[galaxy-dev] Webinar Option Now Available for GCC2022

[Dave Clements]

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 *
*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
,
as defined by the World Bank, please email Jenn Vessio
 before registering and ask for a discount code that you
can apply during registration.*
Register for GCC2022 Webinar Mode

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Anaconda  open source community manager.  If you
need to reach Galaxy Outreach after December 17, please send your email to
outre...@galaxyproject.org.
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[galaxy-dev] GCC2022 Deadlines Extended to June 22 and June 30!

[Dave Clements]

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*  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 .

*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 *

*Three years of waiting and we're down to one month before the #usegalaxy
 community meets
in person at GCC2022! View a summary here
 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 ! *
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

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
.

*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 . *

*Hotel Reservation Deadline EXTENDED*
Be sure to make your hotel reservations

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

Make Hotel Reservations by June 30

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.
-- 
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Anaconda  open source community manager.  If you
need to reach Galaxy Outreach after December 17, please send your email to
outre...@galaxyproject.org.
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[galaxy-dev] November 2021 Galaxy Newsletter

[Dave Clements]

Happy November from Galaxy!

The November newsletter is thin, *but powerful*:

   - Galaxy India Launches this Month
   <https://galaxyproject.org/news/2021-11-galaxy-update/#community-news>
   - 7 new openings (13 total)
   <https://galaxyproject.org/news/2021-11-galaxy-update/#community-news>
   - 9 upcoming Events
   <https://galaxyproject.org/news/2021-11-galaxy-update/#event-news>
   - Blog posts on SARS-CoV-2 training in Africa; Sunsetting CloudLaundh;
   and TIaaS
   <https://galaxyproject.org/news/2021-11-galaxy-update/#galactic-blog-posts>
   - UseGalaxy.* Updates
   <https://galaxyproject.org/news/2021-11-galaxy-update/#galaxy-platforms-news>
   - Other News too: BY-COVID Launches
   <https://galaxyproject.org/news/2021-11-galaxy-update/#other-news>

Have something for the next newsletter? Please let us know and we will
spread the word.

Beatriz Serrano-Solano and Dave Clements, Editors
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[galaxy-dev] October Galaxy News

[Dave Clements]

Hello all,

The October Newsletter is out
<https://galaxyproject.org/news/2021-10-galaxy-update/>. and it covers
Galaxy involvement in Hacktoberfest, and Outreachy, plus a nice batch of
trainings, talks and a Galaxy Papercuts CoFest day too. It also brings news
of new job openings on two continents, two new platforms, blog posts (where
My Little Pony makes an appearance, really), GTN updates (few in number but
big in their coolness), publications, and releases.

In other words, another active month in the Galaxy.

Beatriz Serrano-Solano and Dave Clements, Editors

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[galaxy-dev] September 2021 News: Papercuts resumes; Misconceptions; Hub updated; microGalaxy Community, ...

[Dave Clements]

Hi all,

The September newsletter
<https://galaxyproject.org/news/2021-09-galaxy-update/> brings lots of
news, including

   - 12 recent use cases for UseGalaxy.eu, covering a broad spectrum of
   research.
   - Want to help address misconceptions about Galaxy?
   - The Galaxy Community Hub is now using Gridsome.
   - ELIXIR community updates
   - JXTX Foundation 2021 Awards
   - 7 open positions in Belgium, Italy, and the US
   - The Galaxy YouTube channel is growing up
   - Upcoming events
   - Galaxy Platforms News
   - Recent Blog Posts
   - Doc, Hub, and Training Updates
   - Recent Publications
   - and other news too.

Sit back, get comfortable, and explore the Galaxy...

Beatriz Serrano-Solano and Dave Clements, Editors
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[galaxy-dev] PaperCuts is Resuming this Thursday, Septermber 16

[Dave Clements]

Hello all,

After taking the last 3 months off, PaperCuts is back
.  Galaxy PaperCuts is
a monthly online gathering where we address irritating but relatively easy
to fix bugs in anything related to Galaxy.  This can be code,
documentation, training materials, Ansible recipes, and do on.

We will be on Gitter  for chat all
day long, and on 3 calls spread across the day. Please take advantage of
both to communicate with your collaborators around the world.

   - *Call 1: Oceania, Australia, Asia*
  - 14:00 Australia Eastern time. See your time
  

  .
  - Zoom Link
  
   - *Call 2: Middle East, Europe, Africa*
  - 10:00 Central European Summer time. See your time
  

  .
  - Zoom Link
  

   - *Call 3: Americas*
  - 12:00 US Eastern time. See your time
  

  .
  - Zoom Link
  

If you have any ideas for papercut issues, please add them to the
appropriate repo.

Thanks, and hope to see you soon,
Dave C

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[galaxy-dev] Galaxy Newsletter: July 2021

[Dave Clements]

Hello all,

The big news for July is that the 2021 Galaxy Community Conference
<https://gcc2021.sched.com/> is under way.

With GCC going on, this is one of our thinner newsletters
<https://galaxyproject.org/news/2021-07-galaxy-update/>, but there are
still *open positions
<https://galaxyproject.org/news/2021-07-galaxy-update/#community-news>*, *event
news <https://galaxyproject.org/news/2021-07-galaxy-update/#event-news>*,
*Galaxy
platform news
<https://galaxyproject.org/news/2021-07-galaxy-update/#galaxy-platforms-news>*,
*Galactic blog posts
<https://galaxyproject.org/news/2021-07-galaxy-update/#galactic-blog-activity>*,
*training and doc updates
<https://galaxyproject.org/news/2021-07-galaxy-update/#doc-hub-and-training-updates>*,
recent *open-access Galaxy-related publications
<https://galaxyproject.org/news/2021-07-galaxy-update/#publications>*, *new
releases <https://galaxyproject.org/news/2021-07-galaxy-update/#releases>,
and other news too
<https://galaxyproject.org/news/2021-07-galaxy-update/#other-news>.*

We hope to see you at GCC events this week and next.

Dave Clements and Beatriz Serrano-Solano, Editors
PS: It is too late to register for the 3 day conference next week. It is
also officially too late to sign up for the CoFest on 9-10 July, but
if you follow
this link
<https://docs.google.com/forms/d/e/1FAIpQLScdJHTzw7LWVxFaqGI30COZlcxGPksjGL_UDSwDNsQK1FVFCw/viewform>,
you just mind find yourself invited anyway.
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[galaxy-dev] GCC2021 Deadlines Approaching

[Dave Clements]

Hello all,


The early registration deadline for the 2021 Galaxy Community Conference
has been moved back to June 8. This gives you more time to take advantage
of the 50% discount off full registration prices, so make sure you sign up
now so you don't miss out! Register here
<https://www.vibconferences.be/events/gcc2021-virtual-edition#attendees>.

The draft program <https://gcc2021.sched.com/> and the speakers are now
also available online. Please bear in mind that the times are set for the
Europe/Middle East/Africa - Asia/Pacific window, and that the same schedule
will run 9 hours later for the Americas. The availability of the speakers
for the Q session will depend on the time zone in which they are
located. Posters
and demo sessions can still be submitted
<https://www.vibconferences.be/events/gcc2021-virtual-edition#abstracts>
until the 14th of June.

Feel free to distribute this message further in your network.

We hope to meet you online!
Dave Clements on behalf of the GCC2021 Organizing Committee

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[galaxy-dev] Webinar, Wednesday May 26: Galaxy Resources for Admins and Infrastructure Providers

[Dave Clements]

Hello all,

We are closing the webinar series *"Galaxy Resources for..."* tomorrow with
> Gianmauro Cuccuru and Lucille Delisle. They will talk about the relevant
> resources for *Galaxy admins and infrastructure providers*. Please feel
> free to register and share this link:
>
> https://galaxyproject.org/events/2021-05-gr4-admins/
>

We hope to see you there,
Dave "Blatantly copying Beatriz Serrano-Solano who reminded me to post this
here" C

PS: Also, some GCC2021 news.  The early registration deadline for GCC2021
is Monday, June 1.  We may not have a full talk schedule published by then,
but we do hope to have published a long list of confirmed topics and
presenters by then.  Watch this space .

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[galaxy-dev] May 2021 Galaxy Newsletter: GCC2021 Deadlines Extended

[Dave Clements]

Hello all,


*The May 2021 edition of Galaxy News
<https://galaxyproject.org/news/2021-05-galaxy-update/> is out! *

The big news is that *several deadlines for the 2021 Galaxy Community
Conference
<https://galaxyproject.org/news/2021-05-galaxy-update/#community-news> have
been extended, and the deadline for submitting James Taylor videos
<https://galaxyproject.org/news/2021-05-galaxy-update/#featured-news> has
been extended to this Friday.*

And there are other upcoming deadlines too:

   - *ISMB/ECCB and BOSC 2021 abstracts
   <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> are due
   this Thursday.*
   - *Apply for the Galaxy Australia Variant Calling Workshops
   <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news> by May
   12.*

We also have

   - *open positions
   <https://galaxyproject.org/news/2021-05-galaxy-update/#community-news>*
   - *webinars, CoFests, workshops, community meetups, and other events
   <https://galaxyproject.org/news/2021-05-galaxy-update/#event-news>*,
   - news about *public Galaxy platforms
   
<https://galaxyproject.org/news/2021-05-galaxy-update/#galaxy-platforms-news>*
   ,
   - recent *blog posts
   
<https://galaxyproject.org/news/2021-05-galaxy-update/#galactic-blog-activity>*
   ,
   - *training and doc updates
   
<https://galaxyproject.org/news/2021-05-galaxy-update/#doc-hub-and-training-updates>*
   ,
   - recent *open-access Galaxy-related publications
   <https://galaxyproject.org/news/2021-05-galaxy-update/#publications>*,
   and
   - *new releases
   <https://galaxyproject.org/news/2021-05-galaxy-update/#releases>.*

As always, thanks for using Galaxy,

Dave Clements and Beatriz Serrano-Solano, Editors
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[galaxy-dev] Share your favorite James Taylor Story

[Dave Clements]

Hi All,

In case you missed this
 on other channels,
the deadline is this week:

It's been a year since James Taylor 
passed away. To remember him, and mark his upcoming birthday (May 18) we
would like to create a community video. We are asking you to tell us your
favorite story about James in ~ 30 seconds. We will combine your clips into
a community video that will be prominently featured on all Galaxy-related
sites.

Here is what we will need you to do before April 30:

   1. Think of your favorite story/interaction/event involving James.
   2. Pick a nice location and record the video!
   3. The video should be:
  - in a high-resolution
  - without background noise
  - in a horizontal orientation (not vertical!)
  - ≲ 30 seconds in length
   4. Deposit video file to your Google Drive or Dropbox folder (or any
   other location that would allow us to retrieve it)
   5. Send a link to the video, your name and location as you would like
   them to appear in the final video to: outre...@galaxyproject.org

Thank you all in advance and please feel free to send this to other friends
of James.

Galaxy Outreach

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[galaxy-dev] March 2021 Galaxy Newsletter

[Dave Clements]

Hello all,
It is a very busy time in the Galaxy. 2021 is young, but we have already
had two large training events, including the largest Galaxy event ever -
the GTN Smörgåsbord (with an amazing 1100+ people registered). We are
ramping up for GCC2021, which will be online, global, and affordable, and
will be more accessible (and likely much larger) than an in-person Galaxy
Community Conference.

Galaxy is also shifting with the times, and to reflect how our community
has grown. This newsletter includes a new *Featured News
<https://galaxyproject.org/news/2021-03-galaxy-update/#featured-news>*
section highlighting 1) the *recent explosion of videos* related to Galaxy,
2) a draft *global governance model for Galaxy*, and 3) the new *Galaxy
Career Center.*

That's followed by another new section highlighting *community news
<https://galaxyproject.org/news/2021-03-galaxy-update/#community-news>.*
Arguably, *everything* here is community news, but items listed here
particularly emphasize the community aspects of Galaxy.

The newsletter still includes sections on

   - *upcoming events
   <https://galaxyproject.org/news/2021-03-galaxy-update/#event-news>*,
   - news about *public Galaxy platforms
   
<https://galaxyproject.org/news/2021-03-galaxy-update/#galaxy-platforms-news>*
   ,
   - recent *blog posts
   
<https://galaxyproject.org/news/2021-03-galaxy-update/#galactic-blog-activity>*
   ,
   - *training and doc updates
   
<https://galaxyproject.org/news/2021-03-galaxy-update/#doc-hub-and-training-updates>*
   ,
   - recent *open-access Galaxy-related publications
   <https://galaxyproject.org/news/2021-03-galaxy-update/#publications>*,
   and
   - *new releases
   <https://galaxyproject.org/news/2021-03-galaxy-update/#releases>.*

It's a lot to take in, but it all highlights the breadth and depth of the
Galaxy Community.

Enjoy,

Dave Clements and Beatriz Serrano-Solano, Editors
[image: 2021-03-16_14-51-56-wordcloud.png]
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[galaxy-dev] January 2021 Galaxy Newsletter

[Dave Clements]

Hello all,

We are pleased to announce the first newsletter of 2021. As you can see
there is a lot happening this month, starting with a working groups call
about one hour from now.

Thank you for persevering through 2020, and we hope that 2021 will be a
better year for the world, and for this community.

Dave Clements and Beatriz Serrano-Solano

   - *Event news
   <https://galaxyproject.org/news/2021-01-galaxy-update/#event-news>*:
  - 2nd Galaxy-ELIXIR webinar series, *starts January 20*
  - Galaxy Developer Roundtables, *January 7 & 21*
  - Papercuts CollaborationFest: *January 21*
  - Future Galaxy Admin Trainings, *Register your interest*
  - Tripal CodeFest 2021: *January 11-15*
  - Structural Variant Detection using ONT Data, *January 26*
  - GTN Smörgåsbord: A Global Galaxy Course. *Register by February 1*
  - Single-cell RNA-seq & network analysis using Galaxy and
Cytoscape, *Apply
  by 26 February*
   - *Galaxy platform news
   
<https://galaxyproject.org/news/2021-01-galaxy-update/#galaxy-platforms-news>:*
  - UseGalaxy.no
  - VINYL on Laniakea
  - W4M on UseGalaxy.fr
  - Center for Phage Technology server upgraded and improved
  - Plus more UseGalaxy.* news
   - *Blog posts
   
<https://galaxyproject.org/news/2021-01-galaxy-update/#galactic-blog-activity>:*
  - Involvement of the Galaxy community in OLS-2 and invitation to
  apply to the next cohort
  - DDA and DIA proteomic analysis in Galaxy
  - GTN plant-related trainings
   - *Training material and doc updates
   
<https://galaxyproject.org/news/2021-01-galaxy-update/#doc-hub-and-training-updates>*:

  - Videos: Galactic Introductions
  - Videos: Quick Tips
   - *Publications
   <https://galaxyproject.org/news/2021-01-galaxy-update/#publications>*
  - Metaproteomics, CorGAT (SARS-CoV-2), GAIT-GM (metabolites), and
  training
   - *Q: Who's hiring?
   <https://galaxyproject.org/news/2021-01-galaxy-update/#whos-hiring>*
  - Europe:
 - Norwegian University of Life Science, IFB, VIB
  - North America:
 - Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions)
  - *New releases
   <https://galaxyproject.org/news/2021-01-galaxy-update/#releases>*:
  - Planemo 0.74.1



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[galaxy-dev] Galaxy Papercuts CoFest Day: December 17

[Dave Clements]

Hello all,

The third Galaxy Paper Cuts day will be held on Thursday, December 17.
It will be a day long, around-the-world event, with calls about every
3 hours, plus Gitter chat and support all day. See
  https://galaxyproject.org/events/2020-12-papercuts/

“Paper cuts” are annoying, but relatively easy to fix bugs. They are
also a great way to become familiar with how to contribute code and
other updates. This paper cut event applies to the entire Galaxy
ecosystem.

In addition to learning and fixing, you can also help by
* Creating GitHub issues for anything in Galaxy that bugs you and is
likely to be easy to fix.*
* Advertising this event in your communities. We are particularly
reaching to research software engineers and students.

We hope to see you online on Thursday!

Cheers,
Dave C on behalf of the PaperCuts organizers

* What’s easy to fix? Trust your instincts on this. We want to hear
about glitches, even if they turn out to be harder to fix.


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[galaxy-dev] December 2020 Galaxy Newsletter: And what a month it is

[Dave Clements]

Hello all,

The December 2020 newsletter is out
   https://galaxyproject.org/news/2020-12-galaxy-update/

And there is a lot to it:

Event news:
  Webinars:
Use Galaxy anywhere, right now, December 9
Chloroplast Genome Assembly, December 10
  First Metabolomics Community Call, December 10
  Galaxy Developer Round Table: Working Groups, December 10
  Papercuts CollaborationFest: December 17
  Galaxy Admin Training: Apply by December 18
  Tripal CodeFest 2021: January 11-15
  GTN Smörgåsbord: A Global Galaxy Course. Register by February 1

Galaxy platform news:
  CLIP-Explorer, a new server for CLIP-Seq data
  GenAP expansion funded by CANARIE (Canada!)
  UseGalaxy.eu gets more storage and GPUs through deNBI-Cloud
  Plus more UseGalaxy.* news

Blog posts:
  Outcome of the BioHackathon Europe
  Accessible single-cell RNA-sequencing bioinformatics training
using Galaxy
  TIaaS and training feedback

Training material and doc updates:
  Chloroplast genome assembly
  Compute and analyze Essential Biodiversity Variables with PAMPA
toolsuite
  16S Microbial analysis with Nanopore data

Publications
  Metaproteomics, CLIP-Explorer, GIANT, and package management
is your friend

Q: Who's hiring?
  Europe:
Max Planck IIE, University of Oslo, Hannover Medical School,
  EMBL Rome, Norwegian University of Life Science,
  Sorbonne-Université
  North America:
Roche, Johns Hopkins (AnVIL, 2 positions; Galaxy, 2 Positions),
Cleveland Clinic
  A: Everyone, it seems.

New releases:
  Galaxy 20.09
  ENA submission
  OMERO accessible from Galaxy
  CloudLaunch

Other news too


Happy Holidays!
Dave C and Beatriz, on behalf of, well, everyone

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[galaxy-dev] Re: Two Important Galaxy Calls Next Week

[Dave Clements]

Hi All,

Many thanks to Assunta for pointing out an error:  Dec 3 should say
Dec 9.  So the revised description:

=
Please consider attending this one, and announcing it to your communities:

**Use Galaxy on the web, the cloud, and your laptop too: Options for
using Galaxy: everywhere and right now**

Wednesday, December 9th, 11am Eastern US time (see your time:
https://bit.ly/2VABo3X)
https://galaxyproject.org/events/2020-12-webinar-where/

This Galaxy webinar will introduce the many options for using Galaxy
right now and anywhere in the world. We'll cover
* Publicly accessible Galaxy servers on the web (there are over 100 of them)
* Research and commercial cloud platforms, from Australia (Nectar) to
the US (Jetstream, AnVIL), and everywhere in between (CloudLaunch)
* On your laptop, using pre-packaged containers and virtual machines.

The webinar will be at 11am Eastern US time (see your time). Enis
Afgan, Anton Nekrutenko, and Mike Schatz will present.

Interested? Please sign up now: https://bit.ly/2020-12-webinar-register

==

With many apologies,
Dave C


On Thu, Dec 3, 2020 at 11:31 AM Dave Clements
 wrote:
>
> Hi All,
>
> There are two important Galaxy related calls next week.  Please consider:
> * spreading the word about the first one to your communities.
> * attending both
>
> Details are below.
>
> Thanks,
> Dave C
>
> =
> Please consider attending this one, and announcing it to your communities:
>
> **Use Galaxy on the web, the cloud, and your laptop too: Options for
> using Galaxy: everywhere and right now**
>
> Wednesday, December 3rd, 11am Eastern US time (see your time:
> https://bit.ly/2VABo3X)
> https://galaxyproject.org/events/2020-12-webinar-where/
>
> This Galaxy webinar will introduce the many options for using Galaxy
> right now and anywhere in the world. We'll cover
> * Publicly accessible Galaxy servers on the web (there are over 100 of them)
> * Research and commercial cloud platforms, from Australia (Nectar) to
> the US (Jetstream, AnVIL), and everywhere in between (CloudLaunch)
> * On your laptop, using pre-packaged containers and virtual machines.
>
> The webinar will be at 11am Eastern US time (see your time). Enis
> Afgan, Anton Nekrutenko, and Mike Schatz will present.
>
> Interested? Please sign up now: https://bit.ly/2020-12-webinar-register
>
>
> 
> Please consider attending this one:
>
> **Get Involved with Galaxy: Introducing Galaxy Working Groups**
>
> Thursday, December 10, Noon Eastern US (see your time: https://bit.ly/3g6J8nN)
> https://galaxyproject.org/events/2020-12-10-dev-roundtable/
>
> Galaxy has grown a lot of the years, going from a project at one
> university in 2005 to the global community it is today. Several parts
> of the Galaxy ecosystem have become avowedly and obviously community
> driven during that time, including tools, code, training, and several
> other international efforts. It is past time to push this global model
> to other areas of Galaxy as well.
>
> At the December 10 Galaxy Developer Roundtable we will introduce
> Galaxy Working Groups as a means for the community to help manage and
> contribute to key parts of the Galaxy ecosystem.
>
> If you are interested and are potentially willing to contribute some
> of your time and effort to helping the global Galaxy effort, then
> please attend this roundtable on December 10. If you can't make it,
> the gathering will be recorded and published shortly after the event.
>
> --
> https://galaxyproject.org/



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[galaxy-dev] Two Important Galaxy Calls Next Week

[Dave Clements]

Hi All,

There are two important Galaxy related calls next week.  Please consider:
* spreading the word about the first one to your communities.
* attending both

Details are below.

Thanks,
Dave C

=
Please consider attending this one, and announcing it to your communities:

**Use Galaxy on the web, the cloud, and your laptop too: Options for
using Galaxy: everywhere and right now**

Wednesday, December 3rd, 11am Eastern US time (see your time:
https://bit.ly/2VABo3X)
https://galaxyproject.org/events/2020-12-webinar-where/

This Galaxy webinar will introduce the many options for using Galaxy
right now and anywhere in the world. We'll cover
* Publicly accessible Galaxy servers on the web (there are over 100 of them)
* Research and commercial cloud platforms, from Australia (Nectar) to
the US (Jetstream, AnVIL), and everywhere in between (CloudLaunch)
* On your laptop, using pre-packaged containers and virtual machines.

The webinar will be at 11am Eastern US time (see your time). Enis
Afgan, Anton Nekrutenko, and Mike Schatz will present.

Interested? Please sign up now: https://bit.ly/2020-12-webinar-register



Please consider attending this one:

**Get Involved with Galaxy: Introducing Galaxy Working Groups**

Thursday, December 10, Noon Eastern US (see your time: https://bit.ly/3g6J8nN)
https://galaxyproject.org/events/2020-12-10-dev-roundtable/

Galaxy has grown a lot of the years, going from a project at one
university in 2005 to the global community it is today. Several parts
of the Galaxy ecosystem have become avowedly and obviously community
driven during that time, including tools, code, training, and several
other international efforts. It is past time to push this global model
to other areas of Galaxy as well.

At the December 10 Galaxy Developer Roundtable we will introduce
Galaxy Working Groups as a means for the community to help manage and
contribute to key parts of the Galaxy ecosystem.

If you are interested and are potentially willing to contribute some
of your time and effort to helping the global Galaxy effort, then
please attend this roundtable on December 10. If you can't make it,
the gathering will be recorded and published shortly after the event.

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[galaxy-dev] Galaxy Admin Training, Jan 25-29, online. global, and free.

[Dave Clements]

Hello all,

We are now accepting applications for the January 2021 Galaxy Admin
training workshop.  This will be offered online and around the world, and
will be free:
  https://galaxyproject.org/events/2021-01-admin-training/

If you administer or plan to administer a Galaxy instance then please
consider applying for this workshop.

Space is limited, and we expect applications to be competitive.  The
application deadline is December 18.

Thanks,
Dave C on behalf of the workshop instructors.

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[galaxy-dev] Galaxy Developer Round Table: Working with the GTN, TODAY

[Dave Clements]

Hi All,

The next Galaxy Developer Round Table STARTS IN 30 MINUTES, at
Noon US Eastern.  It will be a discussion about working with the Galaxy
Training Network.

Links are here:
  https://galaxyproject.org/events/2020-11-12-dev-roundtable/

Hope to see you there,
Dave C

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[galaxy-dev] November 2020 Paper Cuts Day: Nov 18

[Dave Clements]

Hello all,

The second Galaxy Paper Cuts day will be held on Wednesday November 18.  It
will be a day long, around-the-world event, with calls about every 3 hours,
plus Gitter chat and support all day.
  https://galaxyproject.org/events/2020-11-papercuts/

"Paper cuts" are annoying, but relatively easy to fix bugs.  They are also
a great way to become familiar with how to contribute code and other
updates. This paper cut event applies to the entire Galaxy ecosystem.

In addition to learning and fixing, you can also help by
1) Creating GitHub issues for anything in Galaxy that bugs you and is
likely to be easy to fix.*
2) Advertising this event in your communities. We are particularly reaching
to research software engineers and students.

We hope to see you online next week!

Cheers,
Dave C on behalf of the PaperCuts organizers

* What's easy to fix?  Trust your instincts on this.  We would like to hear
about glitches, even if they turn out to be harder to fix.

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[galaxy-dev] November 2020 Galaxy News

[Dave Clements]

Hello all,

The November newsletter is out:
  https://galaxyproject.org/news/2020-11-galaxy-update/

Topics:

* JXTX: The James P. Taylor Foundation for Open Science
 New name, and meet our first awardees
* Event news
Lots of them, with one starting today (if you are in Australia / East Asia)
Galaxy Admin Training will be in late January
* Galaxy platform news
GalaxyTrakr, Galaxy Africa, Australia, Europe, and UseGalaxy.*
* Blog post
Advanced Microbiology with Galaxy and TIaaS at Strathclyde
* Training material and doc updates
Metaproteomics, calling variants, and auto-generated video (!)
* Publications
Pub curation is on hiatus, but some pubs just can't be ignored :-)
* Open positions
 At 8 organizations.  (Yes eight!)
* New releases
 The new Galaxy Language Server

Thanks for using Galaxy,
Dave C and Beatriz

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[galaxy-dev] Galaxy Developer Round Table: Tool testing and deployment, Oct 29

[Dave Clements]

Hi All,

The next Galaxy Developer Round Table will be Thursday, October 29, at
Noon US Eastern.  It will be a roundtable discussion on tool testing
and tool deployment issues.

Links (including time zone conversion) are here:
  https://galaxyproject.org/events/2020-10-29-dev-roundtable/

Hope to see you there,
Dave C (channelling actual developers!)

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[galaxy-dev] Galaxy Paper Cuts Day: Wednesday October 19

[Dave Clements]

Hi all,

We are organising the Galaxy Paper Cuts contribution fest this Wednesday*:
   https://galaxyproject.org/events/2020-10-papercuts/

Paper Cuts are small irritants that introduce friction when using or
administering Galaxy.  We want to
1) get rid of them, thus improving Galaxy
2) grow the contributor community!

Want to help / learn / join?  Please sign up. (You can also just show
up, but then you won't get a reminder email.)


Between now and the end of Wednesday, there are a couple of big ways
you can help:
1. Participate!
2. Create GitHub issues for things that you find irritating, in any
part of the Galaxy ecosystem
3. If you manage a Galaxy component (e.g., BioBlend, Planemo, ...)
create a tag for paper cuts, tag any appropriate issues with it, and
then let us know what tag you used.**

Hope to see you on Wednesday,
Dave C channeling Simon, Björn, and Dannon (in time zone order!)


* This Wednesday == 21 hours from now in Australia
** Or just update the paper cuts page in the hub directly.

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[galaxy-dev] October Galaxy Newsletter

[Dave Clements]

Hello all,

The October Galaxy Newsletter is out.
   https://galaxyproject.org/news/2020-10-galaxy-update/

News on
* Event news & JTech Scholarships
* Galaxy platform news: BRIDGE, BioCompute Object, French Galaxies,
PhagePromoter, and UseGalaxy.*
* Blog posts: Remote training, EOSC-Life calls
* Training material and doc updates: refgenie magic
* Publications
* Q: Who's hiring? A: Ten different groups
* New releases
* Other news too

If you have anything to include to next month's newsletter, then
please send it to outre...@galaxyproject.org.

Thanks,
Dave C and Bea



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[galaxy-dev] September 2020 Galaxy Newsletter

[Dave Clements]

Hello all,

After a one month hiatus, the monthly Galaxy newsletter
(https://galaxyproject.org/news/2020-09-galaxy-update/)
is back (and there is a lot going on):

* BCC2020 wrap up, and GCC2021 is on the way
* More event news (some this week)
* Galaxy platform news on
* UseGalaxy.fr (!), ML Workbench, deepTS, BioCompute Object,
  and PiRATE
* Blog posts
* GVL Bets, SARS-CoV-2 (x2), climate science, get your tool in
  Galaxy, and Galaxy hits 10K pubs
* Training material and doc updates (13 new and updated)
* Publications (19 highlighted, 671 total)
* Who's hiring
* Institut Pasteur, UConn, Johns Hopkins, BSC, VIB & NCBI
* New releases of Nebulizer and BioBlend
* And other news too

If you have anything to include in next month's newsletter, then please
send it to outre...@galaxyproject.org.

Cheers,
Dave C


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[galaxy-dev] ***UNCHECKED*** A couple of BCC2020 Deadlines are today

[Dave Clements]

Hi all,

Just a reminder that there are a couple of BCC2020 (BOSC + Galaxy)
deadlines today, July 10:

1. Birds of a feather submissions: https://bit.ly/bcc-propose-a-bof

If you are attending the meeting part of BCC, and you would benefit from
gathering your community at a BoF then please submit a proposal.

We also need these.  Right now we have lots of attendees, and very few BoFs
(https://bcc2020.sched.com/overview/subject/BoF).  This combination may not
work well in an online setting.

We might also extend the deadline to Sunday night.  However, we might not.
So if you see this today, then please submit in the next ~12 or so hours.

2. Early registration closes: https://bcc2020.github.io/Registration/

At US Pacific time. (about 13:45 from right now).  Registration rates
double after that, although they still aren't expensive.  However, this
event might sell out before the end of the day.  So, might want to register
now

Thanks everyone,
Dave C

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[galaxy-dev] July Galaxy News: BCC2020 Deadlines, Schedule, Fellowships; Galaxy Dev Roundtable, ...

[Dave Clements]

The July 2020 Galaxy News is here:
  https://galaxyproject.org/news/2020-07-galaxy-update/

In the July 2020 Issue
* BCC2020 starts July 17
  * Early registration ends July 10
  * BoF proposals due July 10
  * Fellowships due July 5
  * New Silver Sponsor: GalaxyWorks
  * Full training, talk, and poster/demo schedules are online
* Galaxy and the NCBI Sequence Read Archive (SRA)
* Upcoming events
  * Including the new Galaxy Developer Roundtable
* Galaxy Platform News
* Training material and doc updates
* Who's Hiring
* New blog posts
* New Releases

See you online in just over 2 weeks,
Dave C

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[galaxy-dev] June 2020 Galaxy News

[Dave Clements]

Hello all,

The June 2020 issue is hot off the presses:
  https://galaxyproject.org/news/2020-06-galaxy-update/

In this issue:
- James Taylor Foundation
- BCC2020 will be online, global, affordable, and accessible
- Galaxy and the NCBI Sequence Read Archive (SRA)
- Upcoming events
- Galaxy Platform News
- Training material and doc updates
- Who's Hiring
- New Releases
- New publications
- And other cool news too

If you have anything to include to next month's newsletter, then
please send it to outre...@galaxyproject.org.

Thanks,
Dave C

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[galaxy-dev] James Taylor Foundation

[Dave Clements]

Hello all,

The recent passing of Dr. James Taylor, the Ralph S. O’Connor Professor of
Biology and Professor of Computer Science at Johns Hopkins University, has
left an enormous void in the field of computational biology. To help fill
this void and continue James’ efforts, the Galaxy community has established
a memorial foundation in James’ name.

James believed that scientific progress can best be sustained through
mentoring of students and junior faculty. The Junior Training and
Educational Connections Hotspot (JTech) foundation will ensure
implementation of this vision. To begin, JTech will  (1) support  graduate
students to participate in computational biology and data science
conferences, and (2) organize and host mentoring sessions between senior
and junior faculty members at high-profile meetings. JTech will later
expand its reach as a platform for academic mentorship including high
school through college age students.

To make this happen we are accepting contributions here
  https://galaxyproject.org/jxtx/.

Please, help us continue what James has started.

Thank you,
Dave C on behalf of the Galaxy Community

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[galaxy-dev] May News: James Taylor, BCC2020 Abstracts Close Friday, and much, much more.

[Dave Clements]

Hello all,

This is our first newsletter since January.

It has been an eventful and sorrowful four months for the world, and for
the Galaxy Community too: This newsletter starts with the tragic loss of
James Taylor, one of Galaxy’s founders and leaders. We lost James at the
beginning of April. This community, I suspect, will always feel that loss.

The May 2020 issue
https://galaxyproject.org/news/2020-05-galaxy-update/

James Peter Taylor , 1979-2020
* BCC2020 will be online, global, affordable, and accessible
   * All abstracts are due May 8
* Galaxy COVID-19 Response
* Upcoming events
* Blog posts
* Galaxy Platform News
* Training material and doc updates
* Who’s Hiring
* New Releases
* New publications (671 of them)
* And other cool news too

If you have anything to include to next month’s newsletter, then please
send it to outre...@galaxyproject.org.

Thanks, for everything,
Dave C

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[galaxy-dev] BCC2020 Abstract submission and Registration are open

[Dave Clements]

2020 Bioinformatics Community Conference (BCC2020)
Online, July 17-26
https://bcc2020.github.io/

The 2020 Bioinformatics Community Conference (BCC2020) will be online,
global, affordable, and accessible to all.

Key Dates:
May 8:Deadline for submitting talk/poster abstracts (this will not
be extended)
June 6:   Authors notified about talk/poster acceptance
July 10:  Early registration ends
July 17-19: BCC2020 tutorials
July 19-22: BCC2020 main meeting
July 22-24, 24-26: CollaborationFest Core and Encore

BCC2020
-> https://bcc2020.github.io/
BCC2020 is a joint event bringing together the BOSC and Galaxy Communities.
If you are working in data intensive life science research then there will
be no better event this year to share your work, and to learn from others.
BCC2020 will be held July 17-26, and offer 2 days of training, a 3 day
meeting, and a 4 day CollaborationFest.

BCC2020 is Online
->  https://bcc2020.github.io/blog/going-virtual
All BCC2020 events will be held online.  Training will be live and
interactive.  The meeting will feature keynotes, accepted talks, lightning
talks, posters, demos, and birds-of-a-feather and other networking
opportunities.  Talks (with the possible exception of keynotes) will be
pre-recorded.  Posters, demos, and BoFs will be live and interactive.  The
CoFest will also be live and interactive.

BCC2020 is Global
-> https://bcc2020.github.io/blog/going-global
BCC2020 events will be held twice: once in the originally scheduled Toronto
time zone (BCC West), and then again 12 hours later in the Eastern
hemisphere (BCC East).  Training will differ between East and West, with
enrollment open to all, regardless of where you are. The main conference
content will be presented in both East and West.  We are striving to have
the CoFest run continuously, with participants from every part of the world.

BCC2020 is Affordable
-> https://bcc2020.github.io/Registration/
We have slashed registration rates for BCC2020, and are offering even
larger discounts to participants based in low and lower-middle income
countries.  Pricing starts at US$3 per training session, and $12 for the 3
day meeting.  The CoFest is free.

BCC2020 is Accessible
Going online and global, combined with the low registration rates make this
the most accessible Galaxy and BOSC conference ever.  If you work in open
source bioinformatics then this is 2020’s best opportunity to share your
work and learn from others.

Abstracts Due May 8
-> https://bcc2020.github.io/submit/
BCC2020 is seeking oral presentations, lightning talks, posters, and demos,
from researchers working in bioinformatics, and from all over the world.
Abstracts are due May 8 (and that deadline will not be extended).  Please
submit your work today.

Register Now
-> https://bcc2020.github.io/Registration/

BCC2020 registration is now open.  Registering early saves 50% off of the
full rates.

We hope to see you in July at BCC2020,
BCC2020 Organizers

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[galaxy-dev] BCC2020 meeting will be held online

[Dave Clements]

Hello all,

The Organizing Committee of the 2020 Bioinformatics Community
Conference (BCC2020, https://bcc2020.github.io/) has come to the
difficult decision to hold the conference online.

We are making this decision after much consideration of the ongoing
spread of COVID-19, striving to take the most socially responsible
action while maintaining a forum in which our community can share
their work and discovery. It is hard to predict what things will look
like in July, but given current reports and models, it seems unlikely
that the situation will be back to “business as usual”. We also
considered that, even if some people were able to attend, it is
possible that many people would still find it difficult to travel to
Toronto. We believe that making this decision now will allow us to
focus on organizing an engaging conference in this new format.

We will be inviting our community to engage in new ways, and hope that
BCC2020 will be an important space for discussion for the Open Source
bioinformatics community.

The virtual meeting will still take place as planned, on July 18-21.
There will be opportunities for training before the main meeting, and
a CollaborationFest starting on July 22. We are discussing how to
arrange the schedule to allow for participation across the globe; more
details will be coming soon.

Registration will open in a few weeks, and fees will be lower than for
an in-person meeting.

The abstract submission deadline has been postponed to April 30th.
Abstracts will follow the usual submission and review processes.

There are many details to be worked out – for example, a meeting
schedule that takes into account time zones, videoconferencing
technology, ways to enrich our online interactions (while
acknowledging that nothing can replace the vital social interaction
that in-person meetings provide), etc. Many of these aspects are new
for us too; we welcome your input, particularly if you have
suggestions about how to make our first Virtual Bioinformatics
Community Conference a success.

We are looking forward to exploring this new meeting format, and we
hope you will join us.

Stay well,
BCC2020 Organizers

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[galaxy-dev] BCC2020 registration postponed due to COVID-19 uncertainty

[Dave Clements]

Hello all,

We are postponing opening registration for the 2020 Bioinformatics
Community Conference (BCC2020).

See the announcement for details.
  https://bcc2020.github.io/blog/postponement

Dave C, on behalf of the BCC2020 Organizers.

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[galaxy-dev] Fwd: [GMOD-devel] GMOD in Google Summer of Code

[Dave Clements]

Hi All,

Scott's "But WAIT!" comment applies to Galaxy too.  :-)  See below if you
have an idea.

Cheers,
Dave C

-- Forwarded message -
From: Scott Cain 
Date: Thu, Feb 20, 2020 at 6:16 PM
Subject: [GMOD-devel] GMOD in Google Summer of Code
To: gmod-announce , gmod-ajax <
gmod-a...@lists.sourceforge.net>, gmod tripal devel <
gmod-tripal-de...@lists.sourceforge.net>, Gbrowse (E-mail) <
gmod-gbro...@lists.sourceforge.net>, GMOD Schema/Chado List <
gmod-sch...@lists.sourceforge.net>, gmod-devel <
gmod-de...@lists.sourceforge.net>, ,
maker-de...@yandell-lab.org List 


Hello,

I am very pleased to announce that GMOD in conjunction with Reactome,
Galaxy and OICR/WormBase, together forming Open Genome Informatics, has
been accepted for the Google Summer of Code.  If you or someone you know
might be a student interested in participating in GSoC, please take a look
at

  http://gmod.org/wiki/GSOC_Project_Ideas_2020

where there are proposed projects that cover a fair number of
technologies.  Official proposals from students will be due in mid March
(more on that later).

But WAIT! There's more: if you might be interested in being a mentor and
working with a student this summer, it's not too late! You can add new
project ideas to the page above (contact me if you need an account), or you
can even volunteer to add yourself to one of the existing ideas as a
potential mentor.

Please feel free to forward this to other mailing lists or people who might
be interested.  We are already an eclectic, dispersed group, so everyone is
welcome.

Thanks,
Scott


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net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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[galaxy-dev] BCC2020 Training Topic Voting is Open

[Dave Clements]

Hello all,

The The Bioinformatics Community Conference (BCC2020)
, will bring together the Galaxy Community
Conference (GCC) and the Bioinformatics Open Source Conference (BOSC) in
Toronto, Canada in July 2020, following ISMB 2020
 in Montréal.  BCC2020 will start with a
dedicated training day, followed by 3 days of mixed meeting and training
events.

The community (you!) determines what training will be offered at
BCC2020.  *Nominations
from the community * are now ready for
review and voting.  If you are possibly attending BCC2020 then please take
a few minutes to review the nominations and then submit your ballot
.
Voting closes on February 21.

Thanks in advance for your input, and we hope to see you in Toronto,
BCC2020 Organizers

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[galaxy-dev] January Galaxy News: BCC2020, PAG & ABRF; New pubs, platforms, tutorials...

[Dave Clements]

Hello all,

The January 2020 Galactic News is out!
  https://galaxyproject.org/news/2020-01-galaxy-update/

- 13 Upcoming Events
  - BCC2020 training topic nominations, Register for Galaxy Admin
Training, Galaxy @ PAG & ABRF, and training @ Earlham and Rennes.
- 172 new publications
  - Six highlighted pubs from RT-qPCR to functional genomics
- Two new blog posts
  - PGP-UK and Crowdsourcing Science
- Galaxy Platform News
  - Three new platforms, UseGalaxy.* news, and platforms in pubs
- Training material and doc updates
  - R, RStudio, ATAC-Seq, Scanpy, and Single Cell RNA-Seq
-  And other news too

If you have anything to include to next month's newsletter, then
please send it to outre...@galaxyproject.org.

And a happy new year too, :-)
Dave C on behalf of the Galaxy community

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[galaxy-dev] BCC2020 and Galaxy Admin Training

[Dave Clements]

Hello all,

There are three things going on that are of general interest to the Galaxy
and GMOD communities, and that have some urgency to them (and thus this
mid-month email).

BCC2020 Schedule Structure
---
The Bioinformatics Community Conference (BCC2020, https://bcc2020.github.io/)
will be held in July, in Toronto, right after ISMB in Montréal.  This event
brings together the BOSC and Galaxy communities into one gathering.

If you are considering attending BCC2020, then the organizers would like
your input on several scheduling choices, BY JANUARY 7:
  https://bcc2020.github.io/blog/poll

BCC2020 Training Topic Nominations

The training offered at BCC2020 is determined by the community.  We are now
accepting nominations for training sessions.  Nominated topics will be
voted on by the community.  Please submit your ideas by JANUARY 17.
  https://bcc2020.github.io/blog/training-nom

2020 Galaxy Admin Training
---
A week long workshop on setting up your own production-grade Galaxy
instance will be held in Barcelona the first week of March.  Registration
is now open, and is, well, pretty darn cheap too.
  https://galaxyproject.org/events/2020-03-admin/


And, of course, there is a lot of other stuff going on too:
  https://galaxyproject.org/events/

Happy Holidays, and hope to see you in the new year!

Dave C, on behalf of the BCC2020 and Galaxy Admin Training organizers

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[galaxy-dev] December Galaxy News

[Dave Clements]

Hello all,

The December 2019 Galactic News is out!
https://galaxyproject.org/news/2019-12-galaxy-update/

- 12 Upcoming Events
  - India, PAG, HTS, single cell/microbiome, Barcelona, and more
- 191 new publications
- Two new blog posts
  - g:Profiler, GalaxyP
- Galaxy Platform News
  - Systems biology, Laniakea, OpenRefine, ...
- Training material and doc updates
  - defining data types, citing GTN, Windows, account help,
metatranscriptomics, Galaxy for everyone
- Openings
  - with 5 organizations in Denmark, France, US, US, Germany
- Releases
- Galaxy 19.09 is out
- And other news too

Thanks for a superb year, and we are looking forward to an even better 2020.
Dave C, on behalf of everyone


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[galaxy-dev] November Galaxy News

[Dave Clements]

Hello all,

The November 2019 Galactic News includes Galactic news under this or
any other sun:

* 19 Upcoming Events
* 208 new publications
* 2 new blog posts
* Galaxy Platform News
* Training material and doc updates
* Openings with 5 organizations
* Releases
* Other news

See https://galaxyproject.org/news/2019-11-galaxy-update/ for details.

Thanks,
Dave C

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[galaxy-dev] October Galaxy News: Events, pubs, platforms, jobs, training, and more

[Dave Clements]

Hello all,

The October 2019 Galactic News is out!
  https://galaxyproject.org/news/2019-10-galaxy-update/

There is, as always, a lot going on:
- 20 Upcoming Events
- 143 new publications
- Galaxy Platform News
- 6 Openings
- Training material and doc updates
- Other news too

Check it out,
Dave C and the Galaxy Community

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[galaxy-dev] September Galaxy News: INCOB, Galaxy Africa, ACM BCB, GTN, QFAB, ...

[Dave Clements]

Hello all,

The September 2019 Galactic news has been published:

There are a bunch of upcoming events, including Galaxy @ INCOB, Galaxy
Africa, two Bioconda / ToolShed events, a GTN CoFest, QFAB training, a
Galaxy Netherlands gathering, (plus more than 20 more).

We are also highlighting the new Climate Science Workbench Galaxy
server, three recent blog posts, six doc & training updates, and 6 (or
11, depending on how you count) open positions.

Find information on all this and more on the Galaxy Community Hub:
  https://galaxyproject.org/news/2019-09-galaxy-update/

And it's all in a spiffy new format.

Hope to see you in Jakarta, Niagara Falls, Ghana, Brisbane, Utrecht,
Sri Lanka, Ireland, online, ...
Dave C and the Galaxy Community

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[galaxy-dev] August 2019 Galactic News: GCC2019 is done; BCC2020 is coming

[Dave Clements]

Hello all,

The August 2019 Galactic News is here!
   https://galaxyproject.org/news/2019-08-galaxy-update/

* Events:
  * GCC2019 is done (and yow, it was a success)
  * BCC2020 is coming to Toronto!
  * Galaxy ♥ BioHackathon Europe!
  * Plus deadlines this month and 19 other events in the next 90 days.
* 178 new publications, including 5 highlighted ones.
* Two new Galactic Blog posts:
  * Getting the most out of 1) Galaxy on Twitter, and 2) Pan-Galactic Search
* Galaxy Platform News from UseGalaxy.* and the Human Cell Atlas.
* Seven Open positions in four countries on two continents.
* Updates to training materials and documentation.
* New releases.

This month's newsletter was a community effort unlike any before it.
Thanks to everyone who contributed (and keep those contributions
coming!).

See you in San Diego, Milwaukee, Honolulu, Toronto, ...
Dave C


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[galaxy-dev] July Galaxy News: GCC2019 is next week

[Dave Clements]

The July 2019 Galactic News is out!
  https://galaxyproject.org/news/2019-07-galaxy-update/

* GCC2019!
* Plus 17 other upcoming events in the next 90 days
* 153 new publications, great resources lead to great insight.
* Galaxy Platform News for Galaxy Europe, Galaxy Australia, and OpenMinTeD
* At least 6 Open positions in five countries on two continents.
* Updates to training materials and documentation.
* New tools and new releases.
* And some other news too.

Hope to see you in Freiburg next week,
Dave C. Mo, and the Galaxy Community

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[galaxy-dev] June 2019 Galactic News: GCC Deadlines this week and next

[Dave Clements]

Hello all,

The June 2019 Galactic News is here! This is a summary of what is
going on in the Galaxy community:
https://galaxyproject.org/news/2019-06-galaxy-update/

- GCC2019:
  - **Advance registration ends 7 June**
  - **Poster and Demo Abstract Submission deadline: 10 June**
  - Conference schedule is online
- Plus 13 other upcoming events in the next 90 days

- 150 new publications, great resources lead to great insight.
- Galaxy Platform News: New platforms for tranSMART, antibiotic resistance,
phylogeny, long-read data, mass spectrometry Imaging, and Rice!
- A new entry to The Galactic Blog on Galaxy cloud bursting
- At least 8 Open positions in five countries on two continents.
- Updates to training materials and documentation.
- New tools and new releases.

- And some cool other news too:
  - The new Galaxy Services Status Web Site
  - Black Duck Open Hub updates it's Galaxy project stats and we are
doing great.

See you in a month,
Dave C, Mo, and the Galaxy Community


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[galaxy-dev] GCC2019 Early Reg ends this Friday

[Dave Clements]

Hi All,

The latest GCC2019 news:

- A (final) reminder that early registration for the 2019 Galaxy
  Community Conference ENDS THIS FRIDAY NIGHT, 17 May, at
  midnight Freiburg time (CEST / GMT +2).  After that registration
  goes up by ~ 60%. So, register this week!
 https://galaxyproject.org/events/gcc2019/registration/
- All accepted speakers have been notified and talks are being
  added to the schedule as presenters confirm.  There were far
  more talk submissions this year than in any previous year and that
  is reflected in the breadth and quality of the accepted talks.
 https://gcc2019.sched.com/
- Poster and demo submission is still open!  However, space *will*
  fill up and when it's gone, it's gone. Got something to present?
  Submit it *soon*.
 https://galaxyproject.org/events/gcc2019/abstracts/

We hope to see you in Freiburg!
Dave C on behalf of the GCC2019 Organizers

--
2019 Galaxy Community Conference (GCC2019)
1-8 July, Freiburg, Germany
https://galaxyproject.org/gcc2019
--

The 2019 Galaxy Community Conference (GCC2019) will be held 1-8 July
in Freiburg, Germany. GCC brings together hundreds of faculty,
clinicians, researchers, and students, all working in and supporting
data intensive science that is accessible, sharable and reproducible.

GCC2019 features oral presentations, lightning talks, posters, demos,
birds-of-a-feather gatherings (BoFs), training, a CollaborationFest,
and plenty of opportunities for networking.

Presentations will cover the full spectrum of Galaxy applications,
enhancements and deployments. If you are working in data intensive
science then GCC2019 is an ideal conference for sharing your work,
learning from others, and finding new collaborators.

Registration
Early registration starts at €49/day for students and postdocs, and
€79 / day for other academics and non-profit researchers.  Childcare
is available and travel fellowships are available as well.  Early
registration ends 17 May, when rates go up by 60%. So, register early.

About Galaxy
Galaxy (https://galaxyproject.org/) is a platform for data integration
and analysis in the life sciences. It enables researchers to build,
run, share, and repeat their own complex computational analyses using
only a web browser and without having to first learn system
administration and command line interfaces.

The Galaxy Project is driven by a vibrant community who publish
workflows and analyses, wrap new tools, maintain and enhance the
source code, provide support, and write documentation and training
materials. Galaxy is open-source and freely available, and is deployed
in hundreds of organizations, running on everything from laptops
through supercomputers to public and private clouds. Over 150 of these
platforms are publicly available and can be used with little or no
setup.  Thousands of tools have been ported to Galaxy ("wrapped") and
are deployable from the Galaxy Tool Shed. Galaxy was developed to
support life science research, but the software is domain agnostic and
is now used in domains as diverse as natural language processing,
constructive solid geometry, and social science.


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[galaxy-dev] GCC2019 Talk Abstracts due Monday, 22, April

[Dave Clements]

Hello All,

This is just a reminder that oral presentation and lightning talk
submissions for the 2019 Galaxy Community Conference are due on
Monday, 22 April.

And, in case you missed these items:
- There will be childcare
- Travel fellowships are available (application review starts 23 April)

Finally, please redistribute this in any of your communities where
it's relevant.

Thanks,
Dave C


--
2019 Galaxy Community Conference (GCC2019)
1-8 July, Freiburg, Germany
https://galaxyproject.org/gcc2019
--

Deadlines
22 April: Oral Presentation and Lightning Talk abstracts due
17 May: Early registration ends

The 2019 Galaxy Community Conference (GCC2019) will be held 1-8 July
in Freiburg, Germany. GCC brings together hundreds of faculty,
clinicians, researchers, and students, all working in and supporting
data intensive science that is accessible, sharable and reproducible.

GCC2019 features oral presentations, lightning talks, posters, demos,
birds-of-a-feather gatherings (BoFs), training, a CollaborationFest,
and plenty of opportunities for networking.

Presentations will cover the full spectrum of Galaxy applications,
enhancements and deployments. If you are working in data intensive
science then GCC2019 is an ideal conference for sharing your work,
learning from others, and finding new collaborators.

Present your work!
Abstract submission for talks, lightning talks, demos and posters is
now open. If you work in data-intensive science then please consider
presenting your work at GCC2019. This is a chance to present to 200+
researchers, all addressing challenges in data intensive science.
Review of oral presentations starts on 22 April. Submit an abstract
(or two) now!

Registration
Early registration starts at €49/day for students and postdocs, and
€79 / day for other academics and non-profit researchers.  Childcare
is available and travel fellowships are available as well.  Early
registration ends 17 May, when rates go up by 60%. So, register early.

About Galaxy
Galaxy (https://galaxyproject.org/) is a platform for data integration
and analysis in the life sciences. It enables researchers to build,
run, share, and repeat their own complex computational analyses using
only a web browser and without having to first learn system
administration and command line interfaces.

The Galaxy Project is driven by a vibrant community who publish
workflows and analyses, wrap new tools, maintain and enhance the
source code, provide support, and write documentation and training
materials. Galaxy is open-source and freely available, and is deployed
in hundreds of organizations, running on everything from laptops
through supercomputers to public and private clouds. Over 150 of these
platforms are publicly available and can be used with little or no
setup.  Thousands of tools have been ported to Galaxy ("wrapped") and
are deployable from the Galaxy Tool Shed. Galaxy was developed to
support life science research, but the software is domain agnostic and
is now used in domains as diverse as natural language processing,
constructive solid geometry, and social science.

We hope to see you in Freiburg!
GCC2019 Organizers

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[galaxy-dev] Re: GalaxyAdmins online meetup this Thursday

[Dave Clements]

Hello all,

Starting in about 10 minutes:
  https://psu.zoom.us/j/874589458

Cheers,
Dave C

On Tue, Mar 19, 2019 at 3:49 PM Dave Clements 
wrote:

> Hi All,
>
> The GalaxyAdmins group is back (thanks to a rejuvenation by Helena
> Rasche), and will have its first online meetup in over two year this
> Thursday.
>
> *When:* 21 March 2019, 15:00 GMT (see your local time
> <https://www.timeanddate.com/worldclock/fixedtime.html?msg=March+2019+GalaxyAdmins+Meetup=20190321T15=1234=1>
> )
> *Where: *On Zoom <https://zoom.us/>. If you don't already have the Zoom
> client installed, then you'll need to download it
> <https://support.zoom.us/hc/en-us/articles/207373866-Zoom-Installers>
> before the meetup.  *We will publish the Zoom room link here
> <https://galaxyproject.org/community/galaxy-admins/meetups/2019-03-21/> and
> on Twitter <https://twitter.com/galaxyproject> before the meeting.*
> *What:* We will have a general discussion / give and take about Galaxy
> administration and a presentation by Pablo Moreno
> <https://galaxyproject.org/blog/2018-08-cotm-pablo-moreno/> on *Running
> Galaxy on Kubernetes.*
>
>-
>
> Interested?  It would be great to have you join us.
>
> Thanks and hope to see you Thursday,
> Dave C (channeling Helena)
>
> --
> https://galaxyproject.org/
> https://usegalaxy.org/
>
>

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[galaxy-dev] GCC2019 Registration & Abstract Submission are Open

[Dave Clements]

*We are pleased to announce that registration
 and abstract
submission  for the
2019 Galaxy Community Conference (GCC2019)
 are now open.*

GCC2019 will be held 1-8 July in Freiburg, Germany. The *tenth* GCC
 will have many familiar features from
earlier years, including accepted and lightning talks, posters and demos,
birds-of-a-feather gatherings (BoFs), training, and a CollaborationFest.
2019 also brings the most significant conference program update
 in several years:

   - some training will be integrated with the main conference,
   - three days of conference instead of two,
   - several parallel sessions,
   - and a strong emphasis on organizing content by domain.

GCC2019, like every GCC before it, will be built around *community*.
Training topics are nominated, selected, and presented by the community.
Presentations will feature the full spectrum of Galaxy applications,
enhancements and deployments from the community as well.

If you are working in data intensive life science research then there will
not be a better place to share your work, learn from others, and find new
collaborators.

*Registration*

Early registration 
starts at €49/day for students and postdocs, and €79 / day for other
academics and non-profit researchers. Early registration ends 17 May, *when
rates go up by 60%. So, register early
.*

*Present your work!*

Abstract submission 
for talks, lightning talks, demos and posters is now open. If you work in
data-intensive life science (or in other fields using Galaxy) then please
consider presenting your work at GCC2019. This is an ideal chance to
present to 200+ researchers, all addressing common challenges in data
intensive science. Review of oral presentations starts on 22 April, in a
little over a month.

*Submit an abstract (or two) now
!*

*We hope to see you in Freiburg!*

GCC2019 Organizers 


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[galaxy-dev] GalaxyAdmins online meetup this Thursday

[Dave Clements]

Hi All,

The GalaxyAdmins group is back (thanks to a rejuvenation by Helena Rasche),
and will have its first online meetup in over two year this Thursday.

*When:* 21 March 2019, 15:00 GMT (see your local time

)
*Where: *On Zoom . If you don't already have the Zoom
client installed, then you'll need to download it

before the meetup.  *We will publish the Zoom room link here
 and
on Twitter  before the meeting.*
*What:* We will have a general discussion / give and take about Galaxy
administration and a presentation by Pablo Moreno
 on *Running
Galaxy on Kubernetes.*
-
Interested?  It would be great to have you join us.

Thanks and hope to see you Thursday,
Dave C (channeling Helena)

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[galaxy-dev] Galaxy Release 19.01

[Dave Clements]

We are pleased to announce the *release of Galaxy 19.01
*.
A few release highlights are:

Revised UI Style

The Galaxy stylesheet has been substantially reworked resulting in the
largest visual refresh to Galaxy in years.

More Colorful Tags

Use consistently hashed randomized colors for history dataset name tags to
increase visual distinction between tags, making it easier to track data
flow in complex histories. Thanks to @erasche .

Extensive Workflow Enhancements (continued)

Galaxy 18.09 featured a bunch of important and diverse fixes and
enhancements to workflows on both the frontend and backend. That progress
continues in release 19.01.

The workflow editor now features explicit step parameter nodes for non-file
data (integers, strings, booleans, etc) and the ability to connect these to
all tool inputs - not just files. The YAML-based Galaxy Format 2 workflow
language is now included in Galaxy as a beta option and allows import and
export of human readable workflows as well as extensions to allow Galaxy to
serve as a file editor for such workflows. The workflow editor features
more helpful labels on inputs and outputs and important fixes including
logic for connecting collections and dealing with missing tools. The
workflow run form now deals with default values more correctly.

Enhanced Support for Singularity

Singularity  container support in Galaxy has
been brought to parity with Docker container support. Specifically, Galaxy
can now be configured to fetch Biocontainers 
automatically for enabled job destinations. Moreover, explicitly annotated
Docker containers (either in tools or job destinations) can be used with
Singularity. Thanks to @mvdbeek 

Please see the full release notes

for more information, including how to upgrade today!

*Thanks for using Galaxy!*


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[galaxy-dev] February 2019 Galaxy News: VOTE RIGHT NOW, and other stuff too.

[Dave Clements]

Hello all,

The *February 2019 Galactic News*
 is here!

   - Event News
   
  - *Voting on GCC2019 training topics open through February 4th!
  
*
  .
  - *ELIXIR Galaxy Community Workshop
  
*
  pre-registration is open!
   - GalaxyAdmins needs your topic suggestions
  

  .
   - 160 new publications
   ,
   great resources lead to great insight.
   - Some most excellent Galaxy Platform News
   
,
   including proteo-transcriptomics, RNA analyis tools, Genome Browsers, and
   more!
   - The Tutorial of the Month is ... Genome annotation with Prokka
   

   !
   - At least 23 Open positions
    in 6
   countries on 2 continents.
   - Doc, Hub, and Training Updates
   
,
   including *GO enrichment analysis* and *Age prediction using machine
   learning*.
   - ToolShed contributions
   

   .
   - New releases
    of
   galaxy-lib and Planemo.
   - And a bunch of other news
    too.

If you have anything to add to next month's newsletter, then please send it
to outre...@galaxyproject.org.

Thanks,

Dave C on behalf of, well, everyone

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[galaxy-dev] Vote Now: GCC2019 Training Topics

[Dave Clements]

Hello all,

The next 2019 Galaxy Community Conference (GCC2019)
 will be in Freiburg (Germany)
in July. This year the program is specifically aimed at drawing in more
Galaxy end-users, including for training. We are really interested it what
you would like to learn.

*Please take a few minutes to decide

and then vote which training should be offered during GCC2019
!  *If there is *any* chance that
you will attend then we want to hear from you.

*Topic voting closes 4 February.* The Training schedule, including
instructors, will be published before early registration opens.

GCC2019  will be held 1-6 July
in Freiburg, Germany. If you work in data-intensive biomedical research,
there is no better place than GCC2019 to present your work and to learn
from others.

Thanks, and see you in Freiburg

The GCC2019 Organizers


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[galaxy-dev] GalaxyAdmins is returning to a device near you in February 2019, and we need your help

[Dave Clements]

Hi All

After a two year hiatus, the bimonthly online GalaxyAdmins meetups
<https://galaxyproject.org/community/galaxy-admins/meetups/> will
return on February
28 <https://galaxyproject.org/community/galaxy-admins/meetups/2019-02-28/>.
GalaxyAdmins <https://galaxyproject.org/community/galaxy-admins/> is a
discussion group for Galaxy community members who are responsible for
Galaxy installations. Our online meetups are around an hour long and
feature a presentation followed by an open discussion. It's a great place
to catch up on what your fellow admins are thinking about.

*But, before we start meeting next year, we need to know what you care
about
<https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblsto5UhU34gFlXTiPQ/viewform>.*
What do you want to learn? Who do you want to hear from? What's causing you
trouble? Or, what have you worked that your fellow GalaxyAdmins would
benefit from knowing?

Got some ideas? *Nominate them
<https://docs.google.com/forms/d/e/1FAIpQLSfv257YcdQQO7gp3K4USoBzqkd-UDEblsto5UhU34gFlXTiPQ/viewform>*

We hope to see you in February,

Helena Rasche <https://galaxyproject.org/people/helena-rasche/> and Dave
Clements <https://galaxyproject.org/people/dave-clements/>

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[galaxy-dev] Please nominate training topics for GCC2019 by Dec 31

[Dave Clements]

Hi All,

The *2019 Galaxy Community Conference (GCC2019)*
 will be held in be held in
*Freiburg,
Germany, 1-6 July*. Like previous Galaxy Community Conferences
, GCC2019 will feature invited keynotes,
accepted talks, posters, demos, birds-of-a-feather gatherings and *training*.
The format of GCC2019 will be a bit different than the previous years: it
starts with 1 day of training and then 3 days with more specialized
training sessions aligned with talks. *You can read more about the new
format on the conference FAQ
.*

*The training topics that are offered are determined by the community so BY
YOU!
*

Please give some thought to what topics you would like to see offered, or
that you would like to offer, and then submit them as topic nominations

.

Nominated topics can cover a wide range. For example:

   - Introduction to Using Galaxy
   - Scientific topic oriented trainings
   - Community specific trainings
   - Development and administration around Galaxy
   - Train the trainers

This list only shows some examples. *Any topic of interest to the Galaxy
Community can be nominated and you are encouraged to nominate more than one
topic.* If you are looking for ideas, see the topic nominated in: 2016
,
2015
,
2014 ,
2013 
and the Galaxy Events page

.

Training nomination is open from *December, 1st* to *December, 31*. Topics
will be compiled into a uniform list by the GCC2019 Organizing Committee,
and topics will be voted on by the Galaxy Community from *January,
15th* to *January,
31st*.

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Re: [galaxy-dev] Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University

[Dave Clements]

Hi All,

Just a reminder that registration for *the 2019 Galaxy Admin Training
<https://galaxyproject.org/events/2019-admin-training/>* is still open.
Registering now avoids the 45 to 60% price increase when full prices take
effect. The detailed agendas for the basic and advanced sessions are now
available online
<https://github.com/galaxyproject/dagobah-training#timetable> as is
the instructor
list <https://galaxyproject.org/events/2019-admin-training/#instructors>.

We hope to see you in January!


On Wed, Sep 19, 2018 at 12:17 PM Dave Clements 
wrote:

> Hello all,
>
> We are pleased to announce that* the 2019 Galaxy Admin Training
> <https://galaxyproject.org/events/2019-admin-training/> will be offered
> January 28 through February 1 at Penn State University* (where the Galaxy
> Project got started over ten years ago). The workshop offers a 2 day
> introductory session
> <https://github.com/galaxyproject/dagobah-training#basic-sessions>
> followed by a 3 day advanced topics session
> <https://github.com/galaxyproject/dagobah-training#advanced-sessions>.
> Participants can register for one or both sessions.
>
> This workshop will cover what you need to know to set up your own
> high-performance and multi-user production Galaxy instance. Sessions will
> be *intensive and hands-on*, and taught by experienced instructors from
> the Galaxy Community. 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://galaxyproject.org/events/2019-admin-training/#registration> is
> now open and starts at $40 / day for participants from non-profits and
> academia. Early registration ends October 31. However, the 2016 and 2018
> admin training were both full, so you are strongly encouraged to *register
> now*.
>
> *The workshop does have prerequisites
> <https://galaxyproject.org/events/2019-admin-training/#prerequisites>.
> Please read them before you register.*
> Cheers,
> Dave C.
>
>
> *About Galaxy *
> Galaxy 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.
> --
> https://galaxyproject.org/
> https://usegalaxy.org/
>
>

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[galaxy-dev] Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University

[Dave Clements]

Hello all,

We are pleased to announce that* the 2019 Galaxy Admin Training
 will be offered
January 28 through February 1 at Penn State University* (where the Galaxy
Project got started over ten years ago). The workshop offers a 2 day
introductory session
 followed
by a 3 day advanced topics session
.
Participants can register for one or both sessions.

This workshop will cover what you need to know to set up your own
high-performance and multi-user production Galaxy instance. Sessions will
be *intensive and hands-on*, and taught by experienced instructors from the
Galaxy Community. 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
 is now
open and starts at $40 / day for participants from non-profits and
academia. Early registration ends October 31. However, the 2016 and 2018
admin training were both full, so you are strongly encouraged to *register
now*.

*The workshop does have prerequisites
.
Please read them before you register.*
Cheers,
Dave C.


*About Galaxy *
Galaxy 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.
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[galaxy-dev] September 2018 News of the Galaxy

[Dave Clements]

Hello all,

The *September 2018 Galactic News* is here! This is a summary of what is
going on in the Galaxy community. Here's what's happening:

   - Events
  - 2018 SACNAS Workshops
  

  - European Galaxy Days
  
,
  19-20 November, Freiburg, Germany
  - All upcoming events
  
   - New:
  - 80 publications
  
  - Galactic Blog entry: Contributor of the Month: Carrie Ganote
  

  - Public Galaxy Server News
  
:
  epiGeEC and MetaCentrum
  - ToolShed contributions
  

  - Hub and Documentation updates
  

  - CloudBridge v1
   has
  been released!
  - Releases
  
   - And other news
    too

If you have anything to add to next month's newsletter, then please send it
to outre...@galaxyproject.org.
Thanks,

Dave C on behalf of the Galaxy Community

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[galaxy-dev] links to UCSC Genome Browser dev server

[Dave Clements]

Hi All,

If you run a Galaxy server and that server links to the UCSC Genome Browser
*development* server, then you will need to update the URL you link to.
See below for details from Ann Zweig at UCSC.

I am writing because a few of your servers provide links to the UCSC Genome
> Browser development server at genome-test.*cse*.ucsc.edu or genome-test.
> *soe*.ucsc.edu (see list below). This weekend we are retiring that server
> and bringing it back to life next week with a new name: genome-test.*gi*.
> ucsc.edu.


Cheers,

Dave C

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[galaxy-dev] August Galaxy News: GCC2019, Online GTN CoFest, new pubs, servers, tools...

[Dave Clements]

Hello all,

After a two-month hiatus, the August 2018 Galactic News
 is out! Here are some
of the highlights:

   - GCCBOSC 2018
    has
   come and gone, *and the numbers were impressive*
   - GCC2019
   

will be held in Freiburg, Germany, 1-6 July
  - What about BOSC?
  ,
  you ask
   - Other event news:
  - GTN CoFest on Metagenomics Training Material
  
,
  17 August, *online*
  - 2018 SACNAS Workshops
  
  - European Galaxy Days
  
,
  19-20 November, Freiburg, Germany
  - Gateways 2018
   early
  bird deadline *is Monday*.
  - Other Upcoming events
   (on
  three continents in 6 countries)
   - Christophe Caron, 1968-2018
   

   - New:
  - 417 publications
   (that's
  3 month's worth)
  - Two Galactic Blog entries
  
,
  including the first ever *Contributor of the Month* posting.
  - Public Galaxy Server News
  
:
  ProteoRE
  - ToolShed contributions
  
  - Hub and Documentation updates
  
  - Releases
   of
  Galaxy, Planemo, galaxy-lib, ephemeris, and sequence_utils.
   - And other news
    too

See the newsletter  for
the full story.
Thanks for using Galaxy!

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[galaxy-dev] GCCBOSC 2018 Early Registration Ends this Friday (May 11)

[Dave Clements]

Hi All,

Just a reminder that early registration for the Galaxy Community's biggest
annual gathering ends this Friday.  You can also register for housing and
childcare too.

  https://galaxyproject.org/events/gccbosc2018/register/
  https://galaxyproject.org/events/gccbosc2018/venue/#housing
  https://galaxyproject.org/events/gccbosc2018/childcare/

Hope to see you there,

Dave C on behalf of the GCCBOSC 2018 Organizing Committee

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[galaxy-dev] May Galaxy News: GCCBOSC, Training Material Workshop, New pubs, jobs, ...

[Dave Clements]

Hello all,

The May 2018 Galactic News
 highlights what's going
on in the Galaxy this month, including:

   - Lots of GCCBOSC 2018 news
   :
  - *Early registration ends May 11
  
*
  - Galaxy talks have been posted to the schedule
  

  .
  - BOSC deadline for late-breaking lightning talks, demos and posters *is
  May 17
  
*
  - Please welcome *Google Cloud
  
*
   and *Advanced HPC
  * as
  GCCBOSC sponsors. *Both are offering goodies for conference
  participants.*
   - Other event news:
  - ELIXIR Workshop for Galaxy training material and skills improvement
  

   is 21-23 May. Register right now.
  - Galaxy Africa Report
  
  - Other Upcoming events
   (on
  three continents in 6 countries)
   - New:
  - 132 publications
  
  - Openings in 10 groups on 2 continents
  
  - Public Galaxy Server News
  

  : IRProfiler
  
  - ToolShed contributions
  
  - Releases
   of
  BioBlend and Starforge

See the newsletter  for
the full story, and we hope to see you in Portland!
Dave C on behalf of, well, everyone

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[galaxy-dev] April Galactic News: UseGalaxy.org gets some siblings, GCCBOSC and other event news; new pubs, servers, jobs, ...

[Dave Clements]

Hello all,

The April 2018 Galactic News
 highlights what's going
on in the Galaxy (and it's actually quite cool). Take a look:

   - *UseGalaxy.eu and UseGalaxy.org.au Launched
   
*
   - Lots of GCCBOSC 2018 news
   :
  - We are pleased to announce that Lucia Peixoto
   of
  Washington State University will be our third keynote speaker.
  - Please welcome *Google Cloud
  * as
  a GCCBOSC Platinum sponsor.
  - *GCC Lightning talk, poster and demo submissions are due by April
  16
  
*
  - Childcare for GCCBOSC
  !
  Space is limited, so register *now*.
   - Upcoming Events:
  - 2018 Big Genomics Data Skills Training course
  

   - how to integrate genomic data analysis into undergraduate
  coursework
  - Gateways 2018 Call for Participation
  

  - Upcoming events
   (on
  four continents)
   - New:
  - 119 publications
  
(including
  9 highlighted ones)
  - Openings in 9 groups on 2 continents
  
  - Public Galaxy Server News
  

   (a new server and an updated one too)
  - ToolShed contributions
  
  - Releases
   of
  Galaxy, Galaxy Docker, blend4j, and galaxy-lib
   - And other news
    too

See the newsletter  for
the full story, and we hope to see you in Portland!
Dave C, on behalf of the Galaxy

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Re: [galaxy-dev] March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more

[Dave Clements]

Hi All,

In case you aren't on Twitter
<https://twitter.com/galaxyproject/status/974497427506978817>:

The deadline for GCCBOSC 2018 oral presentation abstracts has been extended
to Monday, March 19th.

   - *Submit an abstract
   <https://easychair.org/conferences/?conf=gccbosc2018> (oral presentation
   abstracts deadline extended to March 19)*
   - *Abstract Guidelines
   <https://www.open-bio.org/wiki/BOSC_Abstract_Submission>*
   - Register <https://gccbosc2018.eventbrite.com>
   - Book conference housing <https://gccbosc2018housing.eventbrite.com>

Thanks,

Dave C



On Wed, Mar 14, 2018 at 10:20 AM, Dave Clements <cleme...@galaxyproject.org>
wrote:

> Hi All,
>
> Just a reminder that talk abstracts are *due this Friday*.
>
> Abstract submission, registration & housing are open
>> <https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-registration-and-housing-are-open>
>>
>
> And, we'll be announcing conference-subsidized childcare later this week.
>
> Hope you are in Freiburg right now, in Cape Town next month, and in
> Portland in June!  :)
>
> Dave C
>
> On Thu, Mar 1, 2018 at 12:00 PM, Dave Clements <cleme...@galaxyproject.org
> > wrote:
>
>> Hello all,
>>
>> The March 2018 Galaxy News
>> <https://galaxyproject.org/galaxy-updates/2018-03/> brings more news
>> than usual, with much of it about upcoming meetings, including GCCBOSC, and
>> continental meetings in Europe and Africa.
>>
>>- *Lots* of GCCBOSC 2018 news
>><https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018>:
>>   - Abstract submission, registration & housing are open
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-registration-and-housing-are-open>
>>  - *Oral presentation abstracts due March 16
>>  <https://easychair.org/conferences/?conf=gccbosc2018>*
>>   - Training Schedule set
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#training-schedule-set>
>>  - 17 topics in 22 sessions over two days covering the full
>>  spectrum of open source bioinformatics
>>   - We are pleased to announce two of the keynote speakers
>>   <http://localhost:8080/galaxy-updates/2018-03/#keynote-speakers>:
>>  - Fernando Pérez, of the Berkeley Institute for Data Science,
>>  University of California Berkeley and Project Jupyter
>>  - Tracy K. Teal, of the Carpentries and the *Journal for Open
>>  Scource Software*
>>   - Sponsors
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018-sponsors>
>>   :
>>  - F1000Research
>>  <https://galaxyproject.org/galaxy-updates/2018-03/#f1000research>
>>  - Technology Association of Oregon
>>  
>> <https://galaxyproject.org/galaxy-updates/2018-03/#technology-association-of-oregon>
>>  - Call for sponsors
>>  
>> <https://galaxyproject.org/galaxy-updates/2018-03/#call-for-sponsors>
>>   - *Continental* community meetings:
>>   - *Europe, 14-16 March, Freiburg*
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#elixir-galaxy-community-kickoff-and-meeting-march-freiburg>
>>   - *Africa, 3-5 April, Cape Town*
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#galaxy-africa-3-5-april-cape-town>
>>  - Apply for a Conference Fellowship
>>  
>> <https://galaxyproject.org/galaxy-updates/2018-03/#conference-fellowships>
>>   *by 10 March*.
>>   - Upcoming events
>><https://galaxyproject.org/galaxy-updates/2018-03/#upcoming-events> (on
>>four continents)
>>- New:
>>   - Galactic Blog post from Arun Decano: Coding in the Winter
>>   Wonderland: Galaxy Admin Training
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#new-galactic-blog-entry-coding-in-the-winter-wonderland-galaxy-admin-training>
>>   - 133 publications
>>   <https://galaxyproject.org/galaxy-updates/2018-03/#publications> 
>> (including
>>   5 highlighted ones)
>>   - Openings in 6 groups on 2 continents
>>   <https://galaxyproject.org/galaxy-updates/2018-03/#whos-hiring>
>>   - Public Galaxy Server News
>>   
>> <https://galaxyproject.org/galaxy-updates/2018-03/#public-galaxy-server-news>
>>(a new server and two updated ones)
>>   - ToolShed contributions
>>  

Re: [galaxy-dev] March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more

[Dave Clements]

Hi All,

Just a reminder that talk abstracts are *due this Friday*.

Abstract submission, registration & housing are open
> <https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-registration-and-housing-are-open>
>

And, we'll be announcing conference-subsidized childcare later this week.

Hope you are in Freiburg right now, in Cape Town next month, and in
Portland in June!  :)

Dave C

On Thu, Mar 1, 2018 at 12:00 PM, Dave Clements <cleme...@galaxyproject.org>
wrote:

> Hello all,
>
> The March 2018 Galaxy News
> <https://galaxyproject.org/galaxy-updates/2018-03/> brings more news than
> usual, with much of it about upcoming meetings, including GCCBOSC, and
> continental meetings in Europe and Africa.
>
>- *Lots* of GCCBOSC 2018 news
><https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018>:
>   - Abstract submission, registration & housing are open
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#abstract-submission-registration-and-housing-are-open>
>  - *Oral presentation abstracts due March 16
>  <https://easychair.org/conferences/?conf=gccbosc2018>*
>   - Training Schedule set
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#training-schedule-set>
>  - 17 topics in 22 sessions over two days covering the full
>  spectrum of open source bioinformatics
>   - We are pleased to announce two of the keynote speakers
>   <http://localhost:8080/galaxy-updates/2018-03/#keynote-speakers>:
>  - Fernando Pérez, of the Berkeley Institute for Data Science,
>  University of California Berkeley and Project Jupyter
>  - Tracy K. Teal, of the Carpentries and the *Journal for Open
>  Scource Software*
>   - Sponsors
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#gccbosc-2018-sponsors>
>   :
>  - F1000Research
>  <https://galaxyproject.org/galaxy-updates/2018-03/#f1000research>
>  - Technology Association of Oregon
>  
> <https://galaxyproject.org/galaxy-updates/2018-03/#technology-association-of-oregon>
>  - Call for sponsors
>  <https://galaxyproject.org/galaxy-updates/2018-03/#call-for-sponsors>
>   - *Continental* community meetings:
>   - *Europe, 14-16 March, Freiburg*
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#elixir-galaxy-community-kickoff-and-meeting-march-freiburg>
>   - *Africa, 3-5 April, Cape Town*
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#galaxy-africa-3-5-april-cape-town>
>  - Apply for a Conference Fellowship
>  
> <https://galaxyproject.org/galaxy-updates/2018-03/#conference-fellowships>
>   *by 10 March*.
>   - Upcoming events
><https://galaxyproject.org/galaxy-updates/2018-03/#upcoming-events> (on
>four continents)
>- New:
>   - Galactic Blog post from Arun Decano: Coding in the Winter
>   Wonderland: Galaxy Admin Training
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#new-galactic-blog-entry-coding-in-the-winter-wonderland-galaxy-admin-training>
>   - 133 publications
>   <https://galaxyproject.org/galaxy-updates/2018-03/#publications> 
> (including
>   5 highlighted ones)
>   - Openings in 6 groups on 2 continents
>   <https://galaxyproject.org/galaxy-updates/2018-03/#whos-hiring>
>   - Public Galaxy Server News
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#public-galaxy-server-news>
>(a new server and two updated ones)
>   - ToolShed contributions
>   
> <https://galaxyproject.org/galaxy-updates/2018-03/#toolshed-contributions>
>   - Releases
>   <https://galaxyproject.org/galaxy-updates/2018-03/#releases> of
>   Planemo, Pulsar, and galaxy-lib.
>- And other news
><https://galaxyproject.org/galaxy-updates/2018-03/#other-news> too
>
> See the newsletter <https://galaxyproject.org/galaxy-updates/2018-03/> for
> more.
>
> Hope to see you in Freiburg, Cape Town, and Portland!
>
> Dave C
>
> --
> https://gccbosc2018.sched.com/
> https://galaxyproject.org/
> https://usegalaxy.org/
>
>


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[galaxy-dev] March Galaxy News: GCCBOSC oral presentations due in 2 weeks, plus lots more

[Dave Clements]

Hello all,

The March 2018 Galaxy News
 brings more news than
usual, with much of it about upcoming meetings, including GCCBOSC, and
continental meetings in Europe and Africa.

   - *Lots* of GCCBOSC 2018 news
   :
  - Abstract submission, registration & housing are open
  

 - *Oral presentation abstracts due March 16
 *
  - Training Schedule set
  
 - 17 topics in 22 sessions over two days covering the full
 spectrum of open source bioinformatics
  - We are pleased to announce two of the keynote speakers
  :
 - Fernando Pérez, of the Berkeley Institute for Data Science,
 University of California Berkeley and Project Jupyter
 - Tracy K. Teal, of the Carpentries and the *Journal for Open
 Scource Software*
  - Sponsors
  
  :
 - F1000Research
 
 - Technology Association of Oregon
 

 - Call for sponsors
 
  - *Continental* community meetings:
  - *Europe, 14-16 March, Freiburg*
  

  - *Africa, 3-5 April, Cape Town*
  

 - Apply for a Conference Fellowship
 

  *by 10 March*.
  - Upcoming events
    (on
   four continents)
   - New:
  - Galactic Blog post from Arun Decano: Coding in the Winter
  Wonderland: Galaxy Admin Training
  

  - 133 publications
  
(including
  5 highlighted ones)
  - Openings in 6 groups on 2 continents
  
  - Public Galaxy Server News
  

   (a new server and two updated ones)
  - ToolShed contributions
  
  - Releases
   of
  Planemo, Pulsar, and galaxy-lib.
   - And other news
    too

See the newsletter  for
more.

Hope to see you in Freiburg, Cape Town, and Portland!

Dave C

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[galaxy-dev] GCCBOSC 2018 Abstract Submission & Early Registration are Open

[Dave Clements]

Hello all,

We are pleased to announce that abstract submission and early registration
for GCCBOSC2018  are now open.

   - Submit an abstract
    (oral presentation
   abstracts due March 16)
   - Register 
   - Book conference housing 

GCCBOSC 2018  will be held 25-30 June in
Portland, Oregon, United States. This brings the 2018 Galaxy Community
Conference and the Bioinformatics Open Source Conference together into a
unified week-long event. If you work in open source life science or
data-intensive biomedical research, then there is no better place than
GCCBOSC 2018 to present your work and to learn from others.

Events

GCCBOSC  starts with two days of training
 with a
wide range of topics nominated and selected by our communities. Training is
followed by a two day meeting, with joint and parallel tracks, featuring
oral presentations, posters, demos, lightning talks,
birds-of-a-feather and invited
keynotes from Fernando
Pérez

 of the Berkeley Institute for Data Science  and
 Project Jupyter , and Tracy K. Teal

 of The Carpentries. The week finishes with *CollaborationFest
 Core* and
*Encore*, two or four days of collaborative work on code, documentation,
training and challenging data analysis problems.

Abstract Submission

BOSC and GCC are now accepting abstracts
 for oral
presentations, posters, demos, and lightning talks. We are using EasyChair
 for submissions. If you don't already have an
account, you'll need to create one.

*The deadline for oral presentations is rapidly approaching (March 16) so
plan to submit your abstracts soon.*

Registration

Register now  to take full advantage of
 early registration discounts
 for
students/post-docs (75% off full price), non-profits (67%) and industry
(50%). Early registration rates for students and post-docs average $66 /
day.

Conference Housing

Official conference housing  for
GCCBOSC 2018 is in Reed residence halls. Rooms are within easy walking
distance of all conference venues. Room prices per night drop the longer
the stay. If you prefer to stay elsewhere, Reed College has a list of
recommended hotels , many
offering a discount for those attending events at Reed.

Travel Fellowships

Both OBF and the Galaxy Community Fund Board are offering fellowships to
attend GCCBOSC 2018:

   - OBF Travel Fellowships
   ,
   deadline is April 15.
   - GCC2018 Fellowships
   , first
   deadline is March 16.


See you in Portland!

The GCCBOSC 2018 Organizers




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[galaxy-dev] Galaxy News: GCCBOSC Training Topic Voting closes Wednesday!

[Dave Clements]

Hello all,

The February 2018 Galaxy News
 is out!

   - Events 
  - *GCCBOSC 2018 training topic voting ends tomorrow*
  

 - GCCBOSC Sponsorships
 
:
 highlighting *PeerJ
 * and call
 for sponsors
 
  - *Continental* community meetings in *Europe* (March, Freiburg)
  

   and *Africa* (April, Cape Town)
  

  - The Galaxy Administrators Course
  

   in Oslo is done, and training material and a preview of 18.01
  release from the course are now online.
   - Blog post: Galaxy R Markdown Tools
   

   - 111 new publications
   
   - Openings in 3 groups on 2 continents
   
   - Public Galaxy Server News
   
*(Hint: there are new servers.)*
   - ToolShed contributions
   
   - And other news
    too

See the full newsletter  for
all the news.
Dave C and the Galaxy Community

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[galaxy-dev] GCCBOSC 2018 Training Topic Voting is now open

[Dave Clements]

Hello all,

Voting is now open  on what training topics
 will be
offered at GCCBOSC
2018 .

Your vote  will determine the topics that
are offered, which topics should be offered more than once, and which ones
should not be scheduled at the same time. Your vote matters.

*Topic voting closes January 31.* The Training schedule, including
instructors, will be published before early registration opens.

GCCBOSC2018  will be held 25-30 June in
Portland, Oregon, United States. It will feature two days of training: the
second of which is multi-track and will feature content for both the BOSC
and Galaxy communities. Workshops will be hands-on and participants will be
strongly encouraged to bring a laptop and follow along. If you work in
data-intensive biomedical research, there is no better place than GCCBOSC
2018 to present your work and to learn from others.

Thanks, and see you in Portland!

The GCCBOSC 2018 Organizers

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[galaxy-dev] January Galactic News

[Dave Clements]

Hello all,

The January 2018 Galaxy News
 is out!

   - Upcoming events
   
  - *GCCBOSC 2018 Training Nominations Extended to January 12*
  

  - *ELIXIR Galaxy Community Kickoff and Meeting*
  
,
  March, Freiburg, Germany
  - *Galaxy (and GMOD) at PAG XXVI
  
and
Cal
  State San Marcos
  
*
  - 2018 Big Genomics Data Skills Training course
  

   - Two new blog posts
   
,
   both about Galaksio 
   - 155 new publications
   
   - Openings in 4 groups on 2 continents
   
   - Public Galaxy Server News
   
*(Hint: there are new servers.)*
   - New commercial support option: Intero Life Sciences and Galaxy
   Enterprise
   

   - ToolShed contributions
   
   - New releases
    of
   ephemeris, and blend4php
   - And other news
    too

See the full newsletter  for
all the news.

Wishing you a happy new year from the Galaxy Project,

Dave C

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[galaxy-dev] December 2017 News of the Galaxy

[Dave Clements]

Hello all,

The December 2017 Galaxy News
 is out!

   - Upcoming events
   
  - European Galaxy Administrator Workshop
  

  - Galaxy (and GMOD) at PAG XXVI
  

  - 2018 Big Genomics Data Skills Training course
  

   - Two new blog posts
   
   - 140 new publications
   
   - Public Galaxy Server News
   
   - ToolShed contributions
   
   - New releases
    of Galaxy,
   Galaxy Docker, galaxy-lib, and Planemo

See the full newsletter  for
all the news.
Looking forward to 2018,

Dave C and the Galaxy Team

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[galaxy-dev] European Galaxy Administrator Workshop, 8-12 January 2018, Oslo. FREE

[Dave Clements]

Hello all,

*We are pleased to announce that registration
 is now open for
the European Galaxy Administrator Workshop
*
.

   - Mon 8 January 2018 to Fri 12 January 2018 CET
   - Python room, Blindern, UiO campus, Ole Johan Dahls hus
   ,
   Gaustadalléen 23B, Oslo, 0373, Norway

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. Have a look at the
programme

to
see more details on the planned content of the workshop.

*Maximum number of participants is limited to 30, and we will manage
registrations to allow for geographical distribution and proritize
participants with responsibility of administrating galaxy servers.* After
registering you will get a second confirmation if/when a slot has been
allocated to you.

Although located in Europe, and named to reflect this, the workshop is
definitely *open to a world-wide audience.* The workshop is a result of the
collaboration between the Elixir Galaxy WG
 and the Galaxy
Project, and so far known, this is the only Galaxy Admin workshop planned
for 2018.

*Participants are to cover their own travel and accomodation, while the
workshop participation is free of charge.*

Instructors

   - Björn Grüning  (Elixir Galaxy WG
   , Elixir Germany
   ,
University
   of Freiburg )
   - Marius van den Beek  (Elixir Galaxy WG
   , Institute Curie
   , France)
   - Nicola Soranzo  (Elixir
   Galaxy WG , Earlham
   Institute , UK)
   - Enis Afgan  (Galaxy
   Project , Johns Hopkins University
   , USA)
   - Abdulrahman Azab
   
(Elixir
   Norway ,
   USIT , University of Oslo ,
   Norway)


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[galaxy-dev] November News: Blog, pubs, PAG, servers, tools, ...

[Dave Clements]

Hello all,

The November 2017 Galaxy News
 is out!

   - The Galactic Blog takes off
   
   - Publications
   :
  - The Galaxy Pub library surpasses 5,000 publications
  - 110 new pubs added in October, including 5 highlighted pubs
   - Upcoming events
    (9 this month)
  - Galaxy (and GMOD) at PAG XXVI
  

 - *PAG Early registration ends today.*
  - Public Galaxy Server News
  - 33 pubs in October
  

using,
  referencing or about public Galaxy servers
  - Citations section
  

added
  to public server list
  - New public server: BF2I-MAP
  
  - And the Language Analysis Portal
  

   too
   - ToolShed contributions
   
   - New releases
    of
   StarForge and sequence_utils.

And Other news
 too.

See the full newsletter .
Dave C and the Galaxy Team
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[galaxy-dev] Announcing the Galactic Blog, and a call for posts

[Dave Clements]

Hello all,

I am pleased to announce the *Galactic Blog
,* a place for blogging about Galaxy and
your experiences with it. The blog is on the Galaxy Hub
 and can be reached from the home page and the
Hub's Community menu.

Our very first post
 is
about the ELIXIR Galaxy Community and was written by Frederik Coppens,
Gildas Le Corguillé, and Björn Grüning.  We have a few more posts lined up
over the next week or so, but after that ...

*The Galactic Blog needs you!  *If you've done something that others would
benefit from knowing about then please create a Galactic Blog post
describing your experiences. See the CONTRIBUTING

page. If you have questions, please let me know.

Blog posts can either be directly created in the Galactic Blog (and hosted
on the Galaxy Hub ), or can be posted on your
favorite blogging platform (see, for example, Galactic Engineer
) and linked to from the Galactic
Blog. We'll tweet about every entry and highlight them in the monthly
newsletter as well.

Finally, this was a team effort and I'd particularly like to thank Dannon
Baker, Björn Grüning, and Martin Čech for their contributions.

I look forward to reading your blog posts!

Dave C

PS: The Galactic Blog replaces the former *Community Log* and includes all
content from it (which is why, even though the blog is new, it includes
entries back to 2013).

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[galaxy-dev] October News: Hacktoberfest, Pubs and Pub News, Events, Openings, Servers, ....

[Dave Clements]

Hello all,

The October 2017 Galaxy News
 is out!

   - Hacktoberfest!
   
   - Publications:
  - Galaxy Pub lib moves to Zotero
  

  - Highlighted pubs
  

and
  new tags.
  - 108 new pubs
  
   - Upcoming events
    (14
   this month and next)
   - Galaxy related openings
    at 5
   institutions in France and the US.
   - Public Galaxy Server News
  - 33 pubs in September
  

using,
  referencing or about public Galaxy servers.
  - ImmPort Galaxy: New Release and Feedback Needed
  

  - New server: Codon Harmonizer
  
   - ToolShed contributions
   
   - New releases
    of Pulsar,
   galaxy-lib, Planemo, BioBlend and sequence_utils.

And Other news
 too. See the
full newsletter  for,
well, full details.
Happy October,

Dave C

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[galaxy-dev] September Galaxy Newsletter

[Dave Clements]

Hello all,

The September 2017 Galaxy News
 is out and there are
new publications (122 of them)
, events
, open
positions  in
France and the US, ToolShed contributions
,
and new releases of nebulizer
 and
CloudBridge
.
August also saw the initial release of Takeru Galaxy
, a fully
configured (hardware and software) Galaxy server; and Galaskio
, an easy to
use GUI for running Galaxy workflows.

See the full newsletter .
Thanks for using Galaxy,

The Galaxy Team

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[galaxy-dev] Galaxy Project @ Johns Hopkins is hiring

[Dave Clements]

Hello all,

The Galaxy Project at Johns Hopkins is hiring software engineers and
postdocs:

The Taylor Lab  at Johns Hopkins University
 in Baltimore, Maryland is hiring software engineers and
post-docs  to work on the Galaxy
Project . This is a rare opportunity to perform
research and develop software at the leading edge of life sciences,
genomics, data-intensive computing, and big data analytics. Johns Hopkins
offers a challenging and rewarding work environment and is ranked as a
global top 20 university by Times Higher Education

.

Interested? See the full postings
.

*Watch this space for more upcoming openings...*

 [image: Galaxy Project hiring in the Taylor Lab]
  [image: Johns Hopkins
University] 


Please forward this to anyone who might be interested.

And I can say from experience that it's an excellent team to be a part of.

Thanks,

Dave C

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[galaxy-dev] August News: GCC2018: in Portland (w/ BOSC); GCC2017 & ISMB/BOSC presentations; and more

[Dave Clements]

Hello all,

The August 2017 Galaxy News
 is out!

   -

   Events
   - Save these dates: GCC2018: Portland, Oregon, June 25-30
  

 - And we wil bo colocated with BOSC 2018.
  - GCC2017 Slides, Posters, and Summaries
  
  - Galaxy at the 2017 SACNAS meeting
  

  - Galaxy @ ISMB/ECCB/BOSC 2017 slides and posters
  

  - Other events too
  
   -

   *New, new, new!*
   - Publications
   (298
  of them, 11 highlighted)
  - Open Positions
   (five
  of them)
  - Galaxy server news
  

  - Tools  and
  releases 
   - And other news
   

Thanks,

Dave C on behalf of the Galaxy Community

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[galaxy-dev] Galaxy @ ISMB/ECCB/BOSC 2017: Talks, posters, dinner, BoF, and tutorial

[Dave Clements]

Hello all,

There are Galaxy-related events and presentations every day
 at ISMB/ECCB 2017
 and BOSC 2017
:

   - A tutorial  (
   Friday ,
   still space)
   - 6 BOSC talks (Saturday
   ,
   Sunday )
   - 9 posters (Saturday
   ,
   Sunday 
   , Monday
   ,
   Tuesday
   )
   - 2 ISMB/ECCB talks (Saturday
   ,
   Tuesday
   , both
   by Galaxy PIs)
   - A Galaxy BoF
    (Monday
   )
   - A Galaxy Dinner  (Monday
   , see
   below)

*Galaxy Community Dinner: Monday, 24 June, 8pm*

The Galaxy Community will be gathering at ISMB/ECCB/BOSC 2017 over dinner
on Monday, 24 July at 8pm. Interested? *Then sign up now
!* *Dinner is pay-your-own-way and space
is limited.* Once it's full, it's full, so please signup today. See the sign
up form  for more information.

See you in Prague!

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[galaxy-dev] Galaxy Dinner @ ISMB/ECCB/BOSC 2017

[Dave Clements]

Hello all,

If you are interested in getting together for dinner at ISMB/ECCB/BOSC 2017
#BOSC2017 then please *let us know by Friday:*
  http://bit.ly/ismbdinnerpoll

Thanks,

Dave C

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Re: [galaxy-dev] Admin Training Poll: Where should Galaxy Admin Training be held next?

[Dave Clements]

Hi All,

The correct link to the feedback form is
  http://bit.ly/gatpoll

Thanks,

Dave C

PS: In fairness, I've only been using computers for ~40 years. I should
have this figured out in the next decade or so.  With apologies for the
extra email.

On Mon, Jun 19, 2017 at 12:54 AM, Dave Clements <cleme...@galaxyproject.org>
wrote:

> *Give us your input! <http://bit.ly/gatpoll>*
>
> Hello all,
>
> Last November the Galaxy Project offered it's first ever week-long Galaxy
> Admin Training. It was offered in Salt Lake City and drew ~35 participants
> from all over the world. The material was presented again at another
> training at the Galaxy Australasia Meeting
> <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> in
> February 2017.
>
> For the coming year the project (and other groups) are interested in
> offering it again. *We would like your input
> <http://localhost:8080/news/2017-06-admin-training-poll/(http://bit.ly/gatpoll>*
>  to
> help us to decide where to offer this training again during the coming year.
>
> Please respond <http://bit.ly/gatpoll> by Friday, June 23.
>
> Thanks,
>
> Dave C on behalf of Your friendly Galaxy Admin Trainer Community
>
> --
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> https://getgalaxy.org/
> https://usegalaxy.org/
> https://gcc2017.sciencesconf.org/
>



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[galaxy-dev] Admin Training Poll: Where should Galaxy Admin Training be held next?

[Dave Clements]

*Give us your input! *

Hello all,

Last November the Galaxy Project offered it's first ever week-long Galaxy
Admin Training. It was offered in Salt Lake City and drew ~35 participants
from all over the world. The material was presented again at another
training at the Galaxy Australasia Meeting
 in
February 2017.

For the coming year the project (and other groups) are interested in
offering it again. *We would like your input
*
to
help us to decide where to offer this training again during the coming year.

Please respond  by Friday, June 23.

Thanks,

Dave C on behalf of Your friendly Galaxy Admin Trainer Community

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[galaxy-dev] GCC2017: Talk schedule posted; Register by 16 June

[Dave Clements]

Hello all,


A few GCC2017  things:

1) The presentation schedule  has been posted.

2) The poster and demo schedule will likely be posted later today

3) Lightning talk  and
birds-of-a-feather

submission are still open

4) There is still limited space available for late poster and computer demo
submissions 

5) Register by 16 June 


>From this point on most/all emails about GCC2017 will go only to those that
have registered for it.


The final announcement going out to non-Galaxy mailing lists is below.
Please forward to anyone who you think might be interested.


And, we do hope to see you in Montpellier!


Dave C on behalf of the GCC2017 Organizing Committee



--

2017 Galaxy Community Conference (GCC2017)

26-30 June 2017

Montpellier, France

https://gcc2017.sciencesconf.org/

https://gcc2017.sched.com/

--



The Galaxy Community Conference (GCC) 
brings together researchers working in and supporting data intensive life
science research. There is no better place to share your work and learn
from others that are addressing diverse questions and facing common
challenges in data intensive biology. GCC participants work across the tree
of life, around the world, and represent universities, research
organizations, industry, medical schools and research hospitals.



GCC2017 will be in Montpellier, France, 26-30 June and features two days of
presentations, discussions, poster sessions, lightning talks, computer
demos, keynotes, and birds-of-a-feather meetups
, all about
data-intensive biology and the tools that support it. GCC2017 also
features data
and coding hackathons ,
and two days of training 
covering 16 different topics.  GCC2017 will be held at Le Corum Conference
Centre  in the
heart of Montpellier ,
just 10km from the Mediterranean.



Registration closes 16 June
.  Costs start at 75€
per day for postdocs and students.



If you work in data intensive life science research then GCC2017 is an
ideal opportunity to present your work. Lightning talk
 and birds-of-a-feather

submission are still open, and there is limited space available for late
poster and computer demo submissions
.



About Galaxy

Galaxy  is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
public and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.



We hope to see you in Montpellier!



Au revoir,



The GCC2017 Organising Committee


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https://usegalaxy.org/
https://gcc2017.sciencesconf.org/
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[galaxy-dev] June 2017 News of the Galaxy

[Dave Clements]

Hello all,

The June 2017 Galaxy News
<https://galaxyproject.org/galaxy-updates/2017-06/> is out!

   - 2017 Galaxy Community Conference is almost here
   <https://galaxyproject.org/galaxy-updates/2017-06/#gcc2017-is-almost-here->
  - *Regular registration rates extended
  
<https://galaxyproject.org/galaxy-updates/2017-06/#regular-registration-rates-extended-to-june-16>*
  - Keynote Speakers
  <https://galaxyproject.org/galaxy-updates/2017-06/#keynotes>: Eytan
  Domany
  <https://galaxyproject.org/galaxy-updates/2017-06/#eytan-domany>; Anton
  Nekrutenko & James Taylor
  
<https://galaxyproject.org/galaxy-updates/2017-06/#anton-nekrutenko-james-taylor>
  - Submit a Lightning Talk
  
<https://galaxyproject.org/galaxy-updates/2017-06/#submit-a-lightning-talk->
  - Submit a BoF
  <https://galaxyproject.org/galaxy-updates/2017-06/#gcc2017-call-for-bofs->
  - Capture the flag (what?)
  
<https://galaxyproject.org/galaxy-updates/2017-06/#hack-the-universe-capture-the-flag-at-gcc2017->
   - Making Galaxy Work for You tutorial at ISMB/ECCB 2017
   
<https://galaxyproject.org/galaxy-updates/2017-06/#galaxy-tutorial-ismb-eccb-2017>
   - All upcoming events
   <https://galaxyproject.org/galaxy-updates/2017-06/#all-events>
   - Training Material Re-use Hackathon Reports
   
<https://galaxyproject.org/galaxy-updates/2017-06/#training-material-re-use-hackathon-reports>
   - And *new*:
  - Pubs
  <https://galaxyproject.org/galaxy-updates/2017-06/#new-publications> (85
  of them, 5 highlighted)
  - Positions
  <https://galaxyproject.org/galaxy-updates/2017-06/#who-s-hiring>
  - Public Server News
  
<https://galaxyproject.org/galaxy-updates/2017-06/#public-galaxy-server-news>
  - Tools <https://galaxyproject.org/galaxy-updates/2017-06/#tools>
  - Releases
  <https://galaxyproject.org/galaxy-updates/2017-06/#releases>
   - And other news too
   <https://galaxyproject.org/galaxy-updates/2017-06/#other-news>

Thanks for using Galaxy,

Dave Clements and the Galaxy Community
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Re: [galaxy-dev] [gsoc2017-papers] Project Publication Reference Tracking Tool -- are you interested in?

[Dave Clements]

Hi Anton,

We've already got folks from the Galaxy Project, Reactome, InterMine, and
BioPython on board.  And now several more folks are on the Gitter channel
as well.  I think we may end up with too many people involved.  *(But
that's the kind of problem I want to have!  :-)*

Also, the project isn't about biology per se. It's about finding papers
that reference software projects often in indirect ways.  The software can
be from any domain.

And I would argue that identifying where to search and what to search for
is up to the people using the software (for example, me), rather than the
person developing the software (Chris).

Questions?  I suggest continuing this conversation on gitter
.

Cheers,

Dave C


On Mon, May 15, 2017 at 6:00 AM, Anton Nekrutenko  wrote:

> Krzysztof:
>
> This can be very interesting potentially. However, to be useful such a
> tool needs to take into account how real-world researchers (biologists)
> perform literature searches. Do you have someone who can guide in
> understanding this "very non-linear" process?
>
>
> a.
>
> Anton Nekrutenko
> Professor of Biochemistry
> and Molecular Biology
> Penn State University
> http://nekrut.bx.psu.edu
> (814) 826-9628
>
>
> On Mon, May 15, 2017 at 1:14 AM, Krzysztof Kutt 
> wrote:
> >
> > Hi!
> >
> > We do not know each other yet, so I will briefly introduce myself.
> >
> > I'm Chris, a Polish PhD candidate in Computer Science field at AGH
> University of Science and Technology in Krakow. In my work I deal with the
> broad concept of artificial intelligence. In particular the semantic web
> technologies (RDF, SPARQL, Linked Data) and the ability to support a group
> of knowledge engineers who create knowledge inside (semantic) wiki systems
> - in my PhD I propose some methods and prototypical tools for quality
> management, change management and motivation. I have also finished the
> Master's degree in Psychology and as a result I also deal with Affective
> Computing field.
> >
> > I know, I'm quite far away from bioinformatics :) so, what I am doing
> here?
> > As a part of Google Summer of Code program I will prepare a tool to keep
> track of publications that reference a specific project (project's papers,
> tools, etc). I think that at the end it will be a quite good tool that any
> researcher can use for dealing with the task, regardless of the research
> field.
> >
> > Specifically, it will be a set of Python scripts + GUI that will do four
> tasks:
> > 1) performs database search for new projects (search terms),
> > 2) handles alerts for updating the results later,
> > 3) gives the user the possibility to manually annotate results (e.g. as
> irrelevant),
> > 4) generates citation reports (e.g. list of papers that cite our project
> during last year).
> >
> > If you are interested in such a tool, do not hesitate to:
> > * read the more detailed description placed in the project's github
> wiki: https://github.com/kkutt/references-tracking/wiki/Tool-Description
> > * discuss it on the Gitter channel: https://gitter.im/references-
> tracking/Lobby or simply write me an e-mail
> > We already have interest from members of the Galaxy, Reactome,
> InterMine, and BioPython communities.
> > I am waiting for your comments :)
> >
> > If you are not interested in a project, maybe your colleagues are? :)
> >
> > Best regards,
> > Chris Kutt
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/
>
> ___
> gsoc2017-papers mailing list
> gsoc2017-pap...@lists.galaxyproject.org
> https://lists.galaxyproject.org/listinfo/gsoc2017-papers
>
>


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[galaxy-dev] May 2017 Galaxy News: GCC2017 deadlines, sponsors & BoFs; new papers, openings, tutorials...

[Dave Clements]

Hello all,

The May 2017 Galaxy News  is
out!

   - 2017 Galaxy Community Conference
   

  - *May 15: Early registration ends
  
*
  - *May 27: Poster and Demo submission closes
  
*
  - We are pleased to welcome *GenomeWeb
  *
and *BioTeam
  * as
  returning GCC sponsors (and they both have offers for the Galaxy
community)
  - Got a topic you want to discuss with the community? *Create a Birds
  of a Feather
  
*
   - Making Galaxy Work for You tutorial at ISMB/ECCB 2017
   

   - Gateways 2017 Call for Participation (1st deadline: June 5)
   

   - All upcoming events
   
   - And *new*:
  - Pubs
   (110
  of them, 6 highlighted)
  - Positions
  
  - Public Services and Servers
  

 - CLIMB: UK Galaxy Service for microbial researchers
 

 - Antigen Receptor Galaxy (ARGalaxy)
 

  - Releases
  
  - ToolShed Contributions
  
   - And some pretty cool other news too
   .

Hope to see you in Montpellier!

-- 
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https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/
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[galaxy-dev] GCC2107 Oral presentation abstract deadline extended to 29 April

[Dave Clements]

Hello all,


The deadline for submitting oral presentation abstracts for the 2017 Galaxy
Community Conference  has been extended
to 29 April.


And a reminder of some other GCC2017 
deadlines:


  15 May:  Early registration
 ends

  27 May:  Poster presentation abstracts
 are due.

  27 May:  Visualization and Computer Demo presentation abstracts
 are due.

  31 May:  Regular registration
 ends

  23 June: Lightning Talk presentation abstracts
 are due.

*About GCC2017:*

GCC2017 will be in Montpellier, France, 26-30 June and will feature two
days of presentations, discussions, poster sessions, lightning talks,
computer demos, keynotes, and birds-of-a-feather meetups, all about
data-intensive biology and the tools that support it. GCC2017 also includes
data and coding hackathons ,
and two days of training 
covering 16 different topics.

GCC2017 will be held at Le Corum Conference Centre
 in the heart
of Montpellier , just 10km
from the Mediterranean. This event will gather several hundred researchers
addressing diverse questions and facing common challenges in data intensive
life science research. GCC participants work across the tree of life, come
from around the world, and work at universities, research organizations,
industry, medical schools and research hospitals.  If you work in or
support data intensive life science research then GCC2017 is an ideal
opportunity to present your work.


Early registration  is
starts at less than 55€ / day for post-docs and students.  You can also book
low cost conference housing 
when you register.


GCC2017 has sold out *all* premiere *sponsorship*
 slots (a first). If you
are interested in sponsoring (or know someone who is) there are still
Silver and Bronze and Hackathon sponsorships available. Contact the
organisers if you are interested.

About Galaxy

Galaxy  is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
commercial and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.


We hope to see you this summer in Montpellier!


Au revoir,


The GCC2017 Organising Committee

-- 
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https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/
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[galaxy-dev] GCC2107 Update: Oral presentation abstracts due 15 April

[Dave Clements]

Hello all,


This is just a reminder of some *GCC2017
* deadlines:


  15 April:  Oral presentation abstracts
 are due* this Saturday *at 23:59
Paris local time*.*

  15 May:  Early registration
 ends

  27 May:  Poster presentation abstracts
 are due.

  27 May:  Visualization and Computer Demo presentation abstracts
 are due.

  31 May:  Regular registration
 ends

  23 June: Lightning Talk presentation abstracts
 are due.

*About GCC2017:*

GCC2017 will be in Montpellier, France, 26-30 June and will feature two
days of presentations, discussions, poster sessions, lightning talks,
computer demos, keynotes, and birds-of-a-feather meetups, all about
data-intensive biology and the tools that support it. GCC2017 also includes
data and coding hackathons ,
and two days of training 
covering 16 different topics.

GCC2017 will be held at Le Corum Conference Centre
 in the heart
of Montpellier , just 10km
from the Mediterranean. This event will gather several hundred researchers
addressing diverse questions and facing common challenges in data intensive
life science research. GCC participants work across the tree of life, come
from around the world, and work at universities, research organizations,
industry, medical schools and research hospitals.  If you work in or
support data intensive life science research then GCC2017 is an ideal
opportunity to present your work.


Early registration  is
starts at less than 55€ / day for post-docs and students.  You can also book
low cost conference housing 
when you register.


GCC2017 has sold out *all* premiere *sponsorship*
 slots (a first). If you
are interested in sponsoring (or know someone who is) there are still
Silver and Bronze and Hackathon sponsorships available. Contact the
organisers if you are interested.

About Galaxy

Galaxy  is an open, web-based platform for
data-intensive biomedical analysis used by tens of thousands of researchers
around the world.  It supports ad hoc exploration and analysis through
scalable and repeatable data analysis pipelines for large research studies.
Galaxy is available in over 90 free and publicly accessible web servers, on
commercial and national cloud infrastructures, and is locally installed at
hundreds, if not thousands, of research organisations around the world.


We hope to see you this summer in Montpellier!


Au revoir,


The GCC2017 Organising Committee


-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/
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[galaxy-dev] April 2017 Galaxy News: GCC2017 + new events, papers, jobs, servers, releases, and a milestone

[Dave Clements]

Hello all,

The April 2017 Galaxy News
 is out!

   - Usegalaxy.org passes a milestone
   

   - 2017 Galaxy Community Conference
   

early
   registration and abstract submission are open.
  - Travel fellowships for GCC2017
  

are
  available from the Galaxy Community Fund *(apply by April 5!)*.
  - New GCC2017 Sponsors: ELIXIR and GigaScience
  
   - G-OnRamp Beta Testers Workshop: Invitation
   

   - A whole lot more
   
events
   are coming up.
   - 275 new publications
   ,
   including 12 highlighted pubs.
   - Four open positions
    in
   Europe and North America.
   - Two new public servers, LAPPS Grid looking for collaborators, new
   PhenoMeNal training material
   
   - New releases
    of
   CloudBridge, Planemo, and galaxy-lib.
   - Over 200 new repos
   
in
   the Galaxy Tool Shed.
   - And other news
    too.

Happy April from the Galaxy Team and Community

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[galaxy-dev] GSoC 2017: Project Publication Reference Tracking: Building a community

[Dave Clements]

Hi All,

As you may have heard the Open Genome Informatics proposal
 was accepted for GSoC 2017.  That proposal
covers all the GMOD projects, including Galaxy.  One of projects in the
proposal was:

*Project Publication Reference Tracking (Galaxy/Reactome)
*

Assuming that this item gets prioritized for funding, and that we find a
great student, then this will be worked on this summer.  *Hopefully we'll
end up with a great tool that any open source community can use to keep
track of publications that reference it.*

*If having a tool that helps you track publications that use your resource
interests you then please keep reading below.  *

If not, then thanks for your time,

Dave C


*Building a community*

I've been reading the GSoC Mentoring Manual
 (one of the authors is Duke
Leto) and one of the things it suggests is getting the student engaged with
the community.  The community for this proposal isn't Galaxy or Reactome or
GMOD per se (although GMOD is pretty close).  The community is folks at
open source projects that want to track references to their projects (which
includes those who run bio DBs, public Galaxy Servers, and the various GMOD
component projects).

I'd like to build that community now.  *If you are interested in this
topic, and maybe in helping to provide guidance for a GSoC student then
please let me know.** If I hear from enough people I'll create a mailing
list.  If not, we'll just use email (and probably a Gitter channel).

Also, if anyone knows of tool that already does this, please let me know.
I don't want to reinvent the wheel this summer.  Galaxy does this using
lots of email alerts, CiteULike, and some custom scripts (they work sort
of, but oh the horror!).  I've got a 6 page doc describing the current
process that I've sent to every potential GSoC student who has contacted
me.  First thing I'll do is send that to those that are interested.

Thanks,

Dave C.

* You can also post to the whole list, but I'm trying to cut down on noise
in people's email.


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[galaxy-dev] March 2017 News of the Galaxy

[Dave Clements]

Hello all,

The  March 2017 Galaxy News
 is out!

   - 2017 Galaxy Community Conference
   

early
   registration and abstract submission are open.
   - Travel fellowships for GCC2017
   

are
   available from the Galaxy Community Fund.
   - Metaproteomics of microbiomes at ABRF 2017
   

   , Cycle "Bioinformatique par la pratique" 2017
   

at
   INRA in Jouy-en-Josas, and a whole lot more
   
events
   are coming up.
   - Galaxy is in GSoC 2017
   

   - 199 new publications
   ,
   including 11 highlighted pubs.
   - Four open positions
    in
   Europe and North America.
   - Two new public servers, RNA-Rocket needs some fuel, and Cancer
   Computer upgrades
   

   - New releases
    of
   Galaxy, Planemo, Pulsar, galaxy-lib, Starforge, and (the new)
   sequence_utils.
   - Over 80 new repos
   

in
   the Galaxy Tool Shed.
   - And other news
    too.

Happy March!

Dave C and the Galaxy Team

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Re: [galaxy-dev] GalaxyAdmins online meetup: this Thursday

[Dave Clements]

Hi All,

The links to the online conference room, and (after the meetup) the slides
and video can be found here:
  https://new.galaxyproject.org/community/galaxy-admins/meetups/2017-02-16/

Many thanks to Nuwan and Enis for presenting this.

Hope to see or hear or maybe just sense your presence in about 19 hours,

Dave C


On Tue, Feb 14, 2017 at 6:19 PM, Enis Afgan  wrote:

> This is a reminder that we are going to have a GalaxyAdmins call really
> soon now!
>
> The talk will be held on Thursday Feb 16th at 11AM EST. See your local
> time here .
>
>
> with the following topic being presented:
>
> CloudLaunch  is an application for
> launching Galaxy on the Cloud instances. In this talk, an all-new version
> will be presented. The new CloudLaunch (beta.launch.usegalaxy.org) allows
> multiple flavors of Galaxy to be deployed, Docker images or applications
> other than Galaxy. Each application can have its own custom user interface
> developed to accommodate the specific application needs, which will be
> demonstrated.
>
>
> ___
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>



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[galaxy-dev] Vote for the Training you would like to see at GCC2017

[Dave Clements]

   13. Conda and Containers for Tool Dependencies - A Deployers
  Perspective
  <https://gcc2017.sciencesconf.org/resource/page/id/8#conda_dep>
  14. Introduction to Galaxy Interactive Environments
  <https://gcc2017.sciencesconf.org/resource/page/id/8#ie_intro>
  15. Advanced topics in Galaxy Interactive Environments
  <https://gcc2017.sciencesconf.org/resource/page/id/8#ie_adv>
  16. Galaxy and Tripal - coupling Galaxy to a community database
  <https://gcc2017.sciencesconf.org/resource/page/id/8#tripal>
  17. The Galaxy Genome Annotation project: Dockerized genome
  annotation environment based on Galaxy and GMOD tools
  <https://gcc2017.sciencesconf.org/resource/page/id/8#gap>
  18. Using Hadoop with Galaxy
  <https://gcc2017.sciencesconf.org/resource/page/id/8#hadoop>
   - *Trainer Training Topics
   <https://gcc2017.sciencesconf.org/resource/page/id/8#trainer_training>*
  1. Galaxy for Training and Education
  <https://gcc2017.sciencesconf.org/resource/page/id/8#galaxy_for_training>

Please vote
<https://docs.google.com/forms/d/e/1FAIpQLSdpkLoRuCGZOO3_T6dgRwFeDxVjb_zW-tl1OhfcerMMHItJQA/viewform>!
Your participation helps make Galaxy Community Conferences the successful
and community focused events that they are.  And, thanks to everyone who
nominated topics and/or contributed topic descriptions.

Hope to see you in Montpellier!

Dave Clements, on behalf of the GCC2017 Organising Committee
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Re: [galaxy-dev] Nominate the training topics you want to see at GCC2017

[Dave Clements]

Hello all,

Thanks to everyone who's already nominated topics, and a reminder that

*Topic Nominations close 20 January, which is this Friday.*

You can nominate a topic now:
  http://bit.ly/gcc2017trainingnom

The list of topics nominated thus far is:
  https://gcc2017.sciencesconf.org/page/training

Please nominate the topics you would like to see.  And, if you see a
nominated topic that you would like to provide a more detailed description
for, then please renominate that topic and include the expanded description.

Thanks,

Dave C, on Behalf of the GCC2017 Organising Committee



On Mon, Jan 9, 2017 at 1:02 AM, Olivier Inizan 
wrote:

> Hello all,
>
> Training Day topics are nominated by you, the Galaxy Community. Please
> take a minute to nominate a topic. Any topic of interest to the Galaxy
> Community can be nominated and you are encouraged to nominate more than one
> topic. If you are looking for ideas, see the topic nominated in
>
> - 2016 bit.ly/gcc2016noms,
> - 2015 bit.ly/gcc2015vote,
> - 2014 bit.ly/1s6NtMN,
> - 2013bit.ly/1i2j1gN,
> - and the Galaxy Events page (new.galaxyproject.org/events/).
>
>
> The 2017 Galaxy Community Conference (GCC2017, gcc2017.sciencesconf.org)
> will be held 26-30 in Montpellier, France.
>
> It will feature two days of training: the first day will be single track
> focused on introducing Galaxy for bioinformatics analysis; the second day
> will feature multiple tracks spanning the breadth of Galaxy usage, admin,
> deployment, and tools.
>
>
> Nominated topics will be published on the GCC2017 Training page as they
> come in (gcc2017.sciencesconf.org/).
>
> Topic Nominations close 20 January. Topics will be compiled into a uniform
> list by GCC2017 organizers, and then voted on by the Galaxy Community
> starting one week later.
>
>
> You can nominate a topic now:
> https://t.co/DkOmqELY6h
>
> Olivier Inizan,
>
> On behalf of the GCC2017 Organizing Committee
>
>
>
>
> Olivier Inizan
> 
> Merci de noter ma nouvelle adresse:
>
> olivier.ini...@inra.fr
>
> Unité de Recherches en Génomique-Info (UR INRA 1164),
> INRA, Centre de recherche de Versailles, bat.18
> RD10, route de Saint Cyr
> 78026 Versailles Cedex, FRANCE
>
>
> Tél: +33 1 30 83 38 25
> Fax: +33 1 30 83 38 99
> http://urgi.versailles.inra.fr [urgi.versailles.inra.fr]
> Twitter: @OlivierInizan
>
>
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[galaxy-dev] Fwd: Job: CaliforniaStateU_SanMarcos.PopGenetProgrammer

[Dave Clements]

Hi All,

Cross posting this opening from EvolDir.   This opening was also linked to
from the January newsletter.

Please forward this on to anyone you know who may be looking for a position.

Thanks,

Dave C



-- Forwarded message --
From: 
Date: Mon, Jan 9, 2017 at 11:20 PM
Subject: Job: CaliforniaStateU_SanMarcos.PopGenetProgrammer
To: clementsgal...@gmail.com

Job Description:

The Sethuraman lab of population genetics at California State
University San Marcos is looking to hire a scientific research
programmer. Primary responsibility will be to assist in development of
a model-based population genomics pipeline, and development of a
graphical front-end to be hosted in the Galaxy Project platform. This
position is funded by an NSF grant to Dr. Arun Sethuraman (CSU San
Marcos - www.arunsethuraman.weebly.com) and Dr. Jody Hey (Temple
University - https://bio.cst.temple.edu/~hey/) and will have ample
opportunities for collaborative development of statistical and
evolutionary genetic applications across both labs. The position will
be based out of CSUSM (San Marcos, California). This work requires
experience in C/C++, Perl/Python/Shell across Unix and Windows
platforms. Experience with development of applications for the Galaxy
Project is desired. Experience with software programming best
practices, including test automation (e.x. travis-ci, jenkins.io) and
task management (e.x. Jira, waffle.io) will be an added plus.

The position is funded for three years, with possibilities for
continued funding. The programmer/postdoc will report directly to both
PI's and also have the opportunity to train and mentor graduate and
undergraduate students (2-3 per year) in scientific programming and
software development.

Please contact Arun (asethura...@csusm.edu) with any questions
regarding the position.

Qualifications:

A Master's degree in computer science or bioinformatics with
extensive experience in scientific programming is required. Candidates
with a PhD in computational biology or bioinformatics, or some allied
field will also be considered.

University Auxiliary and Research Services Corporation (UARSC) was
founded in 1990 as a 501(c) 3 public, nonprofit corporation to support
the mission of Cal State San Marcos, the 20th campus in the California
State University system. CSUSM is a recipient of the Chronicle's 2014
Great College to work for. UARSC offers an excellent benefits package
which includes medical, dental, vision, retirement plan, life and long
term disability insurance, paid holidays, and generous vacation and
paid time off leave benefits. For more information about UARSC, visit
our website at www.csusm.edu/uarsc.

"JEANNE CLERY ACT AND CAMPUS FIRE SAFETY RIGHT-TO-KNOW LAW" NOTIFCATION
- See Police Department's website located
at:http://www.csusm.edu/police/Clery.pdf

Application Procedure:

Please apply by clicking "Apply" on this page, and be sure to submit
a cover letter and resume along with your online employment
application. UARSC is an Equal Opportunity Employer and does not
discriminate against persons on the basis of race, color,
creed, religion, ancestry, sex, gender, gender identity, gender
expression, genetic information, pregnancy, sexual orientation, age,
medical condition, military service, veteran's status, marital
status, national origin, physical or mental disability, or any other
status protected by federal, state or local laws.

For questions or if you experience any difficulties with the online
application process, please contact UARSC Human Resources at (760)
750-4700.

--

Thank you!

Arun

Arun Sethuraman, PhD

Assistant Professor
Department of Biological Sciences
California State University San Marcos

http://arunsethuraman.weebly.com/

Arun Sethuraman 




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Re: [galaxy-dev] GalaxyAdmins Online Meetup 15 December

[Dave Clements]

Hi All,

If you missed this, the video for it is now online
<https://new.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_12_15/>.

The video for Nick Hazekamp's August talk on Dynamic Job Expansion:
Experiences using Makeflow in Galaxy is now online too
<https://new.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_08_18/>.

Thanks to Björn Grüning, Bérénice Batut, Dannon Baker, and Nick Hazekamp
for presenting their work.

Cheers,

Dave C

On Mon, Dec 12, 2016 at 8:53 PM, Dave Clements <cleme...@galaxyproject.org>
wrote:

> Hello all,
>
> The next GalaxyAdmins online meetup
> <https://new.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_12_15/>
> is this Thursday, 15 December at [see your local time
> <http://bit.ly/2h2QOsT>].  The meetup will feature two presentations:
>
>- Galaxy Training Materials: Community creation, curation, and use, by
>Björn Grüning and Bérénice Batut, University of Freiburg
>- The new Galaxy Hub: Community creation, curation, and use, by Dannon
>Baker, Johns Hopkins University.
>
> The call will last around an hour, and will include discussion.
>
> Hope to see you there,
>
> Dave C & HAns-Rudolf
>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> https://wiki.galaxyproject.org/
>



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[galaxy-dev] December Galaxy News: New web site, GAMe deadline extended

[Dave Clements]

Hello all,

The *December Galaxy News
<https://new.galaxyproject.org/GalaxyUpdates/2016_12/>* is hot off the
press, *and is was produced on a a hot new press.  *Highlights this month
include:

   - The *Galaxy Community Hub (the Hub)
   
<https://new.galaxyproject.org/GalaxyUpdates/2016_12/#galaxy-community-hub-the-hub->*
will
   be the new home for Galaxy Community documentation, replacing the current
   wiki.
  - And we are asking for help to get it ready for it's official launch
  
<https://new.galaxyproject.org/GalaxyUpdates/2016_12/#the-community-hub-contribution-convergence-chcc-thursday-december-8>
   - *Galaxy Australasia Meeting (GAMe 2017)
   
<https://new.galaxyproject.org/GalaxyUpdates/2016_12/#galaxy-australasia-meeting-game-2017->*:
   February 3-9, Melbourne, Victoria, Australia.
  - *Talk abstract submission extended to 14 December.*
  - *Early registration ends 31 December.*
   - And of course, other upcoming events
   <https://new.galaxyproject.org/GalaxyUpdates/2016_12/#all-upcoming-events>
too

There are also 60 new publications (including eight featured pubs), four
open positions, two new public Galaxy servers, new releases of Planemo &
Pulsar, and other news too.

Dave Clements and the Galaxy Team
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[galaxy-dev] New Galaxy Arabic Community

[Dave Clements]

Hello all,

أرشيف للقائمة البريدية جالاكسي بالعربية يحتوي على الاخبار والمناقشات
والاعلانات الخاصة بمستخدمي جالاكسي من البلاد الناطقة بالعربية نرحب بانضمام
أي شخص مهتم بالجلاكسي بلاتفورم
جالاكسي هي بلاتفورم لتحليل المعلومات الحيوية باستخدام أدوات برمجة أونلاين
مجانا تتميز بأنها متاحة للجميع ونتائجها تتميز بالشفافية وبالقدرة على الحصول
على نفس النتائج عند إجراء التحليل مرات عديدة.
السهولة : يمكن لأي شخص استخدام جالاكسي حتى لو لم تكن لديه خبرة كافية بتحليل
المعلومات الحيوية
النتائج : تحصل على نفس النتائج مهما أجريت التجربة مرات عديدة وهذا يميز
جالاكسي عن العديد من الأدوات الاخرى
الشفافية : يمكنك أن تشارك ما توصلت إليه مع زملائك والعالم كله ويمكنك النشر
أيضا .
جالاكسي مفتوحة لكل المنظمات والسرفر الرئيسي يمكنك من إجراء تحليل على
المعلومات الجينية وإيضا توجد مواد تعليمية للتدريب وأماكن العمل وخدمات النشر
يمكنك استخدام جالاكسي أونلاين ويمكنك أيضا تنزيلها على الكمبيوتر الخاص بك
واستخدامها

--

We are pleased to announce the launch of the *Galaxy Arabic community
<https://wiki.galaxyproject.org/Community/Arabic>.* Galaxy Arabic supports
and promotes Galaxy activity for the Arabic speaking community and in
Arabic speaking regions of the world.

If you are interested in joining the community, please

   -

   Follow @Galaxy_Arabic on Twitter <http://twitter.com/galaxy_arabic>
   -

   Join the Galaxy Arabic mailing list
   <https://lists.galaxyproject.org/listinfo/galaxy-arabic>. Regional
   Galaxy news will be posted here, and you can also ask fellow Arabic
   speakers support questions.
   -

   Join the Galaxy Arabic Facebook group <http://bit.ly/2ek7fTh>

We look forward to connecting and growing the Arabic speaking Galaxy
community.

Thanks,

Abdelazeem Abdelhameed <abdelazeem_abdelhameed2015...@yahoo.com> and Dave
Clements <https://wiki.galaxyproject.org/DaveClements>

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Re: [galaxy-dev] Galaxy Admin Training: November 7-11, Salt Lake City

[Dave Clements]

Hi All,

Just a reminder that registration for the November Galaxy Admin Training in
Salt Lake <https://wiki.galaxyproject.org/Events/AdminTraining2016> *ends
tomorrow (Sunday).*

And in addition to the workshop in Melbourne, there is also this event in
Strasbourg, France in January:

  European Galaxy Developer Workshop
  https://www.france-bioinformatique.fr/evenements/EGDW2017

Registration opens next month.

Hope you'll be there, wherever there is for you.

Thanks,

Dave C


On Wed, Oct 12, 2016 at 4:55 PM, Dave Clements <cleme...@galaxyproject.org>
wrote:

> Hi All,
>
> On-time registration for the November Galaxy Admin Training in Salt Lake
> <https://wiki.galaxyproject.org/Events/AdminTraining2016> *ends this
> Sunday, October 16*.  After Sunday rates go up quite a bit.  There also a
> chance that the sessions will sell out before Sunday.
>
> So, if you are interested, now is a good time to register.
>
> If you are interested, but are based in Australia or Asia, take a look at
> the Galaxy Admin Training being offered in February in Melbourne
> <https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> as
> part of the Galaxy Australasia Meeting
> <https://www.embl-abr.org.au/game2017/>.  Registration is now open for
> that (and it's not yet close to filling up).
>
> Cheers,
>
> Dave C
>
> On Mon, Sep 12, 2016 at 9:43 AM, Dave Clements <cleme...@galaxyproject.org
> > wrote:
>
>> Hello all,
>>
>> *Early registration
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> for
>> Galaxy Admin Training 2016
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016> ends in one week,
>> on Monday, September 19.*
>>
>> Galaxy Admin Training 2016
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016> is a weeklong
>> event offering basic and advanced sessions. It will be held in Salt Lake
>> City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16)
>> <http://sc16.supercomputing.org/> meets in Salt Lake. These workshops
>> are aimed at admins from organizations and labs that are installing,
>> upgrading, or prototyping Galaxy instances.
>>
>>
>> *Basics Session: November 7-8*
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>
>>
>> This two day basics session
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>
>> will introduce participants to what you need to know to get a Galaxy server
>> up and running on a standalone server. You'll also learn how to extend your
>> Galaxy with your own tools and tools from the community, and how to define
>> reference data in your server.
>>
>>
>> *Advanced Session: November 9-11*
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession>
>>
>> The three day advanced session
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession>
>> will build on topics covered in the basics section
>> <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>.
>> This session both extends those topics, such as tool definition, and adds
>> new ones, such as working with compute clusters and heterogeneous
>> resources. The goal of the advanced workshop is to enable Galaxy
>> administrators to create robust, high-performance Galaxy instances that
>> take full advantage of available tools and compute and storage resources.
>>
>>
>> Galaxy Admin Training 2016 is hosted by the University of Utah Center
>> for High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, the USTAR
>> Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>, 
>> 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 <https://wiki.galaxyproject.org/GalaxyTeam>
>>
>>
>> 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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Re: [galaxy-dev] Galaxy Admin Training: November 7-11, Salt Lake City

[Dave Clements]

Hi All,

On-time registration for the November Galaxy Admin Training in Salt Lake
<https://wiki.galaxyproject.org/Events/AdminTraining2016> *ends this
Sunday, October 16*.  After Sunday rates go up quite a bit.  There also a
chance that the sessions will sell out before Sunday.

So, if you are interested, now is a good time to register.

If you are interested, but are based in Australia or Asia, take a look at
the Galaxy Admin Training being offered in February in Melbourne
<https://www.embl-abr.org.au/game2017/training-for-admin-workshop/> as part
of the Galaxy Australasia Meeting <https://www.embl-abr.org.au/game2017/>.
Registration is now open for that (and it's not yet close to filling up).

Cheers,

Dave C

On Mon, Sep 12, 2016 at 9:43 AM, Dave Clements <cleme...@galaxyproject.org>
wrote:

> Hello all,
>
> *Early registration
> <https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> for
> Galaxy Admin Training 2016
> <https://wiki.galaxyproject.org/Events/AdminTraining2016> ends in one week,
> on Monday, September 19.*
>
> Galaxy Admin Training 2016
> <https://wiki.galaxyproject.org/Events/AdminTraining2016> is a weeklong
> event offering basic and advanced sessions. It will be held in Salt Lake
> City, Utah, November 7-11, 2016, the week before Supercomputing 16 (SC16)
> <http://sc16.supercomputing.org/> meets in Salt Lake. These workshops are
> aimed at admins from organizations and labs that are installing, upgrading,
> or prototyping Galaxy instances.
>
>
> *Basics Session: November 7-8*
> <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>
>
> This two day basics session
> <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>
> will introduce participants to what you need to know to get a Galaxy server
> up and running on a standalone server. You'll also learn how to extend your
> Galaxy with your own tools and tools from the community, and how to define
> reference data in your server.
>
>
> *Advanced Session: November 9-11*
> <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession>
>
> The three day advanced session
> <https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession>
> will build on topics covered in the basics section
> <https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession>.
> This session both extends those topics, such as tool definition, and adds
> new ones, such as working with compute clusters and heterogeneous
> resources. The goal of the advanced workshop is to enable Galaxy
> administrators to create robust, high-performance Galaxy instances that
> take full advantage of available tools and compute and storage resources.
>
>
> Galaxy Admin Training 2016 is hosted by the University of Utah Center for
> High Performance Computing (CHPC) <http://www.chpc.utah.edu/>, the USTAR
> Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>, 
> 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 <https://wiki.galaxyproject.org/GalaxyTeam>
>
>
> 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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[galaxy-dev] Fwd: [mailinglist] Call for Submissions: Computer Demo Track at PAGXXV.

[Dave Clements]

Hi All,

Computer demo submissions for Plant and Animal Genome are due October 28.
See below for details.

Galaxy will again have a presence at PAG.  The two-hour Galaxy workshop on
Tuesday will likely focus on genome annotation, and several other proposals
are in the works.

PAG is in San Diego in January.

Hope to see you there,

Dave C


-- Forwarded message --
From: Monica Munoz-Torres 
Date: Fri, Oct 7, 2016 at 3:15 AM
Subject: [mailinglist] Call for Submissions: Computer Demo Track at PAGXXV.
To: mailingl...@biocurator.org
Cc: Monica Munoz-Torres , Brian Smith-White <
smtwh...@ncbi.nlm.nih.gov>


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 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 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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