight plugins for the various GMOD software packages that support them, like JBrowse, Galaxy and Tripal (of course, Galaxy and Tripal have their own sessions, so you should consider submitting to them too). Please get an abstract, brief summary or a vague title to me as soon as possible so I can start getting it put together. Also, if you'd like to be a co-organizer, please let me drop me a line about that too. I might be able to get you some meeting-related niceties for not very much work. For more information about PAG, see: http://www.intlpag.org Thanks and I look forward to seeing in January, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Monica Munoz-T. <mcm...@lb...> - 2016-10-25 20:00:00
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[Second announcement. Submission deadline is this Friday 28 October, 2016.] Dear Colleagues, *International Plant and Animal Genome XXV (PAGXXV)* *January 14-18, 2017. San Diego, California, United States.* http://intlpag.org/ PAGXXV will bring together more than 3,000 leading researchers in plant and animal research, over 130 exhibits, more than 150 workshops, over 1000 posters, *and a computer demo track specifically designed to highlight relevant software and online resources.* PAG is the largest Ag-Genomics meeting in the world. If you work on digital resources that enable life sciences research, please consider submitting an abstract to the PAG ComputerDemonstration Track. Computer demos are 15 or 20 minutes long, and are an excellent way to get resources in front of the people who will benefit the most from them. *The Computer Demo abstract submission deadline is Friday October 28, 2016. * All computer demo presenters must be registered for the conference prior to submitting. Any software which is demonstrated at the PAG Conference must also be available to the scientific community and non-commercial. Visit http://www.intlpag.org/2017/abstracts/computer-demos for additional information and to find a link to the submission form. We hope to see you in San Diego! *Monica Munoz-Torres and Brian Smith-White* *PAGXXV Computer Demo Track Co-Chairs* *[image: Inline image 1]* -- Mentorship Matters! -- Monica Munoz-Torres, PhD. Berkeley Bioinformatics Open-source Projects (BBOP) Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Mailing Address: Lawrence Berkeley National Laboratory 1 Cyclotron Road Mailstop 977 Berkeley, CA 94720 |
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From: Monica Munoz-T. <mcm...@lb...> - 2016-10-07 10:42:16
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Dear Colleagues, *International Plant and Animal Genome XXV (PAGXXV)January 14-18, 2017. San Diego, California, United States.http://intlpag.org/ <http://intlpag.org/>* PAGXXV will bring together more than 3,000 leading researchers in plant and animal research, over 130 exhibits, more than 150 workshops, over 1000 posters, and *a computer demo track specifically designed to highlight relevant software and online resources.* PAG is the largest Ag-Genomics meeting in the world. If you work on digital resources that enable life sciences research, please consider submitting an abstract to the PAG Computer Demonstration Track. Computer demos are 15 or 20 minutes long, and are an excellent way to get resources in front of the people who will benefit the most from them. *The Computer Demo abstract submission deadline is Friday October 28, 2016. * All computer demo presenters must be registered for the conference prior to submitting. Any software which is demonstrated at the PAG Conference must also be available to the scientific community and non-commercial. Visit http://www.intlpag.org/2017/abstracts/computer-demos for additional information and follow the link to the submission form. We hope to see you in San Diego! *Monica Munoz-Torres and Brian Smith-White* *PAGXXV Computer Demo Track Co-Chairs* [image: Inline image 1] -- Mentorship Matters! -- Monica Munoz-Torres, PhD. Berkeley Bioinformatics Open-source Projects (BBOP) Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Mailing Address: Lawrence Berkeley National Laboratory 1 Cyclotron Road Mailstop 977 Berkeley, CA 94720 |
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From: Dave C. <cle...@ga...> - 2016-10-07 05:30:09
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Hello all, Deadline for papers for Biocuration are coming up at the end of this month. See below. Dave C ---------- Forwarded message ---------- From: J. Michael Cherry PhD <ch...@st...> Date: Tue, Oct 4, 2016 at 4:29 PM Subject: [mailinglist] Call for Papers: 10th International Society for Biocuration meeting, DATABASE Journal Virtual Issue To: "mai...@bi..." <mai...@bi...> 2nd notice. Paper submission deadline for the Biocuration 2017 Virtual Issue is the end of this month. Please forward to others that might be interested. — Dear Colleagues, The International Biocuration Conference is a unique event for biocurators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research. For the 10th International Biocuration Conference in Palo Alto, California, you are invited to submit your work for publication. This call for papers is done in collaboration between DATABASE: The Journal of Biological Databases and Curation and the International Society for Biocuration. The DATABASE journal will publish an online Virtual Issue of the accepted papers, see below for a link to last years issue. This is a great occasion to enhance the recognition of your work and of our profession by the greater biological research communities. The Biocuration 2017 program committee will prioritize inclusion of accepted papers for oral presentations at the conference. This year manuscripts are invited for the following topic areas: - Functional Annotation - Phenotypes, genotypes, and variants - Clinical annotations, diseases, drugs - Big data to knowledge - Large scale and predictive annotation - Data standards and ontologies - Crowd/community curation - Data integration, data visualization - Curation standards and best practice; inference from evidence; data and annotation quality - Biocuration and the scholarly communication cycle; data publishing and curation, data sharing Papers on topics outside the above will also be considered for publication. The manuscript review process will be expedited by the journal’s associated editors and they will thus need to be firm on the submission deadlines: Submission deadline: October 31, 2016 First decisions: December 9, 2016 Deadline for revisions: January 23, 2017 Final decisions: February 25, 2017 Conference: March 26-29, 2017 Authors wishing to submit to DATABASE for the 2017 Biocuration Virtual issue should go to the DATABASE home page (<http://database. oxfordjournals.org/>) and click on the "submit now" after having read the "Instructions to Authors". Authors should CLEARLY state that they are submitting the manuscript for consideration for the Biocuration 2017 conference so that the DATABASE staff will ensure appropriate fast-track for inclusion in this meeting's proceedings. In addition, within the database submission form, you should also select "Biocuration Conference Paper" as a manuscript type. We look forward to your participation at Biocuration 2017 the 10th International Biocuration Conference. Submitting a paper to DATABASE does not in itself sign you up to give a talk or poster, you must register your interest separately. Information about abstract submission will be announced soon. The proceedings of the past International Biocuration Conference, the Biocuration Virtual Issue, are online at <http://www.oxfordjournals.org/our_journals/databa/ biocuration_virtual_issue.html> Kind regards, -Biocuration 2017 Organizing Committee bio...@li... -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ |
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From: GRLMC <gr...@gr...> - 2016-09-24 06:28:30
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SLSP 2016: call for participation*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************** 4th INTERNATIONAL CONFERENCE ON STATISTICAL LANGUAGE AND SPEECH PROCESSING SLSP 2016 Pilsen, Czech Republic October 11-12, 2016 Organized by: Department of Computer Science and Engineering Department of Cybernetics University of West Bohemia Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/SLSP2016/ ************************************************************************** PROGRAM Tuesday, October 11 09:00 - 09:30 Registration 09:30 - 09:40 Opening 09:40 - 10:30 Walter Daelemans: Advances in Statistical Approaches to Personality Prediction from Text - Invited lecture 10:30 - 11:00 Coffee break 11:00 - 11:50 Ikbel Hadj Ali and Zied Mnasri: Statistical Analysis of the Prosodic Parameters of a Spontaneous Arabic Speech Corpus for Speech Synthesis Daniil Kocharov, Tatiana Kachkovskaia, Aliya Mirzagitova and Pavel Skrelin: Combining Syntactic and Acoustic Features for Prosodic Boundary Detection in Russian 11:50 - 13:20 Lunch 13:20 - 14:10 Julia Hirschberg: Identifying Sentiment and Emotion in Low Resource Languages - Invited lecture 14:10 - 14:25 Break and Group photo 14:25 - 15:15 Brij Mohan Lal Srivastava and Manish Shrivastava: Articulatory Gesture Rich Representation Learning of Phonological Units in Low Resource Settings Dávid Sztahó and Klára Vicsi: Estimating the Severity of Parkinson’s Disease Using Voiced Ratio and Nonlinear Parameters 15:15 - 15:30 Break 15:30 - Poster presentations 18:00 - 20:00 Social event Wednesday, October 12 09:00 - 09:50 Mari Ostendorf: Continuous-space Language Processing: Beyond Word Embeddings - Invited lecture 09:50 - 10:20 Coffee break 10:20 - 11:35 Antoni Hernández, Bernardino Casas, Ramon Ferrer-i-Cancho and Jaume Baixeries: Testing the Robustness of Laws of Polysemy and Brevity versus Frequency David Marecek: Delexicalized and Minimally Supervised Parsing on Universal Dependencies Ahmet Üstün and Burcu Can: Unsupervised Morphological Segmentation Using Neural Word Embeddings 11:35 - 11:50 Break 11:50 - 13:05 Marie Tahon, Raheel Qader, Gwénolé Lecorvé and Damien Lolive: Optimal Feature Set and Minimal Training Size for Pronunciation Adaptation in TTS Natalia Tomashenko, Yuri Khokhlov and Yannick Estève: A New Perspective on Combining GMM and DNN Frameworks for Speaker Adaptation Matti Varjokallio, Mikko Kurimo and Sami Virpioja: Class n-Gram Models for Very Large Vocabulary Speech Recognition of Finnish and Estonian 13:05 - 13:15 Closing 13:15 - Lunch |
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From: Scott C. <sc...@sc...> - 2016-09-23 15:12:43
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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 -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Dave C. <cle...@ga...> - 2016-09-19 17:47:07
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Hi All, This is just a reminder that early registration closes today. Galaxy Admin Training workshop <https://wiki.galaxyproject.org/Events/AdminTraining2016> November 7-11 Salt Lake City, Utah Thanks, Dave C On Tue, Sep 6, 2016 at 10:41 AM, Dave Clements <cle...@ga...> wrote: > The first Galaxy Admin Training workshop > <https://wiki.galaxyproject.org/Events/AdminTraining2016> will be held > November 7-11 in Salt Lake City, Utah (the week before Supercomputing’16 > <http://sc16.supercomputing.org/> also meets in Salt Lake). The workshop > offers Basic > <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> > and Advanced > <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> > sessions. > > Galaxy <https://galaxyproject.org/> is an open web based platform for > biomedical data integration and analysis. It is deployed at large and small > organizations around the world and used in a broad range of biomedical > research domains, and across the tree of life. Galaxy enables life science > researchers to perform their own data analysis without having to learn > command line interfaces or Linux package management. Galaxy transparently > records all analysis steps and eases workflow reuse and sharing. If your > organization is looking for how to empower your researchers, then please > consider attending one or both sessions. > > > Participants will learn how to install, configure, customize, and extend > their own Galaxy servers. Topics include tool configuration, authentication > and user management, using heterogeneous storage and compute services, and > many other topics that will enable you to get your own Galaxy server up and > running, performing well, and used by your community. > > Registration > <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> is > now open, but space is limited. *Early registration ends September 19*. > Participants can register for one or both sessions. Please review each > session’s prerequisites before registering. > > Galaxy Admin Training 2016 is hosted by the University of Utah Center for > High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, USTAR > Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>, the Department > of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical > & Translational Science Biomedical Informatics Core (CCTS BMIC) > <http://medicine.utah.edu/ccts/bmic/> at the University of Utah > <http://utah.edu/>. > > We hope to see you in Salt Lake! > > The Galaxy Team > > PS: Please share this flier > <https://wiki.galaxyproject.org/Events/AdminTraining2016/Publicity> with > any individuals or groups who might be interested in this event. > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ |
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From: Dave C. <cle...@ga...> - 2016-09-06 17:42:28
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The first Galaxy Admin Training workshop <https://wiki.galaxyproject.org/Events/AdminTraining2016> will be held November 7-11 in Salt Lake City, Utah (the week before Supercomputing’16 <http://sc16.supercomputing.org/> also meets in Salt Lake). The workshop offers Basic <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> and Advanced <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession> sessions. Galaxy <https://galaxyproject.org/> is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life. Galaxy enables life science researchers to perform their own data analysis without having to learn command line interfaces or Linux package management. Galaxy transparently records all analysis steps and eases workflow reuse and sharing. If your organization is looking for how to empower your researchers, then please consider attending one or both sessions. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. Registration <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> is now open, but space is limited. *Early registration ends September 19*. Participants can register for one or both sessions. Please review each session’s prerequisites before registering. Galaxy Admin Training 2016 is hosted by the University of Utah Center for High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, USTAR Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>, the Department of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical & Translational Science Biomedical Informatics Core (CCTS BMIC) <http://medicine.utah.edu/ccts/bmic/> at the University of Utah <http://utah.edu/>. We hope to see you in Salt Lake! The Galaxy Team PS: Please share this flier <https://wiki.galaxyproject.org/Events/AdminTraining2016/Publicity> with any individuals or groups who might be interested in this event. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ |
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From: Scott C. <sc...@sc...> - 2016-09-02 15:08:37
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Hi Hilmar, Definitely true--I made one attempt at moving the gmod wiki a few months ago, and found 1) that just taking everything wholesale and putting it in the right place didn't work, even though I tried to replicate versions as best I could, and 2) when I updated MediaWiki as minimally as possible, I still lost one of the extensions I like best (the tag cloud one) and it will likely have to be replaced with something I like less. On Thu, Sep 1, 2016 at 3:12 PM, Hilmar Lapp <hl...@dr...> wrote: > > On Sep 1, 2016, at 1:24 PM, Dave Clements <cle...@ga...> > wrote: > > *So, my vote is stick with MediaWiki.* I don't think there is any hope > of migrating to GFM without seriously mangling 90%+ of the pages. > > > > I’d mostly agree with that. I think in general the pains of migrating a > MediaWiki are often overestimated, perhaps because most people you speak to > have never done it (or have never had to). I’ve brought up 5 from dumps > over the last couple of months. If you follow the instructions, it usually > works. > > That said, the one factor that in my experience can complicate things (and > explode time needed) tremendously may well apply to the GMOD wiki, and > that’s use of a lot of extensions. Extensions often don’t keep up with the > main MediaWiki version and so aren’t available, or are buggy for the latest > MediaWiki version. Even when they still are available and current, they > sometime have changed their markup rules. Accommodating all that can be a > real pain. > > -hilmar > -- > Hilmar Lapp -:- lappland.io > > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Scott C. <sc...@sc...> - 2016-09-02 15:01:44
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Right, as Dave pointed out, there is quite a bit of custom html and several extensions in use at gmod.org. I have a feeling there would be a loss of functionality (like semi-controlled vocab tagging) as well as content getting "lost" (no longer easy to find, like many presentations, not that anybody is looking up the talks given at the 2005 GMOD meeting :-) Even though I know a migration to another server will not be easy, I think it will be considerably easier. On Fri, Sep 2, 2016 at 10:39 AM, Hilmar Lapp <hl...@dr...> wrote: > It should be noted though that this hasn’t been without its downsides. > Many links don’t work anymore, some content still needs fixes to > formatting, and it was not a small amount of work. > > I think it’s fair to say that it worked best (and arguably well) for those > projects with small wikis that used no or few extensions, and no or little > special HTML formatting. > > -hilmar > > On Sep 2, 2016, at 10:30 AM, Fields, Christopher J <cjf...@il...> > wrote: > > Yep, this is essentially what the Bio* groups did when our AWS server went > down. > > chris > > From: Nathan Dunn > Date: Thursday, September 1, 2016 at 10:58 AM > To: Scott Cain > Cc: gmod-devel, Dave Clements, "gmo...@li...", " > gmo...@li..." > Subject: Re: [Gmod-ajax] [Gmod-tripal] Migrating gmod.org advice/RFC > > > Scott, > > I would advocate moving to GH pages just for the long-term ease of use, > permission management, and cost. There is no server to setup, but you’ll > have to configure a Jekyll theme (http://jekyllthemes.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__jekyllthemes.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=ryxpkC6EWehYCDuuKHKfS1KURvSMvTwhaaOXKnOqAcQ&e=>) and > add the content, which is a PITA unless you create a single-page app (which > I don’t advocate). > > My guess is that actually converting the content will be easier (and I’m > sure folks in the community will be glad to help). > > https://github.com/philipashlock/mediawiki-to-markdown > <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_philipashlock_mediawiki-2Dto-2Dmarkdown&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=j9fv8snqFBe-s77UnlbrVuwXbw-bCDNLcS2JOKrIhDw&e=> > > > Nathan > > On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...> wrote: > > Hi all, > > I'm addressing this to a few of the more heavily trafficked GMOD mailing > lists in hopes of getting some good advice. The server that runs gmod.org > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> > is being retired at the end of the month, so I have to find it a new home. > One option includes leaving it at OICR on a new virtual machine, but it > will require me to port the existing MediaWiki instance, which I already > know won't be fun. > > There are other alternatives though--it was suggested recently that the > content in gmod.org > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> > could be migrated to GitHub pages, which sounds appealing but I have no > idea how much work would be involved. I've also considered migrating to > AWS, which I think will be a similar amount of work as the internal > migration at OICR but would likely be cheaper in the long run. > > Thanks in advance for any insights! > Scott > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=>) > 216-392-3087 > Ontario Institute for Cancer Research > ------------------------------------------------------------ > ------------------ > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal > > > ------------------------------------------------------------ > ------------------ > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel > > > -- > Hilmar Lapp -:- lappland.io > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Hilmar L. <hl...@dr...> - 2016-09-02 14:39:20
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It should be noted though that this hasn’t been without its downsides. Many links don’t work anymore, some content still needs fixes to formatting, and it was not a small amount of work. I think it’s fair to say that it worked best (and arguably well) for those projects with small wikis that used no or few extensions, and no or little special HTML formatting. -hilmar > On Sep 2, 2016, at 10:30 AM, Fields, Christopher J <cjf...@il...> wrote: > > Yep, this is essentially what the Bio* groups did when our AWS server went down. > > chris > > From: Nathan Dunn > Date: Thursday, September 1, 2016 at 10:58 AM > To: Scott Cain > Cc: gmod-devel, Dave Clements, "gmo...@li... <mailto:gmo...@li...>", "gmo...@li... <mailto:gmo...@li...>" > Subject: Re: [Gmod-ajax] [Gmod-tripal] Migrating gmod.org advice/RFC > > > Scott, > > I would advocate moving to GH pages just for the long-term ease of use, permission management, and cost. There is no server to setup, but you’ll have to configure a Jekyll theme (http://jekyllthemes.org/ <https://urldefense.proofpoint.com/v2/url?u=http-3A__jekyllthemes.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=ryxpkC6EWehYCDuuKHKfS1KURvSMvTwhaaOXKnOqAcQ&e=>) and add the content, which is a PITA unless you create a single-page app (which I don’t advocate). > > My guess is that actually converting the content will be easier (and I’m sure folks in the community will be glad to help). > > https://github.com/philipashlock/mediawiki-to-markdown <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_philipashlock_mediawiki-2Dto-2Dmarkdown&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=j9fv8snqFBe-s77UnlbrVuwXbw-bCDNLcS2JOKrIhDw&e=> > > > Nathan > >> On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc... <mailto:sc...@sc...>> wrote: >> >> Hi all, >> >> I'm addressing this to a few of the more heavily trafficked GMOD mailing lists in hopes of getting some good advice. The server that runs gmod.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> is being retired at the end of the month, so I have to find it a new home. One option includes leaving it at OICR on a new virtual machine, but it will require me to port the existing MediaWiki instance, which I already know won't be fun. >> >> There are other alternatives though--it was suggested recently that the content in gmod.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> could be migrated to GitHub pages, which sounds appealing but I have no idea how much work would be involved. I've also considered migrating to AWS, which I think will be a similar amount of work as the internal migration at OICR but would likely be cheaper in the long run. >> >> Thanks in advance for any insights! >> Scott >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/ <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=>) 216-392-3087 >> Ontario Institute for Cancer Research >> ------------------------------------------------------------------------------ >> _______________________________________________ >> Gmod-tripal mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal <https://lists.sourceforge.net/lists/listinfo/gmod-tripal> > > ------------------------------------------------------------------------------ > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel -- Hilmar Lapp -:- lappland.io |
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From: Fields, C. J <cjf...@il...> - 2016-09-02 14:36:13
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… I should add, it might be worth discussing some of the migration issues w/ Peter Cock and Brian Osborne (cc’d), who were instrumental in moving BioPerl and Biopython’s MW to Github Pages; they can probably gives pointers on what worked best. chris On Sep 2, 2016, at 9:30 AM, Fields, Christopher J <cjf...@il...<mailto:cjf...@il...>> wrote: Yep, this is essentially what the Bio* groups did when our AWS server went down. chris From: Nathan Dunn Date: Thursday, September 1, 2016 at 10:58 AM To: Scott Cain Cc: gmod-devel, Dave Clements, "gmo...@li...<mailto:gmo...@li...>", "gmo...@li...<mailto:gmo...@li...>" Subject: Re: [Gmod-ajax] [Gmod-tripal] Migrating gmod.org<http://gmod.org> advice/RFC Scott, I would advocate moving to GH pages just for the long-term ease of use, permission management, and cost. There is no server to setup, but you’ll have to configure a Jekyll theme (http://jekyllthemes.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__jekyllthemes.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=ryxpkC6EWehYCDuuKHKfS1KURvSMvTwhaaOXKnOqAcQ&e=>) and add the content, which is a PITA unless you create a single-page app (which I don’t advocate). My guess is that actually converting the content will be easier (and I’m sure folks in the community will be glad to help). https://github.com/philipashlock/mediawiki-to-markdown<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_philipashlock_mediawiki-2Dto-2Dmarkdown&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=j9fv8snqFBe-s77UnlbrVuwXbw-bCDNLcS2JOKrIhDw&e=> Nathan On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote: Hi all, I'm addressing this to a few of the more heavily trafficked GMOD mailing lists in hopes of getting some good advice. The server that runs gmod.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> is being retired at the end of the month, so I have to find it a new home. One option includes leaving it at OICR on a new virtual machine, but it will require me to port the existing MediaWiki instance, which I already know won't be fun. There are other alternatives though--it was suggested recently that the content in gmod.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> could be migrated to GitHub pages, which sounds appealing but I have no idea how much work would be involved. I've also considered migrating to AWS, which I think will be a similar amount of work as the internal migration at OICR but would likely be cheaper in the long run. Thanks in advance for any insights! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=>) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ _______________________________________________ Gmod-tripal mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-tripal<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dtripal&d=CwMGaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=gNu39iT7G98Gb0zhECXfVOeEXWfHrHgCuA7ECUez7oA&s=mWCuIRi6zHq4wWzNyFIypvnSbeedVi6-l3BnAKLYTww&e=> ------------------------------------------------------------------------------ _______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Fields, C. J <cjf...@il...> - 2016-09-02 14:30:32
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Yep, this is essentially what the Bio* groups did when our AWS server went down. chris From: Nathan Dunn Date: Thursday, September 1, 2016 at 10:58 AM To: Scott Cain Cc: gmod-devel, Dave Clements, "gmo...@li...<mailto:gmo...@li...>", "gmo...@li...<mailto:gmo...@li...>" Subject: Re: [Gmod-ajax] [Gmod-tripal] Migrating gmod.org advice/RFC Scott, I would advocate moving to GH pages just for the long-term ease of use, permission management, and cost. There is no server to setup, but you’ll have to configure a Jekyll theme (http://jekyllthemes.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__jekyllthemes.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=ryxpkC6EWehYCDuuKHKfS1KURvSMvTwhaaOXKnOqAcQ&e=>) and add the content, which is a PITA unless you create a single-page app (which I don’t advocate). My guess is that actually converting the content will be easier (and I’m sure folks in the community will be glad to help). https://github.com/philipashlock/mediawiki-to-markdown<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_philipashlock_mediawiki-2Dto-2Dmarkdown&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=j9fv8snqFBe-s77UnlbrVuwXbw-bCDNLcS2JOKrIhDw&e=> Nathan On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...<mailto:sc...@sc...>> wrote: Hi all, I'm addressing this to a few of the more heavily trafficked GMOD mailing lists in hopes of getting some good advice. The server that runs gmod.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> is being retired at the end of the month, so I have to find it a new home. One option includes leaving it at OICR on a new virtual machine, but it will require me to port the existing MediaWiki instance, which I already know won't be fun. There are other alternatives though--it was suggested recently that the content in gmod.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=> could be migrated to GitHub pages, which sounds appealing but I have no idea how much work would be involved. I've also considered migrating to AWS, which I think will be a similar amount of work as the internal migration at OICR but would likely be cheaper in the long run. Thanks in advance for any insights! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=CojK7Cc18ffp_qBkQhoLF_4YFYOr-zhuUg6c_Au3YnE&s=9SBLwkC1jIxIls9Y3UdT5YDF4GYY0EB0OT8-qrnO0D4&e=>) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ _______________________________________________ Gmod-tripal mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
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From: Raymond W. <rwa...@gm...> - 2016-09-02 04:19:02
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Hi Scott, On Thu, Sep 1, 2016 at 11:46 PM, Scott Cain <sc...@sc...> wrote: > I'm addressing this to a few of the more heavily trafficked GMOD mailing > lists in hopes of getting some good advice. The server that runs gmod.org > is being retired at the end of the month, so I have to find it a new home. > One option includes leaving it at OICR on a new virtual machine, but it will > require me to port the existing MediaWiki instance, which I already know > won't be fun. Though you've received many good opinions already, I'm not sure if I can add more information. But I don't think moving a MediaWiki instance from the current server to a new virtual machine is very difficult. The backup and restore steps are fairly clear -- I've applied them a few times before. If the two versions of MediaWiki are the same (i.e., upgrade the old one before performing the backup), I don't think you should have many problems. In terms of time, I think it would be faster than moving to GitHub. Moving to GitHub would be nice, but "moving servers" + "moving software" seems to be a lot in one go. Maybe it's better to move things one step at a time? > There are other alternatives though--it was suggested recently that the > content in gmod.org could be migrated to GitHub pages, which sounds > appealing but I have no idea how much work would be involved. I've also > considered migrating to AWS, which I think will be a similar amount of work > as the internal migration at OICR but would likely be cheaper in the long > run. Like Dave, I'm happy with AWS but I do have some strange days where my VM should be idle but the load is incredibly high. I did look around and it's probably because another VM on the same server is over-using resources? (I'm not too sure ... don't take my word for it!) It might be because I'm on the absolute lowest AWS tier... In any case, it is true that both OICR and AWS are VMs, but in terms of ease of finding someone to solve some particular problem, I would think it is easier with OICR than AWS? Of course, I don't know the difference in costs between the two... Ray |
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From: Hilmar L. <hl...@dr...> - 2016-09-01 19:36:13
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> On Sep 1, 2016, at 1:24 PM, Dave Clements <cle...@ga...> wrote: > > So, my vote is stick with MediaWiki. I don't think there is any hope of migrating to GFM without seriously mangling 90%+ of the pages. I’d mostly agree with that. I think in general the pains of migrating a MediaWiki are often overestimated, perhaps because most people you speak to have never done it (or have never had to). I’ve brought up 5 from dumps over the last couple of months. If you follow the instructions, it usually works. That said, the one factor that in my experience can complicate things (and explode time needed) tremendously may well apply to the GMOD wiki, and that’s use of a lot of extensions. Extensions often don’t keep up with the main MediaWiki version and so aren’t available, or are buggy for the latest MediaWiki version. Even when they still are available and current, they sometime have changed their markup rules. Accommodating all that can be a real pain. -hilmar -- Hilmar Lapp -:- lappland.io |
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From: Scott C. <sc...@sc...> - 2016-09-01 19:24:37
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Dave, This is good stuff and brought up points I hadn't thought about--thank you! Do you happen to know what the instance size of the Galaxy wiki server is? I suspect that the Galaxy wiki gets more traffic than the GMOD wiki, but they might be at least roughly comparable. Thanks, Scott On Thu, Sep 1, 2016 at 1:24 PM, Dave Clements <cle...@ga...> wrote: > Hi Scott, > > We are in the process of migrating the Galaxy Wiki from MoinMoin to a > GitHub hosted pseudo-wiki (still looking for a good term). The content will > be in GitHub Flavored Markdown (GFM) plus YAML for metadata and structured > content. We'll then use MetalSmith (http://www.metalsmith.io/) to > generate the actual web site, and it's MetalSmith that will process the > YAML. > > Editors will be able to edit local copies of the doc and generate the > website locally, as well as edit doc directly in GitHub. This model will > fully leverage the power of GitHub. > > Moving GMOD.org to straight github would also leverage that power and > community involvement. > > *However, I think this would be tremendously difficult,* and the > advantages of moving from MediaWiki to GitHub are far less than moving from > MoinMoin to GitHub. > > 1) MediaWiki supports a ton of extensions such as Templates, Categories, > and Extensions. GFM does not support any of that. A lot of content on > GMOD.org would have to be disentangled. > > 2) GFM is deliberately crippled. The theory (I think) is that you should > be using CSS for formatting instead of markup. I like that goal, but the > current GMOD.org is chock full of MediaWiki / HTML hacks to achieve > formatting (I put a lot of it there). Translating that to pure GFM / CSS > would be a nightmare. > > GFM does support directly using HTML, but it does not support mixing the > two in many circumstances. For example, tables are all GFM or all HTML. > And GFM tables are painfully limited. Only the simplest tables can be > translated to GFM. If you want row headers, or colspans or rowspans, or > right or center alignment in a cell, or ... you have to translate the whole > table to HTML. And that defeats the whole purpose of having a wiki. > > *So, my vote is stick with MediaWiki.* I don't think there is any hope > of migrating to GFM without seriously mangling 90%+ of the pages. > > I've CC'd Dannon Baker who is also working the Galaxy Wiki move. He's not > familiar with the current GMOD.org implementation, but he knows about > migrating wikis to GitHub. He may have more to add (and might even > contradict me :-). > > And, we've been running our wiki on AWS for years. We've been very happy > with it. > > My 98¢ > > Dave C > > > On Thu, Sep 1, 2016 at 8:58 AM, Nathan Dunn <nat...@lb...> wrote: > >> >> Scott, >> >> I would advocate moving to GH pages just for the long-term ease of use, >> permission management, and cost. There is no server to setup, but you’ll >> have to configure a Jekyll theme (http://jekyllthemes.org/) and add the >> content, which is a PITA unless you create a single-page app (which I don’t >> advocate). >> >> My guess is that actually converting the content will be easier (and I’m >> sure folks in the community will be glad to help). >> >> https://github.com/philipashlock/mediawiki-to-markdown >> >> >> Nathan >> >> On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...> wrote: >> >> Hi all, >> >> I'm addressing this to a few of the more heavily trafficked GMOD mailing >> lists in hopes of getting some good advice. The server that runs >> gmod.org is being retired at the end of the month, so I have to find it >> a new home. One option includes leaving it at OICR on a new virtual >> machine, but it will require me to port the existing MediaWiki instance, >> which I already know won't be fun. >> >> There are other alternatives though--it was suggested recently that the >> content in gmod.org could be migrated to GitHub pages, which sounds >> appealing but I have no idea how much work would be involved. I've also >> considered migrating to AWS, which I think will be a similar amount of work >> as the internal migration at OICR but would likely be cheaper in the long >> run. >> >> Thanks in advance for any insights! >> Scott >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> ------------------------------------------------------------ >> ------------------ >> _______________________________________________ >> Gmod-tripal mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal >> >> >> > > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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