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[GSoC 2023] Announcing Google Summer of Code 2023 - Open Genome Informatics organization application due 7th February
by Robin Haw 31 Jan '23

31 Jan '23

Dear All, Last week, Google announced this years’ Google Summer of Code (GSoC). GSoC is a global, online program focused on bringing new contributors into open source software development. GSoC contributors work with an open source organization on a 12+ week programming project under the guidance of mentors. The Open Genome Informatics team, which I administer with the help of Scott Cain and Marc Gillespie, serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). The list of previously involved projects includes JBrowse, Reactome, Galaxy, WormBase, and others. Over the last 12 years, we have been submitting applications to particiapte in GSoC. We are seeking project ideas to post and attract talented contributors to this years’ Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact me, Marc or Scott. You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2023>. For more information, please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC>. The program is open to students and to beginners in open source software development. The length of the projects is 175 and 350-hours, and there is an option to extend the program from the standard 12 weeks up to 22 weeks. Applications for organizations will close on February 7, 2023 at 18:00 UTC. So, if you are interested in taking part with the team, please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions, please let us know. Thanks, Robin, Scott, and Marc Robin Haw, PhD Program Manager – Genome Informatics and Computational Biology Tel: 647-260-7985 robin.haw(a)oicr.on.ca<mailto:robin.haw@oicr.on.ca> Adaptive Oncology Ontario Institute for Cancer Research MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3 @OICR_news | oicr.on.ca<https://oicr.on.ca/> | genome informatics<https://oicr.on.ca/programs/genome-informatics/> | computational biology<https://oicr.on.ca/programs/computational-biology/> Collaborate. Translate. Change lives. This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

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European Galaxy Days, 3-7 Oct, Freiburg
by Beatriz Serrano-Solano 07 Sep '22

07 Sep '22

Dear all, We would like to invite you to the European Galaxy Days, which will take place in Freiburg (and online) from the 3rd to the 7th of October. The event will feature talks and demos with the latest updates from the community! Please find all the information in the event website: https://galaxyproject.org/events/2022-10-egd/ The registration for talks and demos closes on the 16th of September, registration for attendance to the event will be available until the 23rd of September. As soon as the registration for talks and demos is over, we will publish on the website a detailed program. Kind regards, Beatriz on behalf of the organizing team

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Release of Galaxy 22.05
by Marius van den Beek 23 Aug '22

23 Aug '22

Dear Community, We are pleased to announce the release of Galaxy 22.05. - Developer and admin release announcement <https://docs.galaxyproject.org/en/master/releases/22.05_announce.html>. - User release announcement <https://docs.galaxyproject.org/en/master/releases/22.05_announce_user.html> . A few release highlights are: The New History is Here After years of effort by the development team and community contributors, the new history is finally here. It's a big improvement over the old history interface, both technically and in terms of user experience, but it might take some getting used to. It has a lot of great new features like: - A quick switcher, letting you switch between recent histories - Easily find dataset inputs - Improved history search interface Check it out now! Storage Dashboard (Beta) Have you ever been over your quota? 250 GB sure goes fast! Now with the new Storage Dashboard you can get a quick overview of ways to help clean up deleted datasets and recover some of that quota allocation. This is a beta version of this interface, let us know if you have any issues. In future versions, it will be expanded to help you understand how your allocation is being used, and which histories and datasets should be cleaned up first. Bulk History Operations The new history allows for improved bulk operations, selecting dozens or hundreds of datasets to retag or change the database key automatically, a process that used to require using collections or doing them one by one. Deferred dataset resolution enables running workflows and tools without importing data into Galaxy first It is now possible to defer dataset resolution for datasets imported via URLs and the "Choose remote files" dialog. This means that the deferred dataset will only be downloaded as it is needed during job execution. Deferred datasets will not count towards your storage quota, as the data is not stored by Galaxy. To enable deferred dataset resolution click on "Settings" in the upload dialog. Workflow Improvements You can now see all invocations of a specific workflow, across all of your histories. This is especially useful if you run a single workflow across multiple datasets, and keep them nicely separated in multiple histories. You can see all of the results in a single centralised location. Additional workflow improvements have been made, e.g. numbering of steps in a workflow. Improvements have been made to the internal representation of the workflow that should make the saved .ga and .gxwf.yml files easier to compare across changes. Workflows can also now be zoomed in and out via scrolling, this interface should be more familiar for anyone who has used Google Maps: Saved Rules Do you use the Rule Based Uploader (RBU)? (If not, learn how today! <https://training.galaxyproject.org/training-material/topics/galaxy-interfac…>) The RBU now has a very convenient recently used rule listing, sorted by how recently they were used. You can hover over each entry to also list a preview of what steps were done in that RBU invocation. Scratchbook Upgraded The scratchbook has been updated to a new implementation. Now your views of datasets can overlap, you have much more freedom in the size of each window, and you can minimize datasets like minimizing a window to the taskbar in Windows. OpenAPI Docs The Galaxy API is going through an upgrade to FastAPI, which allows us to generate OpenAPI documentation <https://usegalaxy.org/api/docs>. If you're an API consumer, either via BioBlend or via another system, you can use this to see all of the APIs available from Galaxy and try them out live. Release Notes Please see the full release notes <https://docs.galaxyproject.org/en/master/releases/22.05_announce.html> for a lot more details and instructions for upgrading your Galaxy installation. Thanks for using Galaxy!

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Webinar Option Now Available for GCC2022
by Dave Clements 11 Jul '22

11 Jul '22

Hello all, This is a final reminder that registration is still open for GCC2022 and that you can now register for Webinar mode. See below for details. Hope to see you in Minneapolis in a week, Dave C *2022 Galaxy Community Conference (GCC2022)* July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States *#UseGalaxy2022 <https://twitter.com/hashtag/UseGalaxy2022>* *Unable to join us in Minneapolis for GCC2022? Registration now available for limited Webinar attendance!* Based on popular demand there is now a *Webinar mode* option for GCC2022 attendance. After registering for this option, you will get access to the live stream of the main meeting talks. You will also get invited to the conference Slack where you will have an opportunity to ask any questions of the presenters or poster authors. *Please note that in-person training events and CoFest will not be streamed. Also note that all speakers are required to attend in person. * Webinar Mode Registration Fee: $80 ($10 if working in a low-income country; see below) *If you are currently working in a low-income country <https://drive.google.com/file/d/1PW11lByYd61cIT7wPnGmTQpd9kM79EXX/view?usp=…>, as defined by the World Bank, please email Jenn Vessio <jvessio1(a)jhu.edu> before registering and ask for a discount code that you can apply during registration.* Register for GCC2022 Webinar Mode <https://galaxyproject.org/events/gcc2022/register> -- My last day with Galaxy was December 17, 2021 . After that I will be the Anaconda <https://www.anaconda.com/> open source community manager. If you need to reach Galaxy Outreach after December 17, please send your email to outreach(a)galaxyproject.org.

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Webinar Option Now Available for GCC2022
by Galaxy Community Conference 2022 08 Jul '22

08 Jul '22

GCC2022 July 17-23 ** 2022 Galaxy Community Conference (GCC2022) July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States #UseGalaxy2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ------------------------------------------------------------ Unable to join us in Minneapolis for GCC2022? Registration now available for limited Webinar attendance! Based on popular demand there is now a Webinar mode option for GCC2022 attendance. After registering for this option, you will get access to the live stream of the main meeting talks. You will also get invited to the conference Slack where you will have an opportunity to ask any questions of the presenters or poster authors. Please note that in-person training events and CoFest will not be streamed. Also note that all speakers are required to attend in person. Webinar Mode Registration Fee: $80 ($10 if working in a low-income country; see below) If you are currently working in a low-income country (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) , as defined by the World Bank, please email Jenn Vessio (mailto:jvessio1@jhu.edu) before registering and ask for a discount code that you can apply during registration. Register for GCC2022 Webinar Mode (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ============================================================ ** Twitter (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ** Website (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Copyright © 2022 The Sapphyre Group, All rights reserved. You are receiving this email because you opted in via our website. Our mailing address is: The Sapphyre Group 7042 E Fish Lake Rd Maple Grove, MN 55311-2832 USA Want to change how you receive these emails? You can ** update your preferences (https://sapphyregroup.us14.list-manage.com/profile?u=0f49f912c8c0f3f17b049d…) or ** unsubscribe from this list (https://sapphyregroup.us14.list-manage.com/unsubscribe?u=0f49f912c8c0f3f17b…) . Email Marketing Powered by Mailchimp http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…

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Webinar mode for GCC2022 - Registration open
by Beatriz Serrano-Solano 27 Jun '22

27 Jun '22

Dear all, As you may know, the Galaxy Community Conference (GCC2022) will take place in Minnesota this year. For those that won't attend in person, the GCC Organizing Committee is happy to *announce a virtual webinar-like option*. How can you register? * There is a special *Virtual* option in the registration form <https://galaxyproject.org/events/gcc2022/register> for online only. * Once you are registered and a few days before the conference, you'll receive all the information you need, including: - an invitation to join the GCC2022 Slack space, - a link to a zoom webinar. Is it going to be interactive? There will be a Meeting Owl <https://owllabs.com/> on-site that will show you the room. In the webinar mode, you will have the chance to: * Watch the presentations live (remember the time difference!). * Ask questions. The chat and Q&A functionality will be enabled. There will be someone online in close contact with the moderator in the room. * If there's no time for more questions, you can always post them in the Slack channel. Will you be able to attend the poster session? Partially. The authors will deposit their posters in Sched <https://gcc2022.sched.com/>, and you'll have the chance to ask questions in Slack using the channel *gcc2022-posters-demo*. Their response may be slow, depending on how busy the poster presenters are in real life. How much will the virtual attendance cost? - Regular online registration: $80. - $10 for Low-Income-Countries (check this list <https://drive.google.com/file/d/1PW11lByYd61cIT7wPnGmTQpd9kM79EXX/view> to find out which countries qualify as such). When is the deadline for registration? - July 15. Thank you all for all the interest that you've been showing to join GCC2022, regardless of the format. That's great to see! Cheers, Beatriz on behalf of the GCC2022 Organizing Committee

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GCC2022 Registration Fees Increase Tomorrow
by Galaxy Community Conference 2022 22 Jun '22

22 Jun '22

July 17-23 | Minneapolis, MN ** 2022 Galaxy Community Conference (GCC2022) July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States #UseGalaxy2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ------------------------------------------------------------ Join us next month when the #usegalaxy (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) community meets in person at GCC2022! Registration fees go up tomorrow. View a summary here (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) of what to expect when you join us in Minneapolis. Registration has been EXTENDED to Wednesday, June 22 - register here for GCC2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ! Meeting Registration Fees Full (< June 22) Late (> June 23) Student/postdoc $400 $500 Academic / Non-Profit / Government $550 $750 Industry $900 $1,150 Hotel Reservation Deadline EXTENDED Be sure to make your hotel reservations (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) at our GCC2022 venue the Courtyard Minneapolis Downtown by Thursday, June 30 to get our conference rate of $139/night! Register for GCC2022 by June 22 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Make Hotel Reservations by June 30 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ============================================================ ** Twitter (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ** Website (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Copyright © 2022 The Sapphyre Group, All rights reserved. You are receiving this email because you opted in via our website. Our mailing address is: The Sapphyre Group 7042 E Fish Lake Rd Maple Grove, MN 55311-2832 USA Want to change how you receive these emails? You can ** update your preferences (https://sapphyregroup.us14.list-manage.com/profile?u=0f49f912c8c0f3f17b049d…) or ** unsubscribe from this list (https://sapphyregroup.us14.list-manage.com/unsubscribe?u=0f49f912c8c0f3f17b…) . Email Marketing Powered by Mailchimp http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…

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GCC2022 Deadlines Extended to June 22 and June 30!
by Dave Clements 17 Jun '22

17 Jun '22

Hello all, *The executive summary:* 1. *We have moved our registration deadline to June 22*. Register by the end of Wednesday and save 25% or $200 on your registration. 2. *Hotel rooms can now be booked through June 30*. The hotel is where the conference is, it's a good price, it's in a cool neighborhood, and it's right next to the UMN campus. And if you are wondering what GCC2022 is about... *GCC2022* <https://galaxyproject.org/gcc2022/> brings together hundreds of researchers, trainers, tool developers, software engineers, and computational infrastructure providers, all addressing common challenges in data intensive science using the Galaxy data integration and analysis platform <https://galaxyproject.org/>. *See below for links and more news.* I/We hope to see you in Minneapolis in one month! Dave C, on behalf of the GCC2022 Organizing Committee *2022 Galaxy Community Conference (GCC2022)* July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States *#UseGalaxy2022 <https://twitter.com/hashtag/UseGalaxy2022>* *Three years of waiting and we're down to one month before the #usegalaxy <https://twitter.com/hashtag/usegalaxy?src=hashtag_click> community meets in person at GCC2022! View a summary here <https://galaxyproject.org/blog/2022-06-guide-to-gcc2022/> of what to expect when you join us in Minneapolis.* *Not Registered Yet? There's Still Time!* *Registration has been EXTENDED to Wednesday, June 22 *- *register here for GCC2022 <https://galaxyproject.org/events/gcc2022/register>! * Meeting Registration Fees *Full (< June 22) * *Late (> June 23) * Student/postdoc $400 $500 Academic / Non-Profit / Government $550 $750 Industry $900 $1,150 *Michael Schatz at GCC2022* What do TIME100 <https://time.com/collection/100-most-influential-people-2022/6177818/evan-e…> and GCC2022 have in common? Michael Schatz, that's what! Come talk to him about the future, learn more about his Birds of a Feather session here <https://gcc2022.sched.com/event/13V9n>. *We have a tremendous lineup of speakers for our accepted and invited talks and training sessions! *Get to know who they are by *viewing the entire GCC2022 schedule <https://gcc2022.sched.com/>. * *Hotel Reservation Deadline EXTENDED* Be sure to make your hotel reservations <https://www.marriott.com/event-reservations/reservation-link.mi?id=16458128…> at our GCC2022 venue the Courtyard Minneapolis Downtown by Thursday, June 30 to get our conference rate of $139/night! Register for GCC2022 by June 22 <https://galaxyproject.org/events/gcc2022/register> Make Hotel Reservations by June 30 <https://www.marriott.com/event-reservations/reservation-link.mi?id=16458128…> PS: No, you can never completely leave the Galaxy. You knew this right? PPS: We moved these dates back because a particularly bad interaction between the (spiffy!) MailChimp service we have been using for GCC2022, and Galaxy's (only semi-functional!) MailMan3 server caused no email to be delivered to several mailing lists since the end of April. So, now is your chance. Please do register by Wednesday. -- My last day with Galaxy was December 17, 2021 . After that I will be the Anaconda <https://www.anaconda.com/> open source community manager. If you need to reach Galaxy Outreach after December 17, please send your email to outreach(a)galaxyproject.org.

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GCC2022 Highlights and Updated Deadlines
by Galaxy Community Conference 2022 17 Jun '22

17 Jun '22

July 17-23 | Minneapolis, MN ** 2022 Galaxy Community Conference (GCC2022) July 17-23, 2022 University of Minnesota, Twin Cities Minneapolis, Minnesota, United States #UseGalaxy2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ------------------------------------------------------------ Three years of waiting and we're down to one month before the #usegalaxy (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) community meets in person at GCC2022! View a summary here (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) of what to expect when you join us in Minneapolis. Not Registered Yet? There's Still Time! Registration has been EXTENDED to Wednesday, June 22 - register here for GCC2022 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ! Meeting Registration Fees Full (< June 22) Late (> June 23) Student/postdoc $400 $500 Academic / Non-Profit / Government $550 $750 Industry $900 $1,150 Michael Schatz at GCC2022 What do TIME100 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) and GCC2022 have in common? Michael Schatz, that's what! Come talk to him about the future, learn more about his Birds of a Feather session here (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) . We have a tremendous lineup of speakers for our accepted and invited talks and training sessions! Get to know who they are by viewing the entire GCC2022 schedule (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) . Hotel Reservation Deadline EXTENDED Be sure to make your hotel reservations (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) at our GCC2022 venue the Courtyard Minneapolis Downtown by Thursday, June 30 to get our conference rate of $139/night! Register for GCC2022 by June 22 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Make Hotel Reservations by June 30 (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ============================================================ ** Twitter (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) ** Website (https://sapphyregroup.us14.list-manage.com/track/click?u=0f49f912c8c0f3f17b…) Copyright © 2022 The Sapphyre Group, All rights reserved. You are receiving this email because you opted in via our website. Our mailing address is: The Sapphyre Group 7042 E Fish Lake Rd Maple Grove, MN 55311-2832 USA Want to change how you receive these emails? You can ** update your preferences (https://sapphyregroup.us14.list-manage.com/profile?u=0f49f912c8c0f3f17b049d…) or ** unsubscribe from this list (https://sapphyregroup.us14.list-manage.com/unsubscribe?u=0f49f912c8c0f3f17b…) . Email Marketing Powered by Mailchimp http://www.mailchimp.com/email-referral/?utm_source=freemium_newsletter&utm…

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[GSoC2021] [OGI] Participation in Google Summer of Code 2021
by Robin Haw 15 Mar '22

15 Mar '22

Dear All, The Open Genome Informatics team serves as an “umbrella" organization to support the efforts of many open-access open-source bioinformatics projects for <https://summerofcode.withgoogle.com/> Google Summer of Code (GSoC<https://summerofcode.withgoogle.com/>). Among this list of projects are Reactome and GMOD and its software projects -- JBrowse; Galaxy; WormBase; and others. Call for 2021 Project Ideas and Mentors: We are seeking project ideas to post and attract talented students to this year’s Summer of Code competition. If you have a project idea for which you would like to mentor a student, please contact Robin Haw, Marc Gillespie, and Scott Cain (emails above). You can also submit your ideas here<http://gmod.org/wiki/GSOC_Project_Ideas_2021>. For more information please refer to the Open Genome Informatics page on the GMOD.org website<http://gmod.org/wiki/GSoC><http://gmod.org/wiki/GSoC#Google_Summer_of_Code_2020>. The mentoring organization application deadline with GSoC is February 19th at 2 pm EST. So, if you are interested in taking part with the team please let us know as soon as possible. Please forward this to others who might be interested in taking part. If you have any questions please let us know. Thanks, Robin, Marc, and Scott.

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