gmod-announce — A moderated, low traffic list for announcements of meetings and software release

[Gmod-announce] Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University

[Dave C. <cle...@ga...>]

Hello all,

*The 2019 Galaxy Admin Training
<https://galaxyproject.org/events/2019-admin-training/> will be offered
January 28 through February 1 at Penn State University*. 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.

*Galaxy <https://galaxyproject.org/> is a widely deployed platform for data
integration and analysis in the life sciences.*  It is open source and be
deployed on lab servers, institutional computing resources, and public and
private clouds.  Having your own Galaxy server enables your researchers to
have a customized and collaborative analysis environment that enables then
to learn, perform, and share their own bioinformatics analysis.

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 $65 / day for participants from non-profits and
academia. Advance registration ends December 31. The 2016 and 2018 admin
training workshops were both full, so you are strongly encouraged to *register
now*.
Thanks,
Dave C.


-- 
https://galaxyproject.org/
https://usegalaxy.org/

[Gmod-announce] Call for GMOD/PAG abstracts

[Scott C. <sc...@sc...>]

Hi All,

It's that time of year again: if you would be interested in presenting in
the GMOD workshop at PAG in San Diego this January, please let me know.
You don't have to have a full blown abstract yet; a general idea of what
you'd like to talk about is fine.  If you know anybody who might be
interested but isn't on one of these lists, please feel free to forward
this to them.

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] 2019 Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University

[Dave C. <cle...@ga...>]

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*. 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 <https://galaxyproject.org/> is an open web based platform for
biomedical data integration and analysis. It is deployed at large and small
organizations around the world and used in a broad range of biomedical
research domains, and across the tree of life.  Galaxy has been an active
member of GMOD for over 10 years.

-- 
https://galaxyproject.org/
https://usegalaxy.org/

[Gmod-announce] Fwd: [isb-biocuration] Function @ISMB 2018: Abstract Deadline this week

[Scott C. <sc...@sc...>]

---------- Forwarded message ----------
From: Iddo Friedberg <id...@gm...>
Date: Mon, Apr 2, 2018 at 10:19 AM
Subject: [isb-biocuration] Function @ISMB 2018: Abstract Deadline this week
To: isb...@go...


Call for Abstracts: Function Special Interest Group at ISMB 2018

We call upon all researchers involved in the computational study of
macromolecular function to submit an abstract to the Function-SIG meeting.
Authors of selected abstracts will be invited to give a talk and/or present
a poster.
Travel fellowships will be available for qualifying graduate students and
postdoctoral trainees.

Time and place: Chicago, IL, USA  July 6, 2018
ISMB 2018 home page: https://www.iscb.org/ismb2018


Key Dates:

*Thursday April 5, 2018* Abstract Submission Deadline
*April 26, 2018*: Notification of Acceptance
*July 7, 2018*: Function SIG at ISMB/ECCB 2018


Abstract submission:

http://biofunctionprediction.org/content/submit-abstract



Sequence and structure genomics have generated a wealth of data, but
extracting meaningful information from genomic data is challenging. Both
the number and the diversity of discovered sequences are increasing. In
addition, there is a need for standardized annotation that could be
incorporated into functional annotation on a large scale. Finally, there is
a need to assess the quality of the function prediction algorithms and
software.

For these reasons and many more, automated protein function prediction is
of interest to computational biologists in academia and industry. The
Function-SIG meetings offer researchers and students in the field to meet
with like-minded colleagues, learn about the latest developments in the
field, and forge new collaborations. More on the Function SIG: http://biofu
nctionprediction.org/

We will also present the more results from the third round of the Critical
Assessment of Functional Annotation (CAFA3) and from the additional
CAFA3.14 (CAF-Pi). CAFA is an international computational challenge funded
by the NSF and BBSRC which aims to asses the accuracy of protein
function prediction
methods which is drawing dozens of participating groups worldwide. More on
CAFA: http://biofunctionprediction.org/cafa/



-- 
Iddo Friedberg
http://iddo-friedberg.net/contact.html
++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>>>++++.>
++++++..----.<<<<++++++++++++++++++++++++++++.-----------..>>>+.-----.
.>-.<<<<--.>>>++.>+++.<+++.----.-.<++++++++++++++++++.>+.>.<++.<<<+.>>
>>----.<--.>++++++.<<<<------------------------------------.

-- 
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For more options, visit https://groups.google.com/d/optout.



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] Call for Abstracts: GCCBOSC 2018

[Scott C. <sc...@sc...>]

*GCCBOSC 2018: A Bioinformatics Community Conference*
*Call for Abstracts *



* Dates*: June 25-30, 2018
* Location*: Reed College, Portland, OR
* GCCBOSC website*: https://gccbosc2018.sched.com/
* BOSC website: *https://www.open-bio.org/wiki/BOSC_2018
* Email BOSC organizers*: b <bo...@op...>os...@op...
* BOSC announcements mailing list*: http://lists.open-bio.
org/mailman/listinfo/bosc-announce
* Twitter*: @OBF_BOSC <https://twitter.com/OBF_BOSC>, #GCCBOSC


*Important Dates*

   - *Abstract submission
   <https://www.open-bio.org/wiki/BOSC_Abstract_Submission> deadline: March
   16, 2018*
   - Authors notified: April 10, 2018
   - Travel fellowship
   <https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md>
application
   deadline: April 15, 2017
   - GCCBOSC 2018 Training: June 25-26, 2018
   - GCCBOSC 2018 Talks: June 27-28
   - GCCBOSC CollaborationFest: June 29-30

*About BOSC*
Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has
provided a forum for developers and users to interact and share research
results and ideas in open source bioinformatics. BOSC’s broad spectrum of
topics includes practical techniques for solving bioinformatics problems;
software development practices; standards and ontologies; approaches that
promote open science and sharing of data, results and software; and ways to
grow open source communities while promoting diversity within them.

*Why is BOSC partnering with GCC in 2018?*
In past years, BOSC has been part of the ISMB conference. Because of our
continuing focus on broadening and deepening the BOSC community, we've been
exploring ways to reach those in the bioinformatics community who aren’t
already part of the audience attracted by ISMB. As part of that
exploration, we have looked at other organizations and conferences that
have been successful at establishing a strong and growing community of
participants, such as the Galaxy Community Conference (GCC).

After much discussion and planning, we decided to hold BOSC in conjunction
with GCC in 2018. We hope that this will be an enjoyable and productive
experience for all participants, and we welcome your feedback before,
during and after the event.

As always, BOSC 2018 will include two days of talks and posters, two keynote
speakers <https://galaxyproject.org/events/gccbosc2018/keynotes/>, a panel
discussion, Birds of a Feather, and more. BOSC sessions will run in
parallel with GCC 2018 sessions, with some sessions shared. The two days of
talks will be preceded by two days of training
<https://galaxyproject.org/events/gccbosc2018/training/> on topics
nominated by the community, and will be followed by a two-day
CollaborationFest that merges BOSC's Codefest and Galaxy's Developer and
User Hackathon Days.

*Abstract submission*
We encourage you to submit one-page abstracts (due March 16) on any topic
relevant to open source bioinformatics or open science. After review, some
abstracts will be selected for lightning talks, longer talks, demos and/or
posters. Abstract submission instructions and a link to the EasyChair
submission portal can be found on https://www.open-bio.org/
wiki/BOSC_Abstract_Submission

*BOSC session topics include* (but are not limited to):

   - Open Science and Reproducible Research
   - Open Biomedical Data
   - Citizen/Participatory Science
   - Standards and Interoperability
   - Data Science
   - Workflows
   - Visualization
   - Medical and Translational Bioinformatics
   - Developer Tools and Libraries
   - Bioinformatics Open Source Project Progress Reports

We look forward to receiving your abstract and meeting you at GCCBOSC 2018!

Sincerely,
      BOSC 2018 Organizing Committee: Nomi Harris (chair), Heather Wiencko
(co-chair), Brad Chapman (co-chair), Peter Cock, Christopher Fields,
Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Monica Munoz-Torres


P.S. Don't forget to submit your BOSC abstract by March 16 at
https://www.open-bio.org/wiki/BOSC_Abstract_Submission! Please share this
announcement with your colleagues!



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-announce] GMOD hackathon before PAG San Diego in January

[Scott C. <sc...@sc...>]

Hello,

This is an update on the hackathon.  It is a go; the hackathon page is up
on GMOD.org:

 http://gmod.org/wiki/2018_PAG_Hackathon

And the EventBrite page is up at

  https://www.eventbrite.com/e/gmod-2018-pag-hackathon-tickets-39700164260

Tickets are $50 which covers the costs associated with the room and lunch
on the first day.  Please feel free to add suggested topics to the wiki
page, or send the suggestions to me to add.

Thanks,
Scott


On Thursday, October 12, 2017, Scott Cain <sc...@sc...> wrote:

> Hi all,
>
> This January before PAG on the Wednesday and Thursday before PAG (January
> 10-11) in San Diego we are planning a GMOD hackathon.  We expect that
> participants will be interested in solving problems/creating solutions
> related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
> another GMOD project, by all means, let us know!  We expect this hackathon
> to overlap with the Tripal hackathon that is on January 11 (I'm pretty
> sure; right Stephen?)
>
> If you are interested in attending this hackathon, please let me know so I
> can be sure we have an appropriately sized space.  And if you're coming for
> the pre-PAG hackathon, consider staying for PAG, since there is always a
> lot of GMOD-related content at the meeting!
>
> Thanks,
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] European Galaxy Administrator Workshop, 8-12 January 2018, Oslo. FREE

[Dave C. <cle...@ga...>]

*We are pleased to announce that registration
<https://skjema.uio.no/galaxy-admin-workshop-2018> is now open for
the European Galaxy Administrator Workshop
<https://www.elixir-europe.org/events/european-galaxy-administrator-workshop>*
.

   - Mon 8 January 2018 to Fri 12 January 2018 CET
   - Python room, Blindern, UiO campus, Ole Johan Dahls hus
   <https://www.uio.no/english/about/getting-around/areas/gaustad/ga06/>,
   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
<https://github.com/elixir-no-nels/dagobah-training/blob/2018-oslo/README.md>
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
<https://www.elixir-europe.org/about/groups/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 <https://github.com/bgruening> (Elixir Galaxy WG
   <https://www.elixir-europe.org/about/groups/galaxy-wg>, Elixir Germany
   <https://www.elixir-europe.org/about-us/who-we-are/nodes/germany>,
University
   of Freiburg <https://www.uni-freiburg.de/?set_language=en>)
   - Marius van den Beek <https://github.com/mvdbeek> (Elixir Galaxy WG
   <https://www.elixir-europe.org/about/groups/galaxy-wg>, Institute Curie
   <https://science.institut-curie.org/>, France)
   - Nicola Soranzo <http://www.earlham.ac.uk/nicola-soranzo> (Elixir
   Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Earlham
   Institute <http://www.earlham.ac.uk/>, UK)
   - Enis Afgan <https://galaxyproject.org/people/enis-afgan/> (Galaxy
   Project <https://galaxyproject.org/>, Johns Hopkins University
   <https://jhu.edu/>, USA)
   - Abdulrahman Azab
   <http://www.usit.uio.no/om/organisasjon/itf/ft/ansatte/azab/index.html>
(Elixir
   Norway <https://www.elixir-europe.org/about-us/who-we-are/nodes/norway>,
   USIT <http://www.usit.uio.no/>, University of Oslo <http://www.uio.no/>,
   Norway)

*About Galaxy*

Galaxy <https://galaxyproject.org/> 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 a GMOD component. and 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
organizations around the world.


-- 
https://galaxyproject.org/
https://usegalaxy.org/

[Gmod-announce] Call for presentations at GMOD workshop at PAG

[Scott C. <sc...@sc...>]

Hi all,

This January in San Diego is the annual Plant and Animal Genomes (PAG)
meeting (http://www.intlpag.org).  As in previous PAGs, there will be
several opportunities to present content related to GMOD projects.  If you
are interested in attending PAG and giving a talk at the GMOD workshop on
Wednesday, January 17, please let me know.  Your talk can either be about
new developments/functionality in existing GMOD software, about how your
organization is using the suite of GMOD software to good effect, or about
technologies that you think the GMOD community would be interested in
hearing about.  Please email me directly with a title, an abstract or a
vague idea of what you'd like to talk about.

Also, if you'd really like to come but are having a hard time coming up
with travel funds, please let me know, I might be able to help you with
that too (up to a limit of one person anyway).

Cheers,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] GMOD hackathon before PAG San Diego in January

[Scott C. <sc...@sc...>]

Hi all,

This January before PAG on the Wednesday and Thursday before PAG (January
10-11) in San Diego we are planning a GMOD hackathon.  We expect that
participants will be interested in solving problems/creating solutions
related to Tripal, JBrowse, Apollo, and Galaxy but if you're interested in
another GMOD project, by all means, let us know!  We expect this hackathon
to overlap with the Tripal hackathon that is on January 11 (I'm pretty
sure; right Stephen?)

If you are interested in attending this hackathon, please let me know so I
can be sure we have an appropriately sized space.  And if you're coming for
the pre-PAG hackathon, consider staying for PAG, since there is always a
lot of GMOD-related content at the meeting!

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] Galaxy Community Conference: Register by 16 June

[Dave C. <cle...@ga...>]

Hello all,


A few GCC2017 <https://gcc2017.sciencesconf.org/> things since the previous
announcement:

1) The presentation schedule <https://gcc2017.sched.com/> has been posted.
(In particular, see

http://sched.co/B59G, http://sched.co/B5x9, http://sched.co/B57M)

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

(And some of these are GMOD related as well.)

3) Lightning talk <https://gcc2017.sciencesconf.org/page/submit> and
birds-of-a-feather
<https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m2lHGPLiqJU0Xkzw/viewform>
submission are still open

4) There is still limited space available for late poster and computer demo
submissions <https://gcc2017.sciencesconf.org/page/submit>

5) Register by 16 June <https://gcc2017.sciencesconf.org/page/registration>


This is the last announcement we'll post to the GMOD Lists. Please forward
it 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) <https://gcc2017.sciencesconf.org/>
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
<https://gcc2017.sched.com/overview/type/Conference>, all about
data-intensive biology and the tools that support it. GCC2017 also
features data
and coding hackathons <https://gcc2017.sciencesconf.org/page/hackathon>,
and two days of training <https://gcc2017.sched.com/overview/type/Training>
covering 16 different topics.  GCC2017 will be held at Le Corum Conference
Centre <http://www.montpellier-events.com/en/The-Corum/Presentation> in the
heart of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>,
just 10km from the Mediterranean.



Registration closes 16 June
<https://gcc2017.sciencesconf.org/page/registration>.  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
<https://gcc2017.sciencesconf.org/page/submit> and birds-of-a-feather
<https://docs.google.com/forms/d/e/1FAIpQLSdRCs97OWt47qmMxWZAtSV3TTLJ24IhW0m2lHGPLiqJU0Xkzw/viewform>
submission are still open, and there is limited space available for late
poster and computer demo submissions
<https://gcc2017.sciencesconf.org/page/submit>.



About Galaxy

Galaxy <https://galaxyproject.org/> 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

-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/

[Gmod-announce] Galaxy Community Conference (GCC2017) talk deadline extended

[Dave C. <cle...@ga...>]

*2017 Galaxy Community Conference (GCC2017)*
26-30 June 2017
Montpellier, France
https://gcc2017.sciencesconf.org/
--

*The deadline for submitting oral presentation abstracts for the 2017
Galaxy Community Conference <https://gcc2017.sciencesconf.org/> has been
extended to 29 April.* If you work in data intensive life science research
then GCC2017 is an ideal opportunity to present your work. Posters and
computer demonstration submission closes on 27 May and the lightning talk
submission deadline is 23 June.

The 2017 Galaxy Community Conference will bring together several hundred
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, come from around
the world, and represent universities, research organizations, industry,
medical schools and research hospitals.

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 <https://gcc2017.sciencesconf.org/page/hackathon>,
and two days of training
<https://gcc2017.sched.com/overview/type/Training> covering
16 different topics.  GCC2017 will be held at Le Corum Conference Centre
<http://www.montpellier-events.com/en/The-Corum/Presentation> in the heart
of Montpellier <https://gcc2017.sciencesconf.org/resource/page/id/2>, just
10km from the Mediterranean.

Early registration <https://gcc2017.sciencesconf.org/resource/page/id/6> is
now open and starts at less than 55€ / day for post-docs and students. You
can also book low cost conference housing when you register. Travel
fellowships are being offered by the Galaxy Community Fund for early career
researchers that are travelling from afar.

*About Galaxy*
Galaxy <https://galaxyproject.org/> 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 this summer in Montpellier!

Au revoir,

The GCC2017 Organising Committee

-- 
https://galaxyproject.org/
https://getgalaxy.org/
https://usegalaxy.org/
https://gcc2017.sciencesconf.org/

[Gmod-announce] Galaxy Community Conference (GCC2017), Montpellier, France, 26-30 June

[Dave C. <cle...@ga...>]

*2017 Galaxy Community Conference (GCC2017)*

26-30 June 2017

Montpellier, France

https://gcc2017.sciencesconf.org/

--


The 2017 Galaxy Community Conference <https://gcc2017.sciencesconf.org/>
will bring together several hundred 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, come from around the world, and represent
universities, research organizations, industry, medical schools and
research hospitals.


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 <https://gcc2017.sciencesconf.org/page/hackathon>,
and two days of training <https://gcc2017.sched.com/overview/type/Training>
covering 16 different topics.  GCC2017 will be held at Le Corum Conference
Centre <http://www.montpellier-events.com/en/The-Corum/Presentation>
in the heart
of Montpellier <https://gcc2017.sciencesconf.org/page/location>, just 10km
from the Mediterranean.


Abstract submission <https://gcc2017.sciencesconf.org/page/submit> is now
open.  If you work in or support data intensive life science research then
GCC2017 is an ideal opportunity to present your work. The deadline for oral
presentations is Apr 15 (23:59 Paris local time), and posters and computer
demonstration submission closes on May 27 (23:59 Paris local time). The
Lightning talk submission deadline is June 23 (23:59 Paris time).


Early registration <https://gcc2017.sciencesconf.org/page/registration> is
also open and starts at less than 55€ / day for post-docs and students. You
can also book low cost conference housing
<https://gcc2017.sciencesconf.org/page/lodging> when you register. Travel
fellowships
<https://new.galaxyproject.org/news/2017-03-gcc2017-fellowships/> are being
offered by the Galaxy Community Fund for early career researchers that are
travelling from afar.


About Galaxy

Galaxy <https://galaxyproject.org/> 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 this summer in Montpellier!


Au revoir,


The GCC2017 Organising Committee


PS: Please redistribute this announcement to any interested groups.

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] New Apollo Release 2.0.6(JB#29795a1bbb)

[Monica Munoz-T. <mcm...@lb...>]

*We announce our latest release: Apollo 2.0.6*


*Download our latest release*:
https://github.com/GMOD/Apollo/releases/latest


*New features include: *

   - Improved workflow for optional display of JBrowse native tracks.
   - Improved options to navigate to annotations listed in the *Annotations*
   tab.


*A couple of important bug fixes:  *

   - Fixes problems loading the list of available tracks (*Tracks *tab)
   when switching organisms, specially for slower connections.
   - Fixes naming for annotated genomic elements (other than protein coding
   genes) in the *User-created Annotations* area under various scenarios.


*Apollo for Docker, AMIs:*

   - Our* Docker release* has been updated and is available for download
   at: https://github.com/GMOD/docker-apollo/releases
   - *Amazon Machine Images* for Apollo 2.0.6 (Java 8, Tomcat 8, and Ubuntu
   16.04) are being updated and will be available on AWS in most regions next
   week.


*Thank you!*

We are very thankful to our community of users, admins, and developers who
contribute daily to the improvement of our genome annotation editing tool.

Contribute to this project by visiting our *GitHub tracker* or writing to
the *Mailing List*:

   - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
   - Post your questions on our mailing list at ap...@li...



*Learn More*

* *Detailed, searchable documentation:* pre-requisites, configuration, and
installation guides: http://genomearchitect.readthedocs.io/

* *Detailed account of all changes* available in the Apollo ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo
instances running, you can use your current JBrowse data directories. The
quick-start guide is available at: http://genomearchitect.rea
dthedocs.io/en/stable/Apollo2Build.html

* *Migrating existing annotations:* Please find detailed information about
migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html

** Troubleshooting* guide available at
http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html

** Apollo User Guide* is available at http://genomearchitect.org/use
rs-guide/

** Public Demo: If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo
Demo at http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>*

* More information available on the Apollo Website
<http://genomearchitect.org/> and the Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.


We look forward to hearing from you.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>


[image: Inline image 1]

It is very likely you will receive this message more than once; we offer
our sincere apologies for the redundancy.





-- 
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

[Gmod-announce] New Apollo Release 2.0.5(JB#9334e76fd)

[Monica Munoz-T. <mcm...@lb...>]

*We are pleased to announce the latest Apollo release*

*Apollo 2.0.5 *

*Some of the new features include:*

   - Numerous UI and performance improvements, including easier navigation
   between annotated elements via the Annotator Panel.
   - Better server and client-side reporting.
   - It is now possible to also include metadata on import.
   - Upgrade to Java 8 / GWT 2.8, and updated JBrowse.
   - Apollo 2.0.5 uses the latest JBrowse commit as of 2016-12-09 (
   #9334e76fd
   <https://github.com/GMOD/jbrowse/commit/9334e76fd7530681fa2dcc71d4440141e1414cfd>).
   Use ./apollo clean-all or install from a formal release download for best
   performance.


*Some important bug fixes:*

   - Import script were logging preferences unnecessarily.
   - Improved security for non-public genomes.
   - Fixed for going between logged-out mode and the Annotator Panel while
   retaining history.
   - Improved display of sequence over the annotation after moving the
   annotation to the opposite strand.
   - Users will see a warning message when it is not possible to create an
   intron with canonical splice sites in the selected region.


* The *latest release* can be downloaded from GitHub at:
https://github.com/GMOD/Apollo/releases/latest

* *Detailed, searchable documentation* on pre-requisites, configuration,
and installation guides found at:
http://genomearchitect.readthedocs.io/

* A more *detailed account of all changes* is available in the Apollo
ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

* *Quick-Start Guide for Apollo 2.0.x*: If you already have Apollo
instances running, you can use your current JBrowse data directories. The
quick-start guide is available at: http://genomearchitect.rea
dthedocs.io/en/stable/Apollo2Build.html

* *Migrating existing annotations:* Please find detailed information about
migrating existing installations and their annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html

** Troubleshooting, GitHub tracker, Mailing List: *

   - Browse the Troubleshooting guide at http://genomearchitect.readthe
   docs.io/en/stable/Troubleshooting.html
   <http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html>
   - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
   - Post your questions on our mailing list at ap...@li...

* *The Apollo User Guide* is available at http://genomearchitect.org/use
rs-guide/

** Public Demo: If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo
Demo at http://genomearchitect.org/demo/ <http://genomearchitect.org/demo/>*

* These and more details are available at the Apollo Website
<http://genomearchitect.org/> and the Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.


We look forward to your questions and suggestions.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>

[image: Inline image 1]

It is very likely you will receive this message more than once; we offer
our sincere apologies for the redundancy.
Bee photograph by www.AlexanderWild.com



-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

[Gmod-announce] Galaxy Australasia Meeting, 3-9 February, Melbourne. Abstracts due 30 Nov

[Dave C. <cle...@ga...>]

Hello all,

The 2017 Galaxy Australasia Meeting (GAMe 2017)
<http://www.embl-abr.org.au/game2017/> will be held 3-9 February in
Melbourne, Australia, and  bring together biomedical researchers,
bioinformaticians, infrastructure providers, and data producers from across
Australia and Asia.

GAMe 2017 spans a week and includes a two day conference
<http://www.embl-abr.org.au/game2017/conference>, one day of training for
researchers <https://www.embl-abr.org.au/game2017/training-day/>, and four
days of training for Galaxy administrators
<http://www.embl-abr.org.au/game2017/training-for-admin-workshop>.

The two day conference <http://www.embl-abr.org.au/game2017/conference>
starts 4th February with a BIO day – for Galaxy users (biologists and
bioinformaticians) – followed by an INFO day on 5th February, focussing on
technical aspects of Galaxy – for bioinformaticians, tool and software
developers, and research infrastructure providers. Both days feature
keynotes, accepted and sponsored talks, poster and sponsor sessions,
birds­-of-­a­-feather gatherings, and lots of opportunities for networking.

The conference is preceded by a Researcher Training Day on 3 February for
analysis-focussed biologists and biomedical researchers with limited
experience of Galaxy. A four day intensive Galaxy Admin Training session
for those installing and maintaining Galaxy servers follows the conference.

Talk abstracts <http://www.embl-abr.org.au/game2017/submit-your-talkposter/>
are due 30 November.  Early registration ends 31 December. Register now.
Space is limited.


*About Galaxy:*
Galaxy <https://galaxyproject.org/> is an open web based platform for
biomedical data integration and analysis. It is deployed at large and small
organizations around the world and used in a broad range of biomedical
research domains, and across the tree of life.  Galaxy enables life science
researchers to perform their own data analysis without having to learn
command line interfaces or Linux package management.  Galaxy transparently
records all analysis steps and eases workflow reuse and sharing.  Galaxy is
also a long standing and active member of GMOD.


Please let us know if you have any questions, and we hope to see you in
Melbourne!

The GAMe 2017 Organising Committee
<http://www.embl-abr.org.au/game2017/organisers/>

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] Last Call for GMOD talks at PAG

[Scott C. <sc...@sc...>]

Time is short!

If you want to attend PAG <http://www.intlpag.org/> and would like to
present on a topic that would be of interest to the GMOD community, please
send an abstract or at least a descriptive title to he...@gm.... Types of
talks typically include updates on GMOD software projects, usage stories
for successful sites, proposals for new GMOD projects and descriptions of
plugins for existing GMOD software projects like Tripal
<http://gmod.org/wiki/Tripal>, JBrowse <http://gmod.org/wiki/JBrowse> and
Galaxy <http://gmod.org/wiki/Galaxy>.

Please consider giving a talk and sharing your experience and ideas!
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] Bioinformatician opening at Phoenix Bioinformatics

[Tanya B. <tbe...@ph...>]

Phoenix Bioinformatics, the non-profit organization that runs The
Arabidopsis Information Resource (TAIR), is looking for a
Bioinformatician.  If you think you might be interested, know someone who
might be interested, or can pass this link along to your network, we'd
appreciate your help.

https://my.hirehive.io/phoenix-bioinformatics/jobs/25076/bioinformatician

Thanks very much,

Tanya

Tanya Berardini
TAIR Curator
www.arabidopsis.org

[Gmod-announce] Call for GMOD talks at PAG

[Scott C. <sc...@sc...>]

Hi,

I am pleased to announce a call for talks to be given at the Plant and
Animal Genomes conference this January in the GMOD workshop on Wednesday,
January 18th.  Any talks that involve the development or use of GMOD
software are welcome.  In particular this year, I'd really like to
highlight plugins for the various GMOD software packages that support them,
like JBrowse, Galaxy and Tripal (of course, Galaxy and Tripal have their
own sessions, so you should consider submitting to them too).

Please get an abstract, brief summary or a vague title to me as soon as
possible so I can start getting it put together.  Also, if you'd like to be
a co-organizer, please let me drop me a line about that too.  I might be
able to get you some meeting-related niceties for not very much work.

For more information about PAG, see:

  http://www.intlpag.org

Thanks and I look forward to seeing in January,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] GMOD & JBrowse user servey, 2016

[Scott C. <sc...@sc...>]

Hello Genome Informaticians,

The following survey is aimed at users (and potential users) of GMOD genome
databases, especially the JBrowse genome browser. It will directly inform
the priorities for renewal of the R01 that funds JBrowse software
development and the GMOD helpdesk.

We know surveys are thankless and dull. Your time in filling out this one
is GREATLY appreciated.

https://goo.gl/forms/1bKIuAMjGKrS0hUi1

Thanks & best wishes,
The JBrowse team


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-announce] Galaxy Admin Training: November 7-11, Salt Lake City, Utah

[Dave C. <cle...@ga...>]

The first Galaxy Admin Training workshop
<https://wiki.galaxyproject.org/Events/AdminTraining2016> will be held
November 7-11 in Salt Lake City, Utah (the week before Supercomputing’16
<http://sc16.supercomputing.org/> also meets in Salt Lake).  The workshop
offers Basic
<https://wiki.galaxyproject.org/Events/AdminTraining2016/BasicsSession> and
Advanced
<https://wiki.galaxyproject.org/Events/AdminTraining2016/AdvancedSession>
sessions.

Galaxy <https://galaxyproject.org/> is an open web based platform for
biomedical data integration and analysis. It is deployed at large and small
organizations around the world and used in a broad range of biomedical
research domains, and across the tree of life.  Galaxy enables life science
researchers to perform their own data analysis without having to learn
command line interfaces or Linux package management.  Galaxy transparently
records all analysis steps and eases workflow reuse and sharing.  If your
organization is looking for how to empower your researchers, then please
consider attending one or both sessions.


Participants will learn how to install, configure, customize, and extend
their own Galaxy servers. Topics include tool configuration, authentication
and user management, using heterogeneous storage and compute services, and
many other topics that will enable you to get your own Galaxy server up and
running, performing well, and used by your community.

Registration
<https://wiki.galaxyproject.org/Events/AdminTraining2016/Registration> is
now open, but space is limited.  *Early registration ends September 19*.
Participants can register for one or both sessions. Please review each
session’s prerequisites before registering.

Galaxy Admin Training 2016 is hosted by the University of Utah Center for
High Performance Computing (CHPC) <http://www.chpc.utah.edu/>,  USTAR
Center for Genetic Discovery (UCGD) <http://ucgd.genetics.utah.edu/>,
the Department
of Biomedical Informatics <http://medicine.utah.edu/dbmi/> and the Clinical
& Translational Science Biomedical Informatics Core (CCTS BMIC)
<http://medicine.utah.edu/ccts/bmic/> at the University of Utah
<http://utah.edu/>.

We hope to see you in Salt Lake!

The Galaxy Team

PS: Please share this flier
<https://wiki.galaxyproject.org/Events/AdminTraining2016/Publicity> with
any individuals or groups who might be interested in this event.

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] New Apollo Release 2.0.4 (JB1.12.2-apollo)

[Monica Munoz-T. <mcm...@lb...>]

*We are pleased to announce the latest Apollo release*
*Apollo 2.0.4*

*Some of the new features include: *

   - Users may download genomic sequences from highlighted regions.
   - Information from parent features can be retained when loading
   transcripts onto the 'User-created Annotations' area using the command
   line.
   - REMOTE_USER authentication and user authentication modules are now
   available.
   - Ability to enter pre-specified (canned) values for *Attributes* in the
   'Information Editor', similar to canned *Comments*.
   - Added documentation for using Apollo with Docker
   <https://github.com/GMOD/Apollo/blob/master/docs/Setup.md#configure-for-docker>
   .

*Some important fixes include: *

   - Fixed multiple errors in add_transcript_from_gff3_to_annotations.pl
   script
   - Fixed service timeout / disconnection silent error
   - Fixed several deployment installation issues


* The* latest release* can be downloaded from GitHub at:
*https://github.com/GMOD/Apollo/releases/latest
<https://github.com/GMOD/Apollo/releases/latest>*

** Detailed, searchable documentation* on pre-requisites, configuration,
and installation guides found at:
http://genomearchitect.readthedocs.io/
<http://genomearchitect.readthedocs.io/en/stable/>

*** A more *detailed account of all changes* is available in the Apollo
 ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

** Quick-Start Guide for Apollo 2.0.x:* If you already have Apollo instances
running, you can use your current JBrowse data directories. The quick-start
guide is available at:
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html

** Migrating existing annotations: *You will need to migrate existing
annotations from Web Apollo 1.0.x. Please find detailed information about
migrating annotations at http://genomearchitect.readthedocs.io/en/latest/
Migration.html

** Troubleshooting, GitHub tracker, Mailing List:*

   - Browse the Troubleshooting guide at
   http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
   - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
   - Post your questions on our mailing list at ap...@li...


** The Apollo User Guide* is available at http://genomearchitect.org/
users-guide/

** Public Demo:* If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo Demo
at http://genomearchitect.org/demo/

* *These and more details* are available at the Apollo Website
<http://genomearchitect.org/> and Apollo repository
<https://github.com/GMOD/Apollo/blob/master/README.md>.


We look forward to your questions and suggestions.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>

[image: Inline image 1]

It is very likely you will receive this message more than once. We offer
our sincere apologies for the redundancy.
Bee image CopyRight of www.AlexanderWild.com | DNA image from
ShutterStock.com





-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

[Gmod-announce] New Apollo Release 2.0.3 (JB1.12.2-apollo)

[Monica Munoz-T. <mcm...@lb...>]

*We are pleased to announce the latest Apollo release*
*Apollo 2.0.3*

*Some of the new features include: *

   - Ability to export Apollo annotations into a Chado database - and
   ability to update an existing Chado database.
   - Users now have the ability to change the type of genomic element they
   are annotating after it has been dragged to the User-created Annotations
   area (e.g. from '*gene*' to '*pseudogene*')
   - Users can now have multiple tabs open while simultaneously annotating
   genomic elements for 2 or more different organisms.
   - Usernames are no longer restricted to email addresses.
   - We have upgraded the JBrowse version to 1.12.2-apollo


*Some important fixes include: *

   - Users can now annotate genomic elements using evidence from Canvas
   tracks, using the 'right-click' menu options.
   - Comments are no longer restricted to only 256 characters.
   - The error caused from '*Undo*' operations on a pseudogene has been
   fixed.


* The* latest release* can be downloaded from GitHub at:
https://github.com/GMOD/Apollo/releases/

** Detailed, searchable documentation* on pre-requisites, configuration,
and installation guides found at:
http://genomearchitect.readthedocs.io/
<http://genomearchitect.readthedocs.io/en/stable/>

*** A more *detailed account of all changes* is available in the Apollo
 ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

** Quick-Start Guide for Apollo 2.0.x:* If you already have Apollo instances
running, you can use your current JBrowse data directories. The quick-start
guide is available at:
http://genomearchitect.readthedocs.io/en/stable/Apollo2Build.html

** Migrating existing annotations: *You will need to migrate existing
annotations from Web Apollo 1.0.x. Please find detailed information about
migrating annotations at
http://genomearchitect.readthedocs.io/en/latest/Migration.html

** Troubleshooting, GitHub tracker, Mailing List:*

   - Browse the Troubleshooting guide at
   http://genomearchitect.readthedocs.io/en/stable/Troubleshooting.html
   - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
   - Post your questions on our mailing list at ap...@li...


** The Apollo User Guide* is available at
http://genomearchitect.org/users-guide/

** Public Demo:* If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo Demo
at http://genomearchitect.org/demo/

* *These and more details* are available from the README file on the Apollo
 repository:
https://github.com/GMOD/Apollo/blob/master/README.md




We look forward to your questions and suggestions.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about/>


[image: Inline image 1]
It is very likely you will receive this message more than once. We offer
our sincere apologies for the redundancy.
Bee image CopyRight of www.AlexanderWild.com | DNA image from
ShutterStock.com

-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

[Gmod-announce] GMOD 2016 Meeting early reg ends May 21; Galaxy Conference Deadlines

[Dave C. <cle...@ga...>]

Hello all,

*GMOD will be holding a community meeting on June 30th and July 1st
<http://gmod.org/wiki/Jun_2016_GMOD_Meeting> in Bloomington, Indiana,
United States.*  GMOD Meetings <http://gmod.org/wiki/Meetings> are a mix of
user and developer presentations, and are a great place to find out what is
happening in the project, what's coming up, and what others are doing.

*Early bird registration <https://gmod2016.eventbrite.com/> ends May 21,
this Saturday.*

*For those who would like to present a talk or poster, the meeting
registration form includes a section for submitting the presentation title
and abstract.*

If you have any suggestions or requests for the meeting, please
contact the GMOD
help desk <he...@gm...>.


*GCC2016*

The GMOD Meeting is immediately after the 2016 Galaxy Community Conference
(GCC2016) <https://gcc2016.iu.edu/>, also in Bloomington (and sharing
housing and venue).  If you are interested in Galaxy, *GCC2016 has a number
of deadlines this Friday, May 20*.  See below.

Galaxy is a part of the GMOD project and there are several presentations at
GCC2016 that cover the GMOD integration:

   - Moving data from the warehouse to the workbench: a bridge to Galaxy
   from the Tripal community genome database software platform,
   <http://sched.co/743X> talk presented by Margaret Staton
   - Apollo: Collaborative Manual Annotation for Genomic Sequencing Projects
   <http://sched.co/743i>, talk presented by Nathan Dunn (Apollo will have
   a poster and demo)
   - Hardwood Genomics Database (HGD): a web portal and database resource
   for hardwood tree genomic and genetic research, poster presented by Ming
   Chen and Margaret Staton (posters are not online yet)

More posters and demos are in the works.

Thanks, and hope to see you in Bloomington,

Dave C


---------- Forwarded message ----------
From: Dave Clements <cle...@ga...>
Date: Mon, May 16, 2016 at 9:09 AM
Subject: GCC2016 Deadlines this Friday & Conference schedule
To: Galaxy Announcements List <gal...@li...>,
Galaxy Dev List <gal...@li...>


Hello all,

This is just a reminder that* there are some key deadlines this Friday, May
20:*

   - Early registration ends <https://gcc2016.iu.edu/registration/index.php>.
   After Friday registration rates go up by over 40%.
   - Poster abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due.

   - Demo abstracts <https://gcc2016.iu.edu/abstracts/index.php> are due.
   These are new this year and can complement a poster abstract or stand on
   their own.

If you are wondering what's happening at GCC2016, the training and
conference schedules <https://gcc16.sched.org/> are now online, featuring 21
accepted talks <https://gcc16.sched.org/overview/type/Conference> and 31
training sessions
<https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any>.

And, thanks to Jetstream <http://jetstream-cloud.org/> IU's newest National
Science Foundation-funded project (and in which Galaxy is a partner), and
the National Center for Genome Analysis Support <http://ncgas.org/> at IU
are sponsoring an opening reception on Monday evening <http://sched.co/72bN>
at the IU Cyberinfrastructure Building.  The first ever GCC opening
reception will feature local wine/beer, morsels from local eateries, and
demonstrations of the 15 million+ pixel IQ-Wall, IU's Data Center, Science
on a Sphere, and other IU-centric IT.

Hope to see you there,

Dave C

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] 2016 Galaxy Community Conference: June 25-29, Bloomington, Indiana

[Dave C. <cle...@ga...>]

Hello all,

Here's the official email announcement for the 2016 Galaxy Community
Conference. Please redistribute within your communities, *and also note
that it is immediately before and co-located with the June 2016 GMOD
Meeting
<https://www.eventbrite.com/e/gmod-2016-community-meeting-tickets-22224544210>.*


We hope to see you in Bloomington at both events!


Dave C, on behalf of the GCC2016 Exec

------

*2016 Galaxy Community Conference (GCC2016)*

    *gcc2016.iu.edu <http://gcc2016.iu.edu/>*

    June 25 - 29, 2016

    *Indiana University*

    Bloomington, Indiana

    United States


------


The *2016 Galaxy Community Conference *(*GCC2016*, *gcc2016.iu.edu
<http://gcc2016.iu.edu/>*) 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*. Keynote speakerYoav Gilad
<http://genes.uchicago.edu/directory/yoav-gilad-phd/>, a professor of human
genetics at the University of Chicago, will kick-start the main conference
with a discussion on the analysis of large gene regulatory data sets.
Preconference events include data
<https://gcc2016.iu.edu/hacks/hacks-data.php> and coding
<https://gcc2016.iu.edu/hacks/hacks-coding.php> hackathons
<https://gcc2016.iu.edu/hacks/index.php>, and *two days of training*
<https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> in five
concurrent tracks covering 26 topics.



*GCC2016* will be held at *Indiana University* in Bloomington, Indiana,
June 25-29, 2016.  Since it started seven years ago, GCC has been a
well-attended gathering of biologists, genome researchers,
bioinformaticians, and others in data-intensive biomedical research around
the world.



Galaxy <https://galaxyproject.org/> is an open, web-based platform for
data-intensive biomedical research and enables easy interactive analysis
through the web on arbitrarily large data sets. The Galaxy framework is a
major resource in achieving key research goals within the biological field.
It provides next-generation sequencing (NGS) tools and workflows for
short-read mapping, ChIP-seq, RNA-seq, metagenomics, variant analysis,
visualization, and support for Galaxy in the cloud. There are hundreds of
local installs, and *over 80 publicly accessible servers* around the world.



*Abstract submission** for oral presentations closes March 25. *Abstract
submission for posters and computer demonstrations closes May 20.


*Early registration* is now open. Registration starts at less than $45/day
for post-docs and students. Registering early assures you a place at the
conference and also a spot in the training workshops
<https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> you want to
attend. You can also *book conference housing* when you register. *Registration
and lodging scholarships* are available for attendees from underrepresented
groups and developing countries.


Thanks, and we hope to see you in Bloomington!


The *GCC2016 Exec*

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] New Apollo Release 2.0.2 (JB1.11.6)

[Monica Munoz-T. <mcm...@lb...>]

*We are pleased to announce the latest release for Apollo. *
*Apollo 2.0.2*

*Some of the new features include:*

   - Numerous performance and user interface improvements
   - Expanded web services documentation and examples

*Some important bug fixes:*

   - Fixed bug having to do with navigating history with split and merged
   transcripts
   - Fixed performance and migration errors with MySQL
   - Added back alternate translation table support


* The* latest release* can be downloaded from GitHub at:
https://github.com/GMOD/Apollo/releases/

** Detailed, searchable documentation* on pre-requisites, configuration,
and installation guides found at:
http://webapollo.readthedocs.org

*** A *detailed account of all changes* is available in the Apollo
ChangeLog:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

** Quick-Start Guide for Apollo 2.0.x:* If you already have Apollo
instances running, you can use your current JBrowse data directories. The
quick-start guide is available at:
http://webapollo.readthedocs.org/en/latest/Apollo2Build.html

** Migrating existing annotations: *You will need to migrate existing
annotations from Web Apollo 1.0.x. Please find detailed information about
migrating annotations at
http://webapollo.readthedocs.org/en/latest/Migration.html.

** Troubleshooting, GitHub tracker, Mailing List:*

   - Browse the Troubleshooting guide at
   http://webapollo.readthedocs.org/en/latest/Troubleshooting.html
   - Open a GitHub issue at https://github.com/GMOD/Apollo/issues/
   - Post your questions on our mailing list at ap...@li...


** The Apollo User Guide* is available at
http://genomearchitect.org/web_apollo_user_guide

** Public Demo:* If you are new to Apollo we encourage you to learn more
about our software and its functionality by taking a tour of our Apollo
Demo at http://genomearchitect.org/WebApolloDemo.

* *These and more details* are available from the README file on the Apollo
repository:
https://github.com/GMOD/Apollo/blob/master/README.md




We look forward to receiving your questions and suggestions.

Sincerely,
The Apollo Development Team <http://genomearchitect.org/about-us>
<http://genomearchitect.org/about-us>


[image: Inline image 1]
It is very likely you will receive this message more than once. We offer
our sincere apologies for the redundancy.
p.s: Bee image CopyRight of www.AlexanderWild.com | DNA image from
ShutterStock.com








-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720