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.
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
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!
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.
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
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.
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.