Dear list,
Just found out that conda is not installing on our CentOS6.8
installation (might be related to earlier messages).
The problem is that the shell script installing conda unsets the
LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the
installer).
The command line that is executed during galaxy's installation is
wget -q --recursive -O '/tmp/conda_install7tWo7r.sh'
'https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh'
&& bash '/tmp/conda_install7tWo7r.sh' -b -p
'/gpfs1/data/galaxy_server/galaxy-dev/_conda' &&
/gpfs1/data/galaxy_server/galaxy-dev/_conda/bin/conda install -y -q
conda=4.2.13
Removing the unset LD_LIBRARY_PATH line (and fiddling around with some
file size checks) is (seemingly) successful.
There is an open issue on the conda github:
https://github.com/conda/conda/issues/3632
Any suggestions? The line removal procedure seems to be quite
complicated in an automated ansible installation which I try to achieve.
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
Hello all,
The deadline for submitting oral presentation abstracts for the 2017 Galaxy
Community Conference <https://gcc2017.sciencesconf.org/> has been extended
to 29 April.
And a reminder of some other GCC2017 <https://gcc2017.sciencesconf.org/>
deadlines:
15 May: Early registration
<https://gcc2017.sciencesconf.org/page/registration> ends
27 May: Poster presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> are due.
27 May: Visualization and Computer Demo presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> are due.
31 May: Regular registration
<https://gcc2017.sciencesconf.org/page/registration> ends
23 June: Lightning Talk presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> 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 <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. 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 <https://gcc2017.sciencesconf.org/page/registration> is
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.
GCC2017 has sold out *all* premiere *sponsorship*
<https://gcc2017.sciencesconf.org/page/sponsors> 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 <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
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/
Hello all,
I have updated the NCBI BLAST+ wrappers on the Test Tool Shed,
the wrapper is now at v0.2.00:
https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
The main changes is this now depends on BLAST+ 2.5.0, and that is
available via either BioConda or the Tool Shed:
https://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/
In order for the dependency to work smoothly on both BioConda
and the Tool Shed system, we have changed the package name
from "blast+" to just "blast". Given the NCBI stopped updated the
original "legacy" BLAST some time ago, when combined with the
version number this is no longer ambiguous.
Jumping from using BLAST+ 2.2.31 to using BLAST+ 2.5.0
required updating lots of the test files for NCBI changes, including
dropping the GI numbers in many outputs, expanding the percentage
identity field from 2dp to 3dp, and also changing how -parse_deflines
works with tabular output.
The wrappers (deliberately) do not yet offer any new functionality
added in the recent NCBI BLAST+ updates, in particular BLAST
XML v2 is not yet available as an output with a datatype in Galaxy.
At this point I would welcome feedback from those of you using the
BLAST+ wrappers - including if you were able to install this with the
dependencies from BioConda or the traditional Tool Shed packages.
Once I'm confident that this is all OK, I will update the main Tool Shed
(and think about adding new functionality in 2017).
Thank you all,
Peter
Dear list,
Currently I get SSL certificate errors when I try to install a tool in
Galaxy. I also get the same error when I try to use the galaxy-tools
ansible role (when debugging this I thought this might be because my
local server is on http, since the error appeared seemingly when a
message was posted to the local server -- but I'm not entirely sure).
I'm also missing the "Manage installed tools" link in the admin area
(but maybe this is expected in a fresh install?).
Thanks a lot.
Best,
Matthias
This is the stack trace when I try to install through the web frontend:
141.65.27.89 - - [18/Apr/2017:14:58:19 +0000] "GET
/admin_toolshed/prepare_for_install?changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0)
Gecko/20100101 Firefox/52.0"
Error - <class 'urllib2.URLError'>: <urlopen error [SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:661)>
URL:
http://bioinf2-dev:8080/admin_toolshed/prepare_for_install?changeset_revisi…
File
'/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/middleware/error.py',
line 154 in __call__
app_iter = self.application(environ, sr_checker)
File
'/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/recursive.py',
line 85 in __call__
return self.application(environ, start_response)
File
'/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
line 640 in __call__
return self.application(environ, start_response)
File
'/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py',
line 134 in __call__
return self.handle_request( environ, start_response )
File
'/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/base.py',
line 193 in handle_request
body = method( trans, **kwargs )
File
'/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py',
line 98 in decorator
return func( self, trans, *args, **kwargs )
File
'/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 1035 in prepare_for_install
raw_text = util.url_get( tool_shed_url,
password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ),
pathspec=pathspec, params=params )
File '/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py',
line 1488 in url_get
response = urlopener.open( full_url )
File
'/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py',
line 429 in open
response = self._open(req, data)
File
'/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py',
line 447 in _open
'_open', req)
File
'/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py',
line 407 in _call_chain
result = func(*args)
File
'/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py',
line 1241 in https_open
context=self._context)
File
'/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urllib2.py',
line 1198 in do_open
raise URLError(err)
URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed (_ssl.c:661)>
CGI Variables
-------------
CONTENT_LENGTH: '0'
HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING: 'gzip, deflate'
HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
HTTP_CONNECTION: 'keep-alive'
HTTP_COOKIE:
'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'
HTTP_DNT: '1'
HTTP_HOST: 'bioinf2-dev:8080'
HTTP_UPGRADE_INSECURE_REQUESTS: '1'
HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:52.0)
Gecko/20100101 Firefox/52.0'
PATH_INFO: '/admin_toolshed/prepare_for_install'
QUERY_STRING:
'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F'
REMOTE_ADDR: '141.65.27.89'
REQUEST_METHOD: 'GET'
SERVER_NAME: '0.0.0.0'
SERVER_PORT: '8080'
SERVER_PROTOCOL: 'HTTP/1.1'
WSGI Variables
--------------
application: <paste.recursive.RecursiveMiddleware object at
0x7f2dd8bb5190>
controller_action_key: u'web.admin_toolshed.prepare_for_install'
is_api_request: False
paste.cookies: (<SimpleCookie:
galaxysession='5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa'>,
'galaxysession=5d9fe20b2f75201eeee9486487f5942375617bcc89a7da2cc7e5bd9aff8a0eb130e333f3419e10fa')
paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
object at 0x7f2dd8bb5110>
paste.httpserver.proxy.host: 'dummy'
paste.httpserver.proxy.scheme: 'http'
paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
0x7f2dd875fe10>
paste.parsed_querystring: ([('changeset_revisions', '9ba8ebb636f4'),
('repository_ids', 'd5dd1c5d2070513e'), ('tool_shed_url',
'https://toolshed.g2.bx.psu.edu/')],
'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F')
paste.recursive.forward: <paste.recursive.Forwarder from />
paste.recursive.include: <paste.recursive.Includer from />
paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
from />
paste.recursive.script_name: ''
paste.throw_errors: True
request_id: '7599ea98244711e7941208002755efa5'
webob._parsed_query_vars: (GET([(u'changeset_revisions',
u'9ba8ebb636f4'), (u'repository_ids', u'd5dd1c5d2070513e'),
(u'tool_shed_url', u'https://toolshed.g2.bx.psu.edu/')]),
'changeset_revisions=9ba8ebb636f4&repository_ids=d5dd1c5d2070513e&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F')
wsgi process: 'Multithreaded'
------------------------------------------------------------
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
Hello all,
This is just a reminder of some *GCC2017
<https://gcc2017.sciencesconf.org/>* deadlines:
15 April: Oral presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> are due* this Saturday *at 23:59
Paris local time*.*
15 May: Early registration
<https://gcc2017.sciencesconf.org/page/registration> ends
27 May: Poster presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> are due.
27 May: Visualization and Computer Demo presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> are due.
31 May: Regular registration
<https://gcc2017.sciencesconf.org/page/registration> ends
23 June: Lightning Talk presentation abstracts
<https://gcc2017.sciencesconf.org/page/submit> 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 <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. 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 <https://gcc2017.sciencesconf.org/page/registration> is
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.
GCC2017 has sold out *all* premiere *sponsorship*
<https://gcc2017.sciencesconf.org/page/sponsors> 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 <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
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/
Dear list,
I'm struggling to get jobs running on our cluster (UGE).
In the galaxy log I see:
galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) submitting
file
/gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh
galaxy.jobs.runners.drmaa DEBUG 2017-04-13 12:24:57,799 (10) native
specification is: -l h_rt=60 -l h_vmem=1G -pe smp 2
and I get
galaxy.jobs.runners.drmaa WARNING 2017-04-13 12:24:57,805 (10)
drmaa.Session.runJob() failed, will retry: code 17: error: no suitable
queues
But manual submission works:
qsub -l h_rt=60 -l h_vmem=1G -pe smp 2
/gpfs1/data/galaxy_server/galaxy-dev/database/jobs_directory/000/10/galaxy_10.sh
Your job 161150 ("galaxy_10.sh") has been submitted
So I checked if I can use the drmaa library to submit using the
following python script (based on the example2 included in the library):
"""
#!/usr/bin/env python
from __future__ import print_function
import drmaa
import os
def main():
"""Submit a job.
Note, need file called sleeper.sh in current directory.
"""
s = drmaa.Session()
s.initialize()
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = os.getcwd() + '/sleeper.sh'
jt.args = ['42','Simon says:']
jt.joinFiles=True
jt.nativeSpecification = "-l h_rt=60 -l h_vmem=1G -pe smp 2"
jobid = s.runJob(jt)
print('Your job has been submitted with id ' + jobid)
print('Cleaning up')
s.deleteJobTemplate(jt)
s.exit()
if __name__=='__main__':
main()
"""
This gives me the same error:
drmaa.errors.DeniedByDrmException: code 17: error: no suitable queues
So it seems to be a problem related to the drmaa python library.
Unfortunately I can not try without any native specs, since time, memory
and cores need to be specifies (a suitable queue is chosen automatically).
I found an earlier post with the same error (but this seemed to be
caused by colons in the file name):
http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead…
Does anyone has suggestions for me?
Best regards,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
Hi,
is it possible to implement some kind of login for the usage reports
webapp, so that only admins can see the website? In our current setup
the tool is running on a server with many other users so that anyone who
knows the port can open the website and see potentially sensitive data.
Best regards,
Timo
--
------------------------------------------------------------------------
Timo Janßen
Wissenschaftliche Hilfskraft
Arbeitsgruppe "Anwendungs- und Informationssysteme"
Tel.: +49(0)551/201-1791
E-Mail: timo.janssen(a)gwdg.de
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de
Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
------------------------------------------------------------------------
Dear galaxy-dev list,
The documentation
(https://galaxyproject.org/admin/config/performance/cluster/) mentions
that sudo permissions for /usr/bin/chown are required in order to run
jobs as a real user. This causes quite some headache to our system
admins (understandably).
I tried (unsuccessfully) to dig a bit in the sources to find the
place(s) where sudo chown is called (the idea was to create a small
wrapper which might get sudo permissions).
But I found that there is already scripts/external_chown_script.py
(which is also referred in galaxy.ini). Is it sufficient to make this
script sudo callable? Or where could I invoke a wrapper for sudo chown
in the galaxy code?
Thanks a lot.
Best regards,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
Dear all,
Recent BOSC meetings have had a strong Galaxy presence, so please do
consider submitting an abstract and/or attending BOSC 2017 in Prague.
Thank you,
Peter
Dr. Peter Cock,
Bioinformatician at The James Hutton Institute;
Open Bioinformatics Foundation, board of directors, treasurer;
BOSC 2017 organising committee member.
---------- Forwarded message ----------
From: Nomi Harris <nlharris(a)gmail.com>
Date: Mon, Mar 6, 2017 at 6:50 PM
Subject: [Bosc] BOSC 2017: Call for Abstracts
To: bosc-announce(a)mailman.open-bio.org, bosc-reviewers(a)open-bio.org
Cc: Nomi Harris <nlharris(a)gmail.com>, BOSC 2017 Organizing Committee <
bosc(a)open-bio.org>
*Call for Abstracts for the 18th Annual Bioinformatics Open Source
Conference (BOSC 2017)*
An ISMB/ECCB Community of Special Interest (COSI)
Dates: July 22-23, 2017
Location: Prague, Czech Republic
Web site: http://www.open-bio.org/wiki/BOSC_2017
Email: bosc(a)open-bio.org
BOSC announcements mailing list: http://lists.open-bio.
org/mailman/listinfo/bosc-announce
Twitter: @OBF_BOSC
*Important Dates*
- Call for one-page abstracts
<https://www.open-bio.org/wiki/BOSC_Abstract_Submission> opens: March 6,
2017
- Abstract submission
<https://www.open-bio.org/wiki/BOSC_Abstract_Submission> deadline: April
13, 2017
- Travel fellowship
<https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md>
application
deadline: April 15, 2017
- Authors notified: May 10, 2017
- Codefest 2017 <https://www.open-bio.org/wiki/Codefest_2017>: July
21-22, Prague
- BOSC 2017 <https://www.open-bio.org/wiki/BOSC_2017>: July 22-23,
Prague (days 1 and 2 of ISMB/ECCB)
- ISMB/ECCB 2017 <https://www.iscb.org/ismbeccb2017>: July 21-25, Prague
*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.
In the past, BOSC has taken place the two days before ISMB as a Special
Interest Group (SIG). This year, ISMB is trying a new structure: the SIGs
(now called COSIs) are integrated into the main ISMB meeting. BOSC will
take place the first two full days of ISMB (July 22-23). Attendees will
have the option to register for the full ISMB/ECCB meeting (July 21-25) or
for just two days (there is no single-day registration option this year). A
limited number of partial travel fellowships will be granted to some
accepted speakers who would not otherwise be able to attend BOSC--please
see https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md for
more information.
We encourage you to submit one-page abstracts on any topic of relevance to
open source bioinformatics and open science. After review, some abstracts
will be selected for lightning talks, longer talks, and/or posters.
Abstract submission instructions and a link to the EasyChair portal can be
found on https://www.open-bio.org/wiki/BOSC_Abstract_Submission
*Session topics include:*
- 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
*Sponsorship*
We gratefully accept sponsorships from relevant private companies. These
sponsorships enable us to offer free registration to some BOSC speakers to
help increase diversity at our meeting. Sponsors in 2016 included
Curoverse, the company behind the open source platform Arvados. Please
contact us if you are interested in being a sponsor of BOSC 2017!
Thank you,
BOSC 2017 Organizing Committee: Nomi Harris (chair), Brad Chapman,
Peter Cock, Christopher Fields, Bastian Greshake, Karsten Hokamp, Hilmar
Lapp, Mónica Muñoz-Torres, Heather Wiencko
P.S. Don't forget to submit your BOSC abstract by April 13 at
https://www.open-bio.org/wiki/BOSC_Abstract_Submission!
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