gmod-devel — GMOD developer's mailing list

Re: [GMOD-devel] [Gmod-tripal] Migrating gmod.org advice/RFC

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

Hi Nathan,

I was only vaguely aware of Jekyll and thanks for the extra information.  I
know a lot of projects use Jekyll in combination with GitHub so that is
certainly well-trod territory.

But I would like to, um emphasize that moving from MediaWiki is very
different from moving from MoinMoin.  MoinMoin does not support inline HTML
and this greatly reduced the number of instances where we had to deal with
what are corner cases for GFM.  GMOD.org is chock full of inline HTML and I
think the translation effort would collapse under the diversity of hacks.

My (discounted!) 2¢,

Dave C

On Thu, Sep 1, 2016 at 10:43 AM, Nathan Dunn <nat...@lb...> wrote:

>
> Dave,
>
> I wasn’t advocating using only GitHub Flavored Markdown (GFM), all of
> which I agree with your points on.
>
> GH Pages (https://pages.github.com/) can either use straight HTML or use
> Jekyll (https://jekyllrb.com/ it is basically metalsmith.io on Ruby ),
> which can use either GFM or HTML, which provides a pretty rich UI and
> multiple integrations (http://www.jekyll-plugins.com/) and still allows
> direct editing of content within GitHub.
>
>
>
> Any who, I agree that the easiest option is to grab an AWS instance off of
> the Amazon Market Place to save yourself some time and the cost should be <
> $1K year, as I think you’ll likely lose several days on doing any sort of
> conversion.
>
> https://aws.amazon.com/marketplace/pp/B0078U8W14
>
> Nathan
>
> On Sep 1, 2016, at 10:24 AM, Dave Clements <cle...@ga...>
> wrote:
>
> Hi Scott,
>
> We are in the process of migrating the Galaxy Wiki from MoinMoin to a
> GitHub hosted pseudo-wiki (still looking for a good term). The content will
> be in GitHub Flavored Markdown (GFM) plus YAML for metadata and structured
> content.  We'll then use MetalSmith (http://www.metalsmith.io/) to
> generate the actual web site, and it's MetalSmith that will process the
> YAML.
>
> Editors will be able to edit local copies of the doc and generate the
> website locally, as well as edit doc directly in GitHub.  This model will
> fully leverage the power of GitHub.
>
> Moving GMOD.org <http://gmod.org> to straight github would also leverage
> that power and community involvement.
>
> *However, I think this would be tremendously difficult,* and the
> advantages of moving from MediaWiki to GitHub are far less than moving from
> MoinMoin to GitHub.
>
> 1) MediaWiki supports a ton of extensions such as Templates, Categories,
> and Extensions.  GFM does not support any of that.  A lot of content on
> GMOD.org <http://gmod.org> would have to be disentangled.
>
> 2) GFM is deliberately crippled.  The theory (I think) is that you should
> be using CSS for formatting instead of markup.  I like that goal, but the
> current GMOD.org <http://gmod.org> is chock full of MediaWiki / HTML
> hacks to achieve formatting (I put a lot of it there). Translating that to
> pure GFM / CSS would be a nightmare.
>
> GFM does support directly using HTML, but it does not support mixing the
> two in many circumstances.  For example, tables are all GFM or all HTML.
> And GFM tables are painfully limited. Only the simplest tables can be
> translated to GFM.  If you want row headers, or colspans or rowspans, or
> right or center alignment in a cell, or ... you have to translate the whole
> table to HTML.  And that defeats the whole purpose of having a wiki.
>
> *So, my vote is stick with MediaWiki.*  I don't think there is any hope
> of migrating to GFM without seriously mangling 90%+ of the pages.
>
> I've CC'd Dannon Baker who is also working the Galaxy Wiki move. He's not
> familiar with the current GMOD.org <http://gmod.org> implementation, but
> he knows about migrating wikis to GitHub.  He may have more to add (and
> might even contradict me :-).
>
> And, we've been running our wiki on AWS for years.  We've been very happy
> with it.
>
> My 98¢
>
> Dave C
>
>
> On Thu, Sep 1, 2016 at 8:58 AM, Nathan Dunn <nat...@lb...> wrote:
>
>>
>> Scott,
>>
>> I would advocate moving to GH pages just for the long-term ease of use,
>> permission management, and cost.   There is no server to setup, but you’ll
>> have to configure a Jekyll theme (http://jekyllthemes.org/) and add the
>> content, which is a PITA unless you create a single-page app (which I don’t
>> advocate).
>>
>> My guess is that actually converting the content will be easier (and I’m
>> sure folks in the community will be glad to help).
>>
>> https://github.com/philipashlock/mediawiki-to-markdown
>>
>>
>> Nathan
>>
>> On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...> wrote:
>>
>> Hi all,
>>
>> I'm addressing this to a few of the more heavily trafficked GMOD mailing
>> lists in hopes of getting some good advice.  The server that runs
>> gmod.org is being retired at the end of the month, so I have to find it
>> a new home.  One option includes leaving it at OICR on a new virtual
>> machine, but it will require me to port the existing MediaWiki instance,
>> which I already know won't be fun.
>>
>> There are other alternatives though--it was suggested recently that the
>> content in gmod.org could be migrated to GitHub pages, which sounds
>> appealing but I have no idea how much work would be involved.  I've also
>> considered migrating to AWS, which I think will be a similar amount of work
>> as the internal migration at OICR but would likely be cheaper in the long
>> run.
>>
>> Thanks in advance for any insights!
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> ------------------------------------------------------------
>> ------------------
>> _______________________________________________
>> Gmod-tripal mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>>
>
>
> --
> 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/

Re: [GMOD-devel] [Gmod-tripal] Migrating gmod.org advice/RFC

[Nathan D. <nat...@lb...>]

Dave, 

I wasn’t advocating using only GitHub Flavored Markdown (GFM), all of which I agree with your points on.  

GH Pages (https://pages.github.com/ <https://pages.github.com/>) can either use straight HTML or use Jekyll (https://jekyllrb.com/ <https://jekyllrb.com/> it is basically metalsmith.io on Ruby ), which can use either GFM or HTML, which provides a pretty rich UI and multiple integrations (http://www.jekyll-plugins.com/ <http://www.jekyll-plugins.com/>) and still allows direct editing of content within GitHub. 



Any who, I agree that the easiest option is to grab an AWS instance off of the Amazon Market Place to save yourself some time and the cost should be < $1K year, as I think you’ll likely lose several days on doing any sort of conversion. 

https://aws.amazon.com/marketplace/pp/B0078U8W14 <https://aws.amazon.com/marketplace/pp/B0078U8W14>

Nathan

> On Sep 1, 2016, at 10:24 AM, Dave Clements <cle...@ga...> wrote:
> 
> Hi Scott,
> 
> We are in the process of migrating the Galaxy Wiki from MoinMoin to a GitHub hosted pseudo-wiki (still looking for a good term). The content will be in GitHub Flavored Markdown (GFM) plus YAML for metadata and structured content.  We'll then use MetalSmith (http://www.metalsmith.io/ <http://www.metalsmith.io/>) to generate the actual web site, and it's MetalSmith that will process the YAML.
> 
> Editors will be able to edit local copies of the doc and generate the website locally, as well as edit doc directly in GitHub.  This model will fully leverage the power of GitHub.
> 
> Moving GMOD.org to straight github would also leverage that power and community involvement.
> 
> However, I think this would be tremendously difficult, and the advantages of moving from MediaWiki to GitHub are far less than moving from MoinMoin to GitHub.
> 
> 1) MediaWiki supports a ton of extensions such as Templates, Categories, and Extensions.  GFM does not support any of that.  A lot of content on GMOD.org would have to be disentangled.
> 
> 2) GFM is deliberately crippled.  The theory (I think) is that you should be using CSS for formatting instead of markup.  I like that goal, but the current GMOD.org is chock full of MediaWiki / HTML hacks to achieve formatting (I put a lot of it there). Translating that to pure GFM / CSS would be a nightmare.  
> 
> GFM does support directly using HTML, but it does not support mixing the two in many circumstances.  For example, tables are all GFM or all HTML.  And GFM tables are painfully limited. Only the simplest tables can be translated to GFM.  If you want row headers, or colspans or rowspans, or right or center alignment in a cell, or ... you have to translate the whole table to HTML.  And that defeats the whole purpose of having a wiki.
> 
> So, my vote is stick with MediaWiki.  I don't think there is any hope of migrating to GFM without seriously mangling 90%+ of the pages.
> 
> I've CC'd Dannon Baker who is also working the Galaxy Wiki move. He's not familiar with the current GMOD.org implementation, but he knows about migrating wikis to GitHub.  He may have more to add (and might even contradict me :-). 
> 
> And, we've been running our wiki on AWS for years.  We've been very happy with it.
> 
> My 98¢
> 
> Dave C
> 
> 
> On Thu, Sep 1, 2016 at 8:58 AM, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> Scott,
> 
> I would advocate moving to GH pages just for the long-term ease of use, permission management, and cost.   There is no server to setup, but you’ll have to configure a Jekyll theme (http://jekyllthemes.org/ <http://jekyllthemes.org/>) and add the content, which is a PITA unless you create a single-page app (which I don’t advocate).  
> 
> My guess is that actually converting the content will be easier (and I’m sure folks in the community will be glad to help).  
> 
> https://github.com/philipashlock/mediawiki-to-markdown <https://github.com/philipashlock/mediawiki-to-markdown>
> 
> 
> Nathan
> 
>> On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc... <mailto:sc...@sc...>> wrote:
>> 
>> Hi all,
>> 
>> I'm addressing this to a few of the more heavily trafficked GMOD mailing lists in hopes of getting some good advice.  The server that runs gmod.org <http://gmod.org/> is being retired at the end of the month, so I have to find it a new home.  One option includes leaving it at OICR on a new virtual machine, but it will require me to port the existing MediaWiki instance, which I already know won't be fun.
>> 
>> There are other alternatives though--it was suggested recently that the content in gmod.org <http://gmod.org/> could be migrated to GitHub pages, which sounds appealing but I have no idea how much work would be involved.  I've also considered migrating to AWS, which I think will be a similar amount of work as the internal migration at OICR but would likely be cheaper in the long run.
>> 
>> Thanks in advance for any insights!
>> Scott
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
>> Ontario Institute for Cancer Research
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-tripal mailing list
>> Gmo...@li... <mailto:Gmo...@li...>
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal <https://lists.sourceforge.net/lists/listinfo/gmod-tripal>
> 
> 
> 
> 
> -- 
> http://galaxyproject.org/ <http://galaxyproject.org/>
> http://getgalaxy.org/ <http://getgalaxy.org/>
> http://usegalaxy.org/ <http://usegalaxy.org/>
> https://wiki.galaxyproject.org/ <https://wiki.galaxyproject.org/>

Re: [GMOD-devel] [Gmod-tripal] Migrating gmod.org advice/RFC

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

Hi Scott,

We are in the process of migrating the Galaxy Wiki from MoinMoin to a
GitHub hosted pseudo-wiki (still looking for a good term). The content will
be in GitHub Flavored Markdown (GFM) plus YAML for metadata and structured
content.  We'll then use MetalSmith (http://www.metalsmith.io/) to generate
the actual web site, and it's MetalSmith that will process the YAML.

Editors will be able to edit local copies of the doc and generate the
website locally, as well as edit doc directly in GitHub.  This model will
fully leverage the power of GitHub.

Moving GMOD.org to straight github would also leverage that power and
community involvement.

*However, I think this would be tremendously difficult,* and the advantages
of moving from MediaWiki to GitHub are far less than moving from MoinMoin
to GitHub.

1) MediaWiki supports a ton of extensions such as Templates, Categories,
and Extensions.  GFM does not support any of that.  A lot of content on
GMOD.org would have to be disentangled.

2) GFM is deliberately crippled.  The theory (I think) is that you should
be using CSS for formatting instead of markup.  I like that goal, but the
current GMOD.org is chock full of MediaWiki / HTML hacks to achieve
formatting (I put a lot of it there). Translating that to pure GFM / CSS
would be a nightmare.

GFM does support directly using HTML, but it does not support mixing the
two in many circumstances.  For example, tables are all GFM or all HTML.
And GFM tables are painfully limited. Only the simplest tables can be
translated to GFM.  If you want row headers, or colspans or rowspans, or
right or center alignment in a cell, or ... you have to translate the whole
table to HTML.  And that defeats the whole purpose of having a wiki.

*So, my vote is stick with MediaWiki.*  I don't think there is any hope of
migrating to GFM without seriously mangling 90%+ of the pages.

I've CC'd Dannon Baker who is also working the Galaxy Wiki move. He's not
familiar with the current GMOD.org implementation, but he knows about
migrating wikis to GitHub.  He may have more to add (and might even
contradict me :-).

And, we've been running our wiki on AWS for years.  We've been very happy
with it.

My 98¢

Dave C


On Thu, Sep 1, 2016 at 8:58 AM, Nathan Dunn <nat...@lb...> wrote:

>
> Scott,
>
> I would advocate moving to GH pages just for the long-term ease of use,
> permission management, and cost.   There is no server to setup, but you’ll
> have to configure a Jekyll theme (http://jekyllthemes.org/) and add the
> content, which is a PITA unless you create a single-page app (which I don’t
> advocate).
>
> My guess is that actually converting the content will be easier (and I’m
> sure folks in the community will be glad to help).
>
> https://github.com/philipashlock/mediawiki-to-markdown
>
>
> Nathan
>
> On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...> wrote:
>
> Hi all,
>
> I'm addressing this to a few of the more heavily trafficked GMOD mailing
> lists in hopes of getting some good advice.  The server that runs gmod.org
> is being retired at the end of the month, so I have to find it a new home.
> One option includes leaving it at OICR on a new virtual machine, but it
> will require me to port the existing MediaWiki instance, which I already
> know won't be fun.
>
> There are other alternatives though--it was suggested recently that the
> content in gmod.org could be migrated to GitHub pages, which sounds
> appealing but I have no idea how much work would be involved.  I've also
> considered migrating to AWS, which I think will be a similar amount of work
> as the internal migration at OICR but would likely be cheaper in the long
> run.
>
> Thanks in advance for any insights!
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------
> ------------------
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
>


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

Re: [GMOD-devel] [Gmod-tripal] Migrating gmod.org advice/RFC

[Nathan D. <nat...@lb...>]

Scott,

I would advocate moving to GH pages just for the long-term ease of use, permission management, and cost.   There is no server to setup, but you’ll have to configure a Jekyll theme (http://jekyllthemes.org/ <http://jekyllthemes.org/>) and add the content, which is a PITA unless you create a single-page app (which I don’t advocate).  

My guess is that actually converting the content will be easier (and I’m sure folks in the community will be glad to help).  

https://github.com/philipashlock/mediawiki-to-markdown <https://github.com/philipashlock/mediawiki-to-markdown>


Nathan

> On Sep 1, 2016, at 8:46 AM, Scott Cain <sc...@sc...> wrote:
> 
> Hi all,
> 
> I'm addressing this to a few of the more heavily trafficked GMOD mailing lists in hopes of getting some good advice.  The server that runs gmod.org <http://gmod.org/> is being retired at the end of the month, so I have to find it a new home.  One option includes leaving it at OICR on a new virtual machine, but it will require me to port the existing MediaWiki instance, which I already know won't be fun.
> 
> There are other alternatives though--it was suggested recently that the content in gmod.org <http://gmod.org/> could be migrated to GitHub pages, which sounds appealing but I have no idea how much work would be involved.  I've also considered migrating to AWS, which I think will be a similar amount of work as the internal migration at OICR but would likely be cheaper in the long run.
> 
> Thanks in advance for any insights!
> Scott
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-tripal mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

[GMOD-devel] Migrating gmod.org advice/RFC

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

Hi all,

I'm addressing this to a few of the more heavily trafficked GMOD mailing
lists in hopes of getting some good advice.  The server that runs gmod.org
is being retired at the end of the month, so I have to find it a new home.
One option includes leaving it at OICR on a new virtual machine, but it
will require me to port the existing MediaWiki instance, which I already
know won't be fun.

There are other alternatives though--it was suggested recently that the
content in gmod.org could be migrated to GitHub pages, which sounds
appealing but I have no idea how much work would be involved.  I've also
considered migrating to AWS, which I think will be a similar amount of work
as the internal migration at OICR but would likely be cheaper in the long
run.

Thanks in advance for any insights!
Scott


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

[GMOD-devel] Software engineer position available at Ames, Iowa

[Cannon, E. K [C. S] <ekc...@ia...>]

A Tripal programming position is now open at Iowa State University in Ames, IA:

https://www.iastatejobs.com/postings/20020


The successful applicant will become part of the Legume Federation team<http://legumefederation.org/>, working primarily with the PeanutBase<http://peanutbase.org/> and LegumeInfo<http://legumeinfo.org/> websites on shared development and data exchange with other legume websites.


Ethy

[GMOD-devel] 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-devel] Contribute to the SEMANTiCS Workshops and the DBpedia Day

[Sebastian H. <pr...@in...>]

SEMANTiCS 2016 - The Linked Data Conference
Workshops, Tutorials and the DBpedia Day

12th International Conference on Semantic Systems
Leipzig, Germany
September 12 -15, 2016
_http://2016.semantics.cc/_


*Workshops/Tutorials *

This year's SEMANTiCS is starting on September 12th with a full day of 
exciting and interesting satellite events. In _6 parallel tracks_ 
<http://2016.semantics.cc/satellite-events> scientific and industrial 
workshops and tutorials are scheduled to provide a forum for groups of 
researchers and practitioners to discuss and learn about hot topics in 
Semantic Web research.

Attending the SEMANTiCS workshops and tutorial is _free of charge_, but 
you need to register. Feel free to have a closer look and register for 
the events here: _http://2016.semantics.cc/satellite-events_.


*DBpedia Day - Call for Participation *

Following our successful meetings in Europe & US our next DBpedia 
meeting will be held at Leipzig on September 15th, co-located with 
SEMANTiCS.

_Highlights_

- Keynote #1: Wikidata: bringing structured data to Wikipedia with 16000 
volunteers by Lydia Pintscher, product manager of Wikidata

- Keynote #2: Harald Sack, (title TBA) (Hasso-Plattner-Institut)

- A session for the “_DBpedia references and citations challenge_ 
<http://wiki.dbpedia.org/ideas/idea/261/dbpedia-citations-reference-challenge/>” 


- A _session on DBpedia ontology_ 
<http://mappings.dbpedia.org/index.php/DBpedia_Ontology_Committee> by 
members of the DBpedia ontology committee

- Tell us what cool things you do with 
DBpedia:<https://goo.gl/AieceU>_https://goo.gl/AieceU_

- As always, there will be tutorials to learn about DBpedia and a 
DBpedia showcase session

_Quick facts_

- Web URL: _http://wiki.dbpedia.org/meetings/Leipzig2016_

- When: September 15th, 2016

- Where: University of Leipzig, Augustusplatz 10, 04109 Leipzig

- Call for Contribution: _https://goo.gl/AieceU_ (submission form)

- Registration: Free to participate but only through registration 
(Option for DBpedia support 
tickets)<https://event.gg/3396-7th-dbpedia-community-meeting-in-leipzig-2016>_https://event.gg/3396-7th-dbpedia-community-meeting-in-leipzig-2016_


We are looking forward to your contributions and to seeing you at the 
SEMANTiCS in Leipzig!

[GMOD-devel] open positions in Knoxville, TN

[Meg S. <me...@gm...>]

I am currently recruiting for two positions in my lab to work on Tripal
software in general and the Hardwood Genomics website in particular - a sys
administrator/web developer and a postdoc. Both positions have 3 years of
support.

Web Developer/Systems Admin
https://ut.taleo.net/careersection/ut_knoxville/jobdetail.ftl?job=160000011G

Please note that anyone filling this position would have to the additional
opportunity to pursue a graduate degree at UTK while employed.

Postdoctoral Associate
https://ut.taleo.net/careersection/ut_knoxville/jobdetail.ftl?job=160000011F
Very fun and very publishable objectives for this postdoc - developing
software for genotype/phenotype/location data integration in an online
map-based viewer and Tripal software support for ontologies.

Thanks!
Meg
-- 
Margaret Staton
Assistant Professor
Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

864-506-4515 Mobile
mst...@ut...

[GMOD-devel] SEMANTiCS 2016, Leipzig, Sep 12-15, Contribute to the Vocabulary Carnival

[Sebastian H. <pr...@in...>]

The Vocabulary Carnival at SEMANTiCS 2016 is a unique opportunity for 
vocabulary publishers to showcase and share their work, meet the growing 
community of vocabulary publishers and users, and build useful semantic, 
technical and social links.

*When?* The Vocabulary Carnival is part of the SEMANTiCS programme with 
the Carnival Minute Madness on the 13th of September and on the 
industrial marketplace.

*What kind of vocabularies do we expect?*

  *

    *Any kind!* For this event we use a very open definition of what a
    vocabulary is. Ontologies, classifications, thesauri, concept and
    metadata schemes, whatever their format, in RDF or not, are all welcome.

  *

    *Bootstrap your new Vocabulary project:* At the carnival you can
    present your ideas and early stage vocabs to find the right people
    to get the Vocab discussion going. We require at least a project web
    site.

*What is your benefit of submitting?*

  *

    *attention*: make people aware of your work

  *

    *feedback*: a room full of other vocabulary creators will guarantee
    expert feedback

  *

    *linking*: discover links from your vocabulary to others on-site

*How to submit your Vocabulary to the Carnival?*

 1.

    Make sure your vocabulary is accessible on the Web through a public URI.

 2.

    Communicate your intention to participate at
    _https://goo.gl/mV3VpZ_ by joining and posting your vocabulary
    link and writing “See you at the Carnival in Leipzig” or send an
    email to mon...@cs... , with subject “Vocabulary
    Carnival”.

 3.

    Register to
    SEMANTiCS:<http://2014.semantics.cc/www.semantics.cc/registration/index.html>_http://2016.semantics.cc/registration/_
    <http://2014.semantics.cc/www.semantics.cc/registration/index.html>

 4.

    Submissions will be handled on a *first come, first serve basis*

*Are there any technical requirements?*

Your vocabulary submission will be evaluated in accordance to the 
following criteria:

  *

    *Reusability* - Which vocabularies and/or ontology design patterns
    have been reused in its development? Has it been mapped, aligned,
    imported within other ontologies yet? If not, where do you foresee
    potential reuse?

  *

    *Value addition* - How does the vocabulary provide value addition
    for the intended project or domain as compared to previous efforts
    and to Semantic Web in general?

  *

    *Design and Technical quality* - how do the ontologies incorporate
    best practices in design, i.e., using ontology design patterns or
    extending from upper level ontologies?

  *

    *Documentation* - does the vocabulary provide both human and machine
    readable documentation using for e.g., rdfs:label, rdfs:comment and
    HTML documentation?

  *

    *Availability*: We expect your vocabulary (terminology, taxonomy,
    ontology, etc.) to be hosted on the Web at a persistent URI (PURL,
    w3id, ODI) and with an appropriate licence specification. If it is
    not Linked Data or uploaded
    to<http://lov.okfn.org/>_http://lov.okfn.org_ <http://lov.okfn.org/>
    you can get technical help and advise at the conference.

  *

    *Usage*: Which academic/industrial projects have adopted the
    vocabulary? Which datasets have been annotated using the vocabulary?


*At the SEMANTiCS 2016 Conference:*

  *

    Prepare a poster (max format A0) presenting your vocabulary:
    description, purpose, history and link to its publication page. Your
    description of the vocabulary must include the above criteria.

  *

    Present your poster in the dedicated space at SEMANTiCS conference.

  *

    Brace yourself to participate in the Vocabulary Minute Madness,
    where every vocabulary will have one minute to convince of its
    usefulness and quality. Sporting your vocabulary colors at this
    occasion is optional, but will be much appreciated.

  *

    An independent jury will select the best vocabulary poster and
    presentation.

*Vocabulary Carnival and LOV*

  *

    If your vocabulary is already recorded
    at<http://lov.okn.org/>_http://lov.okn.org_ <http://lov.okn.org/>,
    check its record to see if everything is OK. Ping the LOV curators
    if something is missing or inaccurate, or if you brush up a brand
    new version for the Carnival. If you think your vocabulary is
    LOV-able but not yet recorded, submit its URI
    at<http://lov.okfn.org/dataset/lov/suggest/>_http://lov.okfn.org/dataset/lov/suggest/_

  *

    If your vocabulary is not yet meeting the technical requirements to
    be included in LOV, and you wish it could, we can help you to
    achieve that during the Carnival.

*About the Vocabulary Carnival*

The Vocabulary Carnival will be hosted at the SEMANTiCS conference, Sep 
12-15 2016


*Contact*

Monika Solanki (_mo...@cs....uk_ 
<mailto:mon...@cs...>)

Ghislain Atemezing (_ghislain.atemezing@mondeca.com_ 
<mailto:ghi...@mo...>)

[GMOD-devel] ISWC 2016 Benchmarking Linked Data Workshop

[Axel N. <pr...@in...>]

Metadata
======

Call for Papers
Submission deadline: July 7th 2016
EasyChair submission page: 
https://easychair.org/conferences/?conf=blink2016
Accepted papers: Short (8 pages) and long (16 pages)
Workshop page: http://project-hobbit.eu/events/blink-2016/
Conference: ISWC - Kobe, Japan - October, 17th or 18th, 2016

Description
=======
BLINK will provide a forum where topics related to the evaluation 
(included, but not limited to the performance, accuracy, expressive 
power and usability) of Linked Data Technologies for different steps of 
the Linked Data lifecycle can be discussed and elaborated upon.
Linked Data now part of the new data economy and Big Linked Data is 
gaining in use and traction. Systems are constantly being developed in 
order to support the booming exchange of data (existing in numerous 
formats) in the Web and the Enterprise. Linked Data benchmarks can 
function as valuable tools to objectively depict and illustrate the 
level of adequacy and thus performance provided by the existing Linked 
Data systems.
This workshop aims to bring together a broad range of attendants 
interested in benchmarking Linked Data and aims at identifying the 
specific needs and challenges of the domain in order to foster 
interdisciplinary collaborations towards attaining these challenges.
More specifically the objectives of this workshop are to:
create a discussion forum where researchers and industrials can meet and 
discuss topics related to the performance of Linked Data systems and
expose and initiate discussions on best practices, different application 
needs and scenarios related to Linked Data management.

Topics of Interest
===============
We welcome contributions presenting experiences with benchmarking Linked 
Data technologies as well as technical contributions regarding the 
development of benchmarks for all aspects of the Linked Data/Big Data 
lifecycle. All domains (e.g., life science, social networks, smart 
cities, news, digital forensics, e-science and geo-spatial data 
management)  are welcome.

Topics of interest include but are not limited to:
* Linked Data benchmarks
* Novel benchmarking results
* Analysis of existing benchmarks
* Novel measures for benchmarking Linked Data
* Linked Data benchmark evaluation
* Complex benchmarking pipelines
* Application of benchmarks in academic/industrial settings
* Tools and methodologies for the linked data generation and 
acquisition, analytics and processing,  storage and curation, 
visualization and data access.

This series of workshops are supported by H2020 European Project HOBBIT 
(Holistic Benchmarking of Big Linked Data), see http://project-hobbit.eu/.

Paper Submission
===========
The workshop will accept two types of submissions: short papers (8 
pages) will be either position papers or describe early works in the 
area of benchmarking. Long papers (up to 16 pages) will describe 
benchmarks, benchmarking techniques or benchmarking results along the 
linked data lifecycle. Details on the submission process can be found at 
http://project-hobbit.eu/events/blink-2016/

Important Dates:
July 7th, 2016: paper submission deadline
July 31st 2016: Notifications send to authors
August 25th 2016: Camera-ready papers for workshops
October 17th or 18th: Workshop

Submission Details
============
The workshop is now accepting paper submissions. Long papers (up to 16 
pages) and short papers (up to 8 pages) describing approaches or ideas / 
challenges on the topics of the workshop are invited. Submissions must 
be in PDF, formatted in the style of the Springer Publications format 
for Lecture Notes in Computer Science (LNCS). For details on the LNCS 
style, see Springer’s Author Instructions. Papers should be submitted 
through the EasyChair system 
https://easychair.org/conferences/?conf=blink2016 no later than midnight 
Hawaii time July 7th, 2016. Submissions will be reviewed by members of 
the workshop program committee. Accepted papers will be included in the 
ISWC 2016 Workshop on Benchmarking Linked Data (BLINK) proceedings.

[GMOD-devel] SEMANTiCS 2016, Leipzig, Sep 12-15, Extended Submission Deadline July 1, 2016

[Sebastian H. <pr...@in...>]

***DEADLINE EXTENSION***

2nd Call for Posters & Demos
SEMANTiCS 2016 - The Linked Data Conference
Transfer // Engineering // Community

12th International Conference on Semantic Systems
Leipzig, Germany
September 12 -15, 2016
http://2016.semantics.cc

Important Dates (Posters & Demos)
* Submission Deadline:                        extended: July 1, 2016 
(11:59 pm, Hawaii time)
* Notification of Acceptance:                 extended: August 2, 2016 
(11:59 pm, Hawaii time)
* Camera-Ready Paper:                         extended: August 10, 2016 
(11:59 pm, Hawaii time)

Submissions via Easychair: 
https://easychair.org/conferences/?conf=semantics2016research

The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, who understand its benefits and 
encounter its limitations. Every year, SEMANTiCS attracts information 
managers, IT-architects, software engineers and researchers from 
organisations ranging from NPOs, through public administrations to the 
largest companies in the world. Attendees learn from industry experts 
and top researchers about emerging trends and topics in the fields of 
semantic software, enterprise data, linked data & open data strategies, 
methodologies in knowledge modelling and text & data analytics. The 
SEMANTiCS community is highly diverse; attendees have responsibilities 
in interlinking areas like knowledge management, technical 
documentation, e-commerce, big data analytics, enterprise search, 
document management, business intelligence and enterprise vocabulary 
management.
The success of last year’s conference in Vienna with more than 280 
attendees from 22 countries proves that SEMANTiCS 2016 will continue a 
long tradition of bringing together colleagues from around the world. 
There will be presentations on industry implementations, use case 
prototypes, best practices, panels, papers and posters to discuss 
semantic systems in birds-of-a-feather sessions as well as informal 
settings. SEMANTICS addresses problems common among information 
managers, software engineers, IT-architects and various specialist 
departments working to develop, implement and/or evaluate semantic 
software systems.

The SEMANTiCS program is a rich mix of technical talks, panel 
discussions of important topics and presentations by people who make 
things work - just like you. In addition, attendees can network with 
experts in a variety of fields. These relationships provide great value 
to organisations as they encounter subtle technical issues in any stage 
of implementation. The expertise gained by SEMANTiCS attendees has a 
long-term impact on their careers and organisations. These factors make 
SEMANTiCS for our community the major industry related event across Europe.

SEMANTiCS 2016 will especially welcome submissions for the following hot 
topics:
* Data Quality Management
* Data Science (Data Mining, Machine Learning, Network Analytics)
* Semantics on the Web, Linked (Open) Data & schema.org
* Corporate Knowledge Graphs
* Knowledge Integration and Language Technologies
* Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:
Horizontals:
* Enterprise Linked Data & Data Integration
* Knowledge Discovery & Intelligent Search
* Business Models, Governance & Data Strategies
* Big Data & Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management
* Smart Connectivity, Networking & Interlinking
* Smart Data & Semantics in IoT
* Semantics for IT Safety & Security
* Semantic Rules, Policies & Licensing
* Community, Social & Societal Aspects

Verticals:
* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* Galleries, Libraries, Archives & Museums (GLAM)
* Education & eLearning
* Media & Data Journalism
* Publishing, Marketing & Advertising
* Tourism & Recreation
* Financial & Insurance Industry
* Telecommunication & Mobile Services
* Sustainable Development: Climate, Water, Air, Ecology
* Energy, Smart Homes & Smart Grids
* Food, Agriculture & Farming
* Safety & Security
* Transport, Environment & Geospatial


Posters & Demos Track
The Posters & Demonstrations Track invites innovative work in progress, 
late-breaking research and innovation results, and smaller contributions 
in all fields related to the broadly understood Semantic Web. These 
include submissions on innovative applications with impact on end users 
such as demos of solutions that users may test or that are yet in the 
conceptual phase, but are worth discussing, and also applications or 
pieces of code that may attract developers and potential research or 
business partners. This also concerns new data sets made publicly available.

The informal setting of the Posters & Demonstrations Track encourages 
participants to present innovations to the research community, business 
users and find new partners or clients and engage in discussions about 
the presented work. Such discussions can be invaluable inputs for the 
future work of the presenters, while offering conference participants an 
effective way to broaden their knowledge of the emerging research trends 
and to network with other researchers.

Poster and demo submissions should consist of a paper of 1-4 pages that 
describe the work, its contribution to the field or novelty aspects. 
Submissions must be original and must not have been submitted for 
publication elsewhere. All submissions should follow the ACM ICPS 
guidelines for formatting. The layout templates can be found here: 
http://www.acm.org/sigs/publications/proceedings-templates. The best 
posters (5-6 papers) will be published in the digital library of the ACM 
ICP Series. The other papers will be published in the 
http://ceur-ws.org/. Papers should be submitted through EasyChair 
(https://easychair.org/conferences/?conf=semantics2016research). Papers 
must be submitted in PDF (Adobe's Portable Document Format) format. 
Other formats will not be accepted. For the camera-ready version, the 
source files (Latex, Word) will also be needed.
Submissions will be reviewed by experienced and knowledgeable 
researchers and practitioners; each submission will receive a detailed 
feedback. For demos, it would be beneficial to include also links 
enabling the reviewers testing the application or reviewing the component.

Important Dates (Posters & Demos)
* Submission Deadline:                extended: July 1, 2016 (11:59 pm, 
Hawaii time)
* Notification of Acceptance:         extended: August 2, 2016 (11:59 
pm, Hawaii time)
* Camera-Ready Paper:                 extended: August 10, 2016 (11:59 
pm, Hawaii time)

Poster and Demo Chairs:
* Michael Martin, University of Leipzig
* Martí Cuquet, Semantic Technology Institute, University of Innsbruck
* Erwin Folmer, University of Twente, Kadaster and Geonovum

Contact email address: sem...@gm...

Conference Chairs:
* Sebastian Hellmann, AKSW/KILT, InfAI, Leipzig University
* Tassilo Pellegrini, UAS St. Pölten

[GMOD-devel] 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-devel] SEMANTiCS 2016, Leipzig, Sep 12-15, Call for Posters & Demos

[Sebastian H. <pr...@in...>]

Call for Posters & Demos
SEMANTiCS 2016 - The Linked Data Conference
Transfer // Engineering // Community

12th International Conference on Semantic Systems
Leipzig, Germany
September 12 -15, 2016
http://2016.semantics.cc

Important Dates (Posters & Demos)
* Submission Deadline:                        June 17, 2016 (11:59 pm, 
Hawaii time)
* Notification of Acceptance:                 July 15, 2016 (11:59 pm, 
Hawaii time)
* Camera-Ready Paper:                         August 1, 2016 (11:59 pm, 
Hawaii time)

Submissions via Easychair: 
https://easychair.org/conferences/?conf=semantics2016research

The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, who understand its benefits and 
encounter its limitations. Every year, SEMANTiCS attracts information 
managers, IT-architects, software engineers and researchers from 
organisations ranging from NPOs, through public administrations to the 
largest companies in the world. Attendees learn from industry experts 
and top researchers about emerging trends and topics in the fields of 
semantic software, enterprise data, linked data & open data strategies, 
methodologies in knowledge modelling and text & data analytics. The 
SEMANTiCS community is highly diverse; attendees have responsibilities 
in interlinking areas like knowledge management, technical 
documentation, e-commerce, big data analytics, enterprise search, 
document management, business intelligence and enterprise vocabulary 
management.

The success of last year’s conference in Vienna with more than 280 
attendees from 22 countries proves that SEMANTiCS 2016 will continue a 
long tradition of bringing together colleagues from around the world. 
There will be presentations on industry implementations, use case 
prototypes, best practices, panels, papers and posters to discuss 
semantic systems in birds-of-a-feather sessions as well as informal 
settings. SEMANTICS addresses problems common among information 
managers, software engineers, IT-architects and various specialist 
departments working to develop, implement and/or evaluate semantic 
software systems.

The SEMANTiCS program is a rich mix of technical talks, panel 
discussions of important topics and presentations by people who make 
things work - just like you. In addition, attendees can network with 
experts in a variety of fields. These relationships provide great value 
to organisations as they encounter subtle technical issues in any stage 
of implementation. The expertise gained by SEMANTiCS attendees has a 
long-term impact on their careers and organisations. These factors make 
SEMANTiCS for our community the major industry related event across Europe.

SEMANTiCS 2016 will especially welcome submissions for the following hot 
topics:
* Data Quality Management
* Data Science (Data Mining, Machine Learning, Network Analytics)
* Semantics on the Web, Linked (Open) Data & schema.org
* Corporate Knowledge Graphs
* Knowledge Integration and Language Technologies
* Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:
Horizontals:
* Enterprise Linked Data & Data Integration
* Knowledge Discovery & Intelligent Search
* Business Models, Governance & Data Strategies
* Big Data & Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management
* Smart Connectivity, Networking & Interlinking
* Smart Data & Semantics in IoT
* Semantics for IT Safety & Security
* Semantic Rules, Policies & Licensing
* Community, Social & Societal Aspects

Verticals:
* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* Galleries, Libraries, Archives & Museums (GLAM)
* Education & eLearning
* Media & Data Journalism
* Publishing, Marketing & Advertising
* Tourism & Recreation
* Financial & Insurance Industry
* Telecommunication & Mobile Services
* Sustainable Development: Climate, Water, Air, Ecology
* Energy, Smart Homes & Smart Grids
* Food, Agriculture & Farming
* Safety & Security
* Transport, Environment & Geospatial

Posters & Demos Track
The Posters & Demonstrations Track invites innovative work in progress, 
late-breaking research and innovation results, and smaller contributions 
in all fields related to the broadly understood Semantic Web. These 
include submissions on innovative applications with impact on end users 
such as demos of solutions that users may test or that are yet in the 
conceptual phase, but are worth discussing, and also applications or 
pieces of code that may attract developers and potential research or 
business partners. This also concerns new data sets made publicly available.

The informal setting of the Posters & Demonstrations Track encourages 
participants to present innovations to the research community, business 
users and find new partners or clients and engage in discussions about 
the presented work. Such discussions can be invaluable inputs for the 
future work of the presenters, while offering conference participants an 
effective way to broaden their knowledge of the emerging research trends 
and to network with other researchers.

Poster and demo submissions should consist of a paper of 1-4 pages that 
describe the work, its contribution to the field or novelty aspects. 
Submissions must be original and must not have been submitted for 
publication elsewhere. All submissions should follow the ACM ICPS 
guidelines for formatting. The layout templates can be found here: 
http://www.acm.org/sigs/publications/proceedings-templates. The best 
posters (5-6 papers) will be published in the digital library of the ACM 
ICP Series. The other papers will be published in the 
http://ceur-ws.org/. Papers should be submitted through EasyChair 
(https://easychair.org/conferences/?conf=semantics2016research). Papers 
must be submitted in PDF (Adobe's Portable Document Format) format. 
Other formats will not be accepted. For the camera-ready version, the 
source files (Latex, Word) will also be needed.
Submissions will be reviewed by experienced and knowledgeable 
researchers and practitioners; each submission will receive a detailed 
feedback. For demos, it would be beneficial to include also links 
enabling the reviewers testing the application or reviewing the component.

Important Dates (Posters & Demos)
* Submission Deadline:                June 17, 2016 (11:59 pm, Hawaii time)
* Notification of Acceptance:         July 15, 2016 (11:59 pm, Hawaii time)
* Camera-Ready Paper:                 August 1, 2016 (11:59 pm, Hawaii 
time)


Poster and Demo Chairs:
* Michael Martin, University of Leipzig
* Martí Cuquet, Semantic Technology Institute, University of Innsbruck
* Erwin Folmer, University of Twente, Kadaster and Geonovum

Contact email address: sem...@gm...

Conference Chairs:
* Sebastian Hellmann, AKSW/KILT, InfAI, Leipzig University
* Tassilo Pellegrini, UAS St. Pölten

[GMOD-devel] 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-devel] Fwd: BioCreative 2016 Extension to May 5th for Abstract Submission

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

Hello all,

Forwarding from ISB list.

Dave C.


---------- Forwarded message ----------
From: Cecilia Neomi Arighi <ar...@db...>
Date: Fri, Apr 22, 2016 at 5:22 AM
Subject: BioCreative 2016 Extension to May 5th for Abstract Submission
To: IS...@li...


*Call for participation (CFP) for BioCreative 2016*


We would like to announce that the deadline for abstract and award
submissions have been extended to May 5th.


Find below the CFP with updated information:


We would like to invite you to participate in the *BioCreative** 2016 *in
Corvallis, Oregon, USA, on August 1-2, 2016*.* BioCreative 2016 this year
will run joint with the *Annual International Conference on Biological
Ontology (ICBO)*, August 1-4, 2016, and both events will have shared
sessions and invited speakers on August 2, 2016. The aim is to foster
discussion, exchange, and innovation in research and development in the
areas of text mining and Biomedical Ontology (including plants,
agriculture, environment and biomes).



BioCreative 2016 solicits papers/presentations for the following
topics/sessions:

   1. Text mining-facilitated models of curation, Lynette Hirschman and
   Rezarta Islamaj Dogan, on application of text mining methods in areas such
   as crowdsourcing, database curation, publication process, and metagenomics.
   2. Text mining in precision medicine, Zhiyong Lu, Martin Krallinger and
   Fabio Rinaldi, on methods for annotations such as disease, phenotype, and
   adverse reactions in different text sources literature, clinical records
   and social media
   3. Domain portability or generalizability across medical literature,
   Donald Comeau and Kevin Bretonnel Cohen, on methods to achieve
   interoperability, generalizability and scalability in text mining: BioC,
   RDF and semantic web, among others
   4. Text mining and ontologies, Cecilia Arighi and ICBO, on application
   of ontologies in text mining, and text mining as ontology builder.



Submission: http://icbo.cgrb.oregonstate.edu/Biocreative_submission



Important dates:

May 5, 2016:               2-page extended abstract submission deadline

May 25, 2016:             Author notification

July 1, 2016:               Camera-ready copies deadline

August 1-2, 2016:        BioCreative 2016



Travel awards:

Funds are available for US participants for the amount up to $700 to
participate in BioCreative workshop 2016. To apply complete the application
<http://www.biocreative.org/media/store/files/2016/Travel_Award_Application_Form_BC2016.docx>
by
May 5. Women, under-represented minorities, students, and post-doctoral
fellows are encouraged to apply.



For more details, please check:
http://icbo.cgrb.oregonstate.edu/Biocreative_submission


We are looking forward to your participation!


Regards,


The BioCreative 2016 organizing committee




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

[GMOD-devel] SEMANTiCS 2016, Leipzig, Sep 12-15, Extended Submission Deadline May 10, 2016

[Sebastian H. <pr...@in...>]

**** DEADLINE EXTENSION****

3rd Call for Research & Innovation Papers
SEMANTiCS 2016 - The Linked Data Conference
Transfer // Engineering // Community

12th International Conference on Semantic Systems
Leipzig, Germany
September 12 -15, 2016
http://2016.semantics.cc

Important Dates (Research & Innovation)
* Abstract Submission Deadline:        extended: May 3, 2016 (11:59 pm, 
Hawaii time)
* Paper Submission Deadline:                extended: May 10, 2016 
(11:59 pm, Hawaii time)
* Notification of Acceptance:                 extended: June 7, 2016 
(11:59 pm, Hawaii time)
* Camera-Ready Paper:                         extended: July 1, 2016 
(11:59 pm, Hawaii time)

Submissions via Easychair: 
https://easychair.org/conferences/?conf=semantics2016research
As in the previous years, SEMANTiCS’16 proceedings are expected to be 
published by ACM ICP.

The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, who understand its benefits and 
encounter its limitations. Every year, SEMANTiCS attracts information 
managers, IT-architects, software engineers and researchers from 
organisations ranging from NPOs, through public administrations to the 
largest companies in the world. Attendees learn from industry experts 
and top researchers about emerging trends and topics in the fields of 
semantic software, enterprise data, linked data & open data strategies, 
methodologies in knowledge modelling and text & data analytics. The 
SEMANTiCS community is highly diverse; attendees have responsibilities 
in interlinking areas like knowledge management, technical 
documentation, e-commerce, big data analytics, enterprise search, 
document management, business intelligence and enterprise vocabulary 
management.

The success of last year’s conference in Vienna with more than 280 
attendees from 22 countries proves that SEMANTiCS 2016 will continue a 
long tradition of bringing together colleagues from around the world. 
There will be presentations on industry implementations, use case 
prototypes, best practices, panels, papers and posters to discuss 
semantic systems in birds-of-a-feather sessions as well as informal 
settings. SEMANTICS addresses problems common among information 
managers, software engineers, IT-architects and various specialist 
departments working to develop, implement and/or evaluate semantic 
software systems.

The SEMANTiCS program is a rich mix of technical talks, panel 
discussions of important topics and presentations by people who make 
things work - just like you. In addition, attendees can network with 
experts in a variety of fields. These relationships provide great value 
to organisations as they encounter subtle technical issues in any stage 
of implementation. The expertise gained by SEMANTiCS attendees has a 
long-term impact on their careers and organisations. These factors make 
SEMANTiCS for our community the major industry related event across Europe.


SEMANTiCS 2016 will especially welcome submissions for the following hot 
topics:
* Data Quality Management
* Data Science (Data Mining, Machine Learning, Network Analytics)
* Semantics on the Web, Linked (Open) Data & schema.org
* Corporate Knowledge Graphs
* Knowledge Integration and Language Technologies
* Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:
Horizontals
* Enterprise Linked Data & Data Integration
* Knowledge Discovery & Intelligent Search
* Business Models, Governance & Data Strategies
* Big Data & Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management
* Smart Connectivity, Networking & Interlinking
* Smart Data & Semantics in IoT
* Semantics for IT Safety & Security
* Semantic Rules, Policies & Licensing
* Community, Social & Societal Aspects

Verticals
* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* Galleries, Libraries, Archives & Museums (GLAM)
* Education & eLearning
* Media & Data Journalism
* Publishing, Marketing & Advertising
* Tourism & Recreation
* Financial & Insurance Industry
* Telecommunication & Mobile Services
* Sustainable Development: Climate, Water, Air, Ecology
* Energy, Smart Homes & Smart Grids
* Food, Agriculture & Farming
* Safety, Security & Privacy
* Transport, Environment & Geospatial

Research / Innovation Papers
The Research & Innovation track at SEMANTiCS welcomes the submission of 
papers on novel scientific research and/or innovations relevant to the 
topics of the conference. Submissions must be original and must not have 
been submitted for publication elsewhere. The Research & Innovation 
track at SEMANTiCS is a single-blind review process (author names are 
visible to reviewers, reviewers stay anonymous). The submitted abstract 
and the topics are leveraged to find adequate reviewers for submitted 
papers. Please write an email to 
sem...@ea..., if you have any questions.

Papers should follow the ACM ICPS guidelines for formatting and must not 
exceed 8 pages in length for full papers and 4 pages for short papers, 
including references and optional appendices. The layout templates can 
be found here: 
http://www.acm.org/sigs/publications/proceedings-templates All accepted 
full papers and short papers will be published in the digital library of 
the ACM ICP Series. Research & Innovation papers should be submitted 
through EasyChair at: 
https://easychair.org/conferences/?conf=semantics2016research. Papers 
must be submitted in PDF (Adobe's Portable Document Format) format. 
Other formats will not be accepted. For the camera-ready version, the 
source files (Latex, WordPerfect, Word) will also be needed.

Important Dates (Research & Innovation)
* Abstract Submission Deadline:                extended: May 3, 2016 
(11:59 pm, Hawaii time)
* Paper Submission Deadline:                extended: May 10, 2016 
(11:59 pm, Hawaii time)
* Notification of Acceptance:                 extended: June 7, 2016 
(11:59 pm, Hawaii time)
* Camera-Ready Paper:                         extended: July 1, 2016 
(11:59 pm, Hawaii time)

Research and Innovation Chairs:
* Anna Fensel, University of Innsbruck
* Amrapali Zaveri, Stanford University
Contact email address: sem...@ea...

Research and Innovation Deputy Chairs:
* Bernhard Haslhofer, Austrian Institute of Technology
* Artem Revenko, Semantic Web Company

Conference Chairs:
* Sebastian Hellmann, AKSW/KILT, InfAI, Leipzig University
* Tassilo Pellegrini, UAS St. Pölten

Senior Program Committee:
* Paul Buitelaar, Insight - National University of Ireland, Galway
* Oscar Corcho, Universidad Politécnica de Madrid
* Claudia D'Amato, University of Bari
* Brian Davis, National University of Ireland, Galway
* Victor de Boer, VU Amsterdam
* Christian Dirschl, Wolters Kluwer Germany
* Michel Dumontier, Stanford University
* Agata Filipowska, Department of Information Systems, Poznan University 
of Economics
* Bernhard Haslhofer, AIT-Austrian Institute of Technology
* Sebastian Hellmann, AKSW/KILT, InfAI, Leipzig University
* Andreas Hotho, University of Wuerzburg
* Jose Emilio Labra Gayo, Universidad de Oviedo
* Peter Mika, Yahoo! Research
* Axel-Cyrille Ngonga Ngomo, University of Leipzig
* Josiane Xavier Parreira, Siemens AG Österreich
* Heiko Paulheim, University of Mannheim
* Tassilo Pellegrini, University of Applied Sciences St. Pölten
* Marta Sabou, Vienna University of Technology
* Harald Sack, Hasso-Plattner-Institute for IT Systems Engineering, 
University of Potsdam
* Pierre-Yves Vandenbussche, Fujitsu
* Ruben Verborgh, Ghent University - iMinds
* Maria Esther Vidal, Universidad Simon Bolivar, Dept. Computer Science

Re: [GMOD-devel] [go-discuss] GAFs, GPADs, LEGO and GMOD

[Chris M. <cjm...@lb...>]

On 7 Apr 2016, at 9:30, Siddhartha Basu wrote:

> Hi Chris,
> I have a quick look and using owl for modeling GO
> annotations makes more sense. GO annotations now a days have linked
> data(annotation extensions) and the flat file format is really getting
> stretched. The implicit dependencies and connections in the flat file 
> is just impossible
> to express.

Exactly

> So, this is something i would like to revisit
> in detail besides modeling GPAD into chado. For the time being just 
> want
> to brainstorm few ideas/questions that comes from the first look.
> * Unless we go full owl for modeling annotations, we have to use 
> owltools command to
>   convert gpad into lego compatible owl.

you mean (lossy) lego->gpad,gaf?

Yes, you can use our converter to do that --- but you won't have to. The 
GOC is committed to continued support for annotations in GAF/GPAD. You 
should just be aware that this will not capture the richness of the lego 
model. But we're not forcing anyone to do any extra work.

Note that for particular kinds of bioinformatics application, other 
kinds of lossy transformation may be fine - e.g. getting files for use 
in cytoscape.

I would say that GMOD ultimately has a broader picture though.

> * How do we store these owl model for querying it.
>   Could we just shove it in a triple store like Jena TDB. Is there any
>   other options.

There are a variety of options - LEGO fits naturally into a graph or RDF 
store (as its native form is RDF/OWL). We are also storing the graph 
blobs in a Solr index for fast access and querying via AmiGO. This isn't 
intended to support rich queries involving pathway connections, but 
rather for things like "which models have mouse genes with kinase 
activity"

And you could use a relational store if you really wanted to. You don't 
need to express all of OWL. You could design a datamodel around the 
types we use in LEGO - functions, processes, components, molecular 
entities, causal links. But we'd probably both be in agreement that it 
would be more natural to use a graph-level abstraction.

The question for GMOD is do we want to consolidate everything into one 
store, or have a federated approach, with different data types in 
different kinds of store, optimized for that datatype? If things are 
consolidated, is that via incremental extensions of existing schemas, or 
through of a redesign, with (for example) a rdf/graph store front and 
center?

There are multiple possibilities here. For example, a GMOD application 
like Tripal could integrate the AmiGO LEGO widget, and have that 
communicate with our service. Or we could explore the route of having a 
tighter coupling.

> * How do we query that model. Is sparql an option. Or there is an high
>   level api.

Within GO, there will be a mixture of both. For retrieval purposes, we 
have an unpublished very high level API for fetching entire models based 
on what genes they contain etc, for this use case: 
https://github.com/geneontology/noctua/issues/221

> * How does noctua fits here. It seems to have its own customized 
> stack.
>   Does it play well with other generic rdf/semantic/linked data tool.

It's primarily an editing tool so it has its own custom stack for 
handing distributed simultaneous editing of models. But the back-end 
component is mostly a layer on top of OWL. So it depends exactly what 
you mean, but one thing to note is that as the native form is rdf/owl, 
so anything in the semweb stack will work on it out of the box.

Hope this answers some of your questions,
Chris

> thanks,
> -sidd
>
>
> On Tue, 05 Apr 2016, Chris Mungall wrote:
>
>> Dear GMODders,
>>
>> Following on from a recent discussion on gmod-schema involving Eric
>> and Siddhartha, I thought this would be a good opportunity to
>> clarify some differences between some existing GO association
>> formats, and to give you a heads-up about a new more expressive way
>> of doing GO annotation you'll be seeing soon.
>>
>> I posted some details here:
>> http://geneontology.org/article/gaf-gpad-and-lego
>>
>> In particular, I wanted to draw your attention to the more
>> expressive form of LEGO annotations. The best way to grok this is by
>> having a look at some existing annotations and documentation here:
>> http://noctua.berkeleybop.org/
>>
>> Although I think it's too early to start thinking about integrating
>> this into the GMOD stack, we can still have a conversation about how
>> this might work. For example, WormBase are exploring the addition of
>> a Noctua widget into their pages. What we learn from this could feed
>> into generic GMOD tools like Tripal - it would be great to see LEGO
>> diagrams in there.
>>
>> I'd be happy to answer any questions over on the GMOD lists. Also,
>> if any of you are at ISB/Biocuration then there will be many GO
>> experts there, as well as the Noctua developer, Seth. Paul Thomas
>> will be giving a talk about the modeling paradigm. Feel free to ask
>> us questions!
>>
>> Cheers,
>> Chris
>> _______________________________________________
>> go-discuss mailing list
>> go-...@li...
>> https://mailman.stanford.edu/mailman/listinfo/go-discuss
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

Re: [GMOD-devel] [go-discuss] GAFs, GPADs, LEGO and GMOD

[Siddhartha B. <bi...@gm...>]

Hi Chris,
I have a quick look and using owl for modeling GO
annotations makes more sense. GO annotations now a days have linked
data(annotation extensions) and the flat file format is really getting
stretched. The implicit dependencies and connections in the flat file is just impossible
to express. 
So, this is something i would like to revisit
in detail besides modeling GPAD into chado. For the time being just want
to brainstorm few ideas/questions that comes from the first look.
* Unless we go full owl for modeling annotations, we have to use owltools command to
  convert gpad into lego compatible owl.
* How do we store these owl model for querying it.
  Could we just shove it in a triple store like Jena TDB. Is there any
  other options.
* How do we query that model. Is sparql an option. Or there is an high
  level api.
* How does noctua fits here. It seems to have its own customized stack.
  Does it play well with other generic rdf/semantic/linked data tool.

thanks,
-sidd


On Tue, 05 Apr 2016, Chris Mungall wrote:

> Dear GMODders,
> 
> Following on from a recent discussion on gmod-schema involving Eric
> and Siddhartha, I thought this would be a good opportunity to
> clarify some differences between some existing GO association
> formats, and to give you a heads-up about a new more expressive way
> of doing GO annotation you'll be seeing soon.
> 
> I posted some details here:
> http://geneontology.org/article/gaf-gpad-and-lego
> 
> In particular, I wanted to draw your attention to the more
> expressive form of LEGO annotations. The best way to grok this is by
> having a look at some existing annotations and documentation here:
> http://noctua.berkeleybop.org/
> 
> Although I think it's too early to start thinking about integrating
> this into the GMOD stack, we can still have a conversation about how
> this might work. For example, WormBase are exploring the addition of
> a Noctua widget into their pages. What we learn from this could feed
> into generic GMOD tools like Tripal - it would be great to see LEGO
> diagrams in there.
> 
> I'd be happy to answer any questions over on the GMOD lists. Also,
> if any of you are at ISB/Biocuration then there will be many GO
> experts there, as well as the Noctua developer, Seth. Paul Thomas
> will be giving a talk about the modeling paradigm. Feel free to ask
> us questions!
> 
> Cheers,
> Chris
> _______________________________________________
> go-discuss mailing list
> go-...@li...
> https://mailman.stanford.edu/mailman/listinfo/go-discuss

[GMOD-devel] GAFs, GPADs, LEGO and GMOD

[Chris M. <cjm...@lb...>]

Dear GMODders,

Following on from a recent discussion on gmod-schema involving Eric and 
Siddhartha, I thought this would be a good opportunity to clarify some 
differences between some existing GO association formats, and to give 
you a heads-up about a new more expressive way of doing GO annotation 
you'll be seeing soon.

I posted some details here:
http://geneontology.org/article/gaf-gpad-and-lego

In particular, I wanted to draw your attention to the more expressive 
form of LEGO annotations. The best way to grok this is by having a look 
at some existing annotations and documentation here: 
http://noctua.berkeleybop.org/

Although I think it's too early to start thinking about integrating this 
into the GMOD stack, we can still have a conversation about how this 
might work. For example, WormBase are exploring the addition of a Noctua 
widget into their pages. What we learn from this could feed into generic 
GMOD tools like Tripal - it would be great to see LEGO diagrams in 
there.

I'd be happy to answer any questions over on the GMOD lists. Also, if 
any of you are at ISB/Biocuration then there will be many GO experts 
there, as well as the Noctua developer, Seth. Paul Thomas will be giving 
a talk about the modeling paradigm. Feel free to ask us questions!

Cheers,
Chris

Re: [GMOD-devel] 2016 Galaxy Community Conference: June 25-29, Bloomington, Indiana

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

Hello all,

*The oral presentation abstract deadline
<https://gcc2016.iu.edu/abstracts/index.php>** for GCC2016 has just been
extended to April 8*.  Scholarship applications are still open as well.  A
revised announcement is below.

Thanks,

Dave C

---------------------


*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 speaker Yoav 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 <https://gcc2016.iu.edu/index.php>* will be held at *Indiana
University <http://indiana.edu/>* 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
<https://wiki.galaxyproject.org/PublicGalaxyServers>* around the world.

*Abstract submission <https://gcc2016.iu.edu/abstracts/index.php>** for
oral presentations closes April 8. *Abstract submission for posters and
computer demonstrations closes May 20.

*Early registration <https://gcc2016.iu.edu/registration/index.php>* 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
<https://gcc2016.iu.edu/location/index.php>* when you register. *Registration
and lodging scholarships
<https://wiki.galaxyproject.org/News/GCC2016Scholarships>* are available
for attendees from underrepresented groups and developing countries.

Thanks, and we hope to see you in Bloomington!

The *GCC2016 Exec <https://gcc2016.iu.edu/organizers/index.php>*


On Wed, Mar 9, 2016 at 9:28 AM, Dave Clements <cle...@ga...>
wrote:

> 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
>


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

[GMOD-devel] SEMANTiCS 2016, Leipzig, Sep 12-15, 2nd Call for Research & Innovation Papers

[Sebastian H. <pr...@in...>]

Apologies for cross-posting

2nd Call for Research & Innovation Papers

SEMANTiCS 2016 - The Linked Data Conference
Transfer // Engineering // Community

12th International Conference on Semantic Systems
Leipzig, Germany
September 12 -15, 2016
http://2016.semantics.cc

Important Dates (Research & Innovation)
* Abstract Submission Deadline:       April 14, 2016 (11:59 pm, Hawaii 
time)
* Paper Submission Deadline:           April 21, 2016 (11:59 pm, Hawaii 
time)
* Notification of Acceptance:            May 26, 2016 (11:59 pm, Hawaii 
time)
* Camera-Ready Paper:                    June 16, 2016 (11:59 pm, Hawaii 
time)

Submissions via Easychair: 
https://easychair.org/conferences/?conf=semantics2016research
As in the previous years, SEMANTiCS’16 proceedings are expected to be 
published by ACM ICP.

The annual SEMANTiCS conference is the meeting place for professionals 
who make semantic computing work, who understand its benefits and 
encounter its limitations. Every year, SEMANTiCS attracts information 
managers, IT-architects, software engineers and researchers from 
organisations ranging from NPOs, through public administrations to the 
largest companies in the world. Attendees learn from industry experts 
and top researchers about emerging trends and topics in the fields of 
semantic software, enterprise data, linked data & open data strategies, 
methodologies in knowledge modelling and text & data analytics. The 
SEMANTiCS community is highly diverse; attendees have responsibilities 
in interlinking areas like knowledge management, technical 
documentation, e-commerce, big data analytics, enterprise search, 
document management, business intelligence and enterprise vocabulary 
management.
The success of last year’s conference in Vienna with more than 280 
attendees from 22 countries proves that SEMANTiCS 2016 will continue a 
long tradition of bringing together colleagues from around the world. 
There will be presentations on industry implementations, use case 
prototypes, best practices, panels, papers and posters to discuss 
semantic systems in birds-of-a-feather sessions as well as informal 
settings. SEMANTICS addresses problems common among information 
managers, software engineers, IT-architects and various specialist 
departments working to develop, implement and/or evaluate semantic 
software systems.

The SEMANTiCS program is a rich mix of technical talks, panel 
discussions of important topics and presentations by people who make 
things work - just like you. In addition, attendees can network with 
experts in a variety of fields. These relationships provide great value 
to organisations as they encounter subtle technical issues in any stage 
of implementation. The expertise gained by SEMANTiCS attendees has a 
long-term impact on their careers and organisations. These factors make 
SEMANTiCS for our community the major industry related event across Europe.


#SEMANTiCS 2016 will especially welcome submissions for the following 
hot topics:
* Data Quality Management
* Data Science (Data Mining, Machine Learning, Network Analytics)
* Semantics on the Web, Linked (Open) Data & schema.org
* Corporate Knowledge Graphs
* Knowledge Integration and Language Technologies
* Economics of Data, Data Services and Data Ecosystems

Following the success of previous years, the ‘horizontals’ (research) 
and ‘verticals’ (industries) below are of interest for the conference:
Horizontals
* Enterprise Linked Data & Data Integration
* Knowledge Discovery & Intelligent Search
* Business Models, Governance & Data Strategies
* Big Data & Text Analytics
* Data Portals & Knowledge Visualization
* Semantic Information Management
* Document Management & Content Management
* Terminology, Thesaurus & Ontology Management
* Smart Connectivity, Networking & Interlinking
* Smart Data & Semantics in IoT
* Semantics for IT Safety & Security
* Semantic Rules, Policies & Licensing
* Community, Social & Societal Aspects

Verticals
* Industry & Engineering
* Life Sciences & Health Care
* Public Administration
* Galleries, Libraries, Archives & Museums (GLAM)
* Education & eLearning
* Media & Data Journalism
* Publishing, Marketing & Advertising
* Tourism & Recreation
* Financial & Insurance Industry
* Telecommunication & Mobile Services
* Sustainable Development: Climate, Water, Air, Ecology
* Energy, Smart Homes & Smart Grids
* Food, Agriculture & Farming
* Safety, Security & Privacy
* Transport, Environment & Geospatial

#Research / Innovation Papers
The Research & Innovation track at SEMANTiCS welcomes the submission of 
papers on novel scientific research and/or innovations relevant to the 
topics of the conference. Submissions must be original and must not have 
been submitted for publication elsewhere. The Research & Innovation 
track at SEMANTiCS is a single-blind review process (author names are 
visible to reviewers, reviewers stay anonymous). The submitted abstract 
and the topics are leveraged to find adequate reviewers for submitted 
papers. Please write an email to 
sem...@ea..., if you have any questions.

Papers should follow the ACM ICPS guidelines for formatting and must not 
exceed 8 pages in length for full papers and 4 pages for short papers, 
including references and optional appendices. The layout templates can 
be found here: 
http://www.acm.org/sigs/publications/proceedings-templates All accepted 
full papers and short papers will be published in the digital library of 
the ACM ICP Series. Research & Innovation papers should be submitted 
through EasyChair at: 
https://easychair.org/conferences/?conf=semantics2016research. Papers 
must be submitted in PDF (Adobe's Portable Document Format) format. 
Other formats will not be accepted. For the camera-ready version, the 
source files (Latex, WordPerfect, Word) will also be needed.

Important Dates (Research & Innovation)
* Abstract Submission Deadline:            April 14, 2016 (11:59 pm, 
Hawaii time)
* Paper Submission Deadline:                April 21, 2016 (11:59 pm, 
Hawaii time)
* Notification of Acceptance:                 May 26, 2016 (11:59 pm, 
Hawaii time)
* Camera-Ready Paper:                         June 16, 2016 (11:59 pm, 
Hawaii time)

Research and Innovation Chairs:
* Anna Fensel, University of Innsbruck
* Amrapali Zaveri, Stanford University
Contact email address: sem...@ea...

Research and Innovation Deputy Chairs:
* Bernhard Haslhofer, Austrian Institute of Technology
* Artem Revenko, Semantic Web Company

Conference Chairs:
* Sebastian Hellmann, AKSW/KILT, InfAI, Leipzig University
* Tassilo Pellegrini, UAS St. Pölten

Senior Program Committee:
* Paul Buitelaar, Insight - National University of Ireland, Galway
* Oscar Corcho, Universidad Politécnica de Madrid
* Claudia D'Amato, University of Bari
* Brian Davis, DERI NUIG
* Victor de Boer, VU Amsterdam
* Christian Dirschl, Wolters Kluwer Germany
* Michel Dumontier, Stanford University
* Agata Filipowska, Department of Information Systems, Poznan University 
of Economics
* Bernhard Haslhofer, AIT-Austrian Institute of Technology
* Sebastian Hellmann, AKSW/KILT, InfAI, Leipzig University
* Andreas Hotho, University of Wuerzburg
* Jose Emilio Labra Gayo, Universidad de Oviedo
* Peter Mika, Yahoo! Research
* Axel-Cyrille Ngonga Ngomo, University of Leipzig
* Josiane Xavier Parreira, Siemens AG Österreich
* Heiko Paulheim, University of Mannheim
* Tassilo Pellegrini, University of Applied Sciences St. Pölten
* Marta Sabou, Vienna University of Technology
* Harald Sack, Hasso-Plattner-Institute for IT Systems Engineering, 
University of Potsdam
* Pierre-Yves Vandenbussche, Fujitsu
* Ruben Verborgh, Ghent University - iMinds
* Maria Esther Vidal, Universidad Simon Bolivar, Dept. Computer Science

[GMOD-devel] WebST 2016: early registration deadline 6 April

[GRLMC <gr...@gr...>]

WebST 2016: early registration deadline 6 April*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line*

 

*****************************************************************************
INTERNATIONAL SUMMER SCHOOL ON WEB SCIENCE AND TECHNOLOGY

 
WebST 2016

 
Bilbao, Spain

 
July 18-22, 2016

 

Organized by:

University of Deusto

Rovira i Virgili University

 

http://grammars.grlmc.com/webst2016/

*****************************************************************************

 
--- Early registration deadline: April 6, 2016 ---

 

********************************************************

 
AIM:

 

WebST 2016 is a research training event addressed to graduates and postgraduates in the first steps of their academic career. With a global scope, it aims at updating them about the most recent advances in the critical, multidisciplinary and fast developing area of web studies, which covers a large spectrum of current exciting research and industrial innovation from computing and technologies to social sciences and the humanities and has turned out to be the largest socio-technical infrastructure in human history. Renowned academics and industry pioneers will lecture and share their views with the audience.

 

Most subareas of web science and technology will be displayed, namely: content analysis and information extraction, information networks, search, data and semantics, ontologies, user behavior and personalization, online communities, social networks, economic transactions, mobility, security and privacy, graph analysis, web mining and applications. Main challenges and opportunities will be identified through 4 keynote lectures, 19 six-hour courses, and 1 round table, which will tackle the most active and promising topics from various perspectives: philosophy, sociology, politics, digital humanities, economics, computer science, engineering and mathematics. The organizers believe outstanding speakers will attract the brightest and most motivated students. Interaction will be a main component of the event. Moreover, an open session will give participants the opportunity to present their own work in progress in 5 minutes.

 
ADDRESSED TO:

 

Graduates and postgraduates from around the world. There are no formal pre-requisites in terms of academic degrees. However, since there will be differences in the course levels, specific knowledge background may be assumed for some of them. WebST 2016 is also appropriate for more senior people who want to keep themselves updated on recent developments and future trends. All will surely find it fruitful to listen and discuss with major researchers, scholars, industry leaders and innovators.

 
REGIME:

 

In addition to keynotes, at least 2 courses will run in parallel during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another.

 
VENUE:

 

WebST 2016 will take place in Bilbao, a city famous for its gastronomy and the seat of the Guggenheim Museum. The venue will be:

 

DeustoTech, School of Engineering

University of Deusto

Avda. Universidades, 24

48014 Bilbao

 
KEYNOTE SPEAKERS:

 

Ricardo Baeza-Yates (Pompeu Fabra University), Distributed Web Search

 

Jiawei Han (University of Illinois, Urbana-Champaign), From Data to Knowledge: A Data-to-Network-to-Knowledge (D2N2K) Paradigm

 

Prabhakar Raghavan (Google), Three Vignettes from the Theory and Practice of Large Data Analysis

 

Amit P. Sheth (Wright State University), Semantic, Cognitive and Perceptual Computing – three intertwined strands of a golden braid of intelligent computing

 
PROFESSORS AND COURSES:

 

Timothy Baldwin (University of Melbourne), [intermediate] Social Media and Text Analytics

 

Boualem Benatallah (University of New South Wales), [advanced] API Engineering and Management

 

Vassilis Christophides (INRIA, Paris), [introductory/intermediate] Entity Resolution in the Web of Data

 

Brian D. Davison (Lehigh University), [introductory] Useful Web Mining with R

 

Marco Gori (University of Siena), [advanced] Learning Semantic-based Structures from Textual Sources

 

Alon Halevy (Recruit Institute of Technology), [introductory] Structured Data on the Web

 

Jiawei Han (University of Illinois, Urbana-Champaign), [intermediate] Construction and Mining of Text-Rich Heterogeneous Information Networks

 

Andreas Hotho (University of Würzburg), [intermediate] Social Semantics in the Web

 

Ravi Kumar (Google), [introductory/intermediate] Computing at Scale: Models and Algorithms

 

Haewoon Kwak (Qatar Foundation), [introductory/intermediate] From Social Network Analysis to Social Media Analytics and beyond: Challenges and Opportunities

 

Cathy Marshall (Texas A&M University), [introductory] Qualitative Methods for Studying Users on the Web

 

Mirco Musolesi (University College London), [introductory/intermediate] Mining Big (and Small) Mobile Data

 

Bijan Parsia (University of Manchester), [introductory] The Semantic Web and Linked Data

 

Prabhakar Raghavan (Google), [intermediate] How To Build a Search Engine

 

Uli Sattler (University of Manchester), [introductory] OWL, Underlying Logics, and What This Reasoning Is All about

 

Munindar P. Singh (North Carolina State University), [introductory/intermediate] Web Applications as Sociotechnical Systems: A Basis for a Science of Security and Privacy

 

Barry Smith (University at Buffalo), [introductory] Towards Ontological Foundations for​ Web Science

 

Raphael Volz (Pforzheim University of Applied Science), [introductory] Improving Prediction Models with Open Data

 
OPEN SESSION

 

An open session will collect 5-minute presentations of work in progress by participants. They should submit a half-page abstract containing title, authors, and summary of the research to florentinalilica.voicu (at) urv.cat by July 15, 2016.

 
ORGANIZING COMMITTEE:

 

Carlos Martín-Vide (co-chair)

Manuel Jesús Parra Royón

Borja Sanz (co-chair)

Florentina Lilica Voicu

 
REGISTRATION:

 

It has to be done at

 

http://grammars.grlmc.com/webst2016/Registration.php

 

The selection of up to 8 courses requested in the registration template is only tentative and non-binding. For the sake of organization, it will be helpful to have an approximation of the respective demand for each course.

 

Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed and the on-line registration facility disabled when the capacity of the venue will be complete. It is much recommended to register prior to the event.

 
FEES:

 

Fees are a flat rate covering the attendance to all courses during the week. There are several early registration deadlines. Fees depend on the registration deadline.

 
ACCOMMODATION:

 

A suggestion of accommodation is available on the webpage.

 
CERTIFICATE:

 

Participants will be delivered a certificate of attendance.

 
QUESTIONS AND FURTHER INFORMATION:

 

florentinalilica.voicu (at) urv.cat

 
ACKNOWLEDGEMENTS:

 

University of Deusto

Rovira i Virgili University

Re: [GMOD-devel] Testing a migration of gmod.org

[Todd H. <tod...@gm...>]

t2.nanos also don't have very much allocated network bandwidth and can become unresponsive under modest loads. 

Todd

> On Mar 16, 2016, at 8:50 PM, Scott Cain <sc...@sc...> wrote:
> 
> Thanks Hilmar,
> 
> I wasn't really thinking I'd be able to get away with using a t2.nano forever, it's just the size machine I was using while migrating and testing.  I also was hoping to not need a medium but I'm wondering what will happen the first time the google bot hits it :-/  Is the only thing running on the OBF machine the wikis for the various projects or are there other processes as well?
> 
> Thanks,
> Scott
> 
> 
>> On Tue, Mar 15, 2016 at 5:46 PM, Hilmar Lapp <hl...@dr...> wrote:
>> Scott, 
>> 
>> The needs of and traffic for the GMOD wiki might be small, but as a point of reference and comparison, a t1.medium AWS VM has shown too small for running the OBF member project wikis. They go down at least once a week due to memory issues, and that's  despite daily MySQL restarts.
>> 
>> That doesn't mean a t2.nano can't work for you, but you may want to be prepared for upgrading to a medium at least.
>> 
>> -hilmar
>> 
>> Sent from away
>> 
>>> On Mar 15, 2016, at 4:04 PM, Scott Cain <sc...@sc...> wrote:
>>> 
>>> Hi all,
>>> 
>>> I'm working on migrating the gmod.org wiki away from OICR servers and I currently have a test machine running on AWS (a t2.nano machine) and I think I've implemented every extension that is in use on the current wiki.  Would you mind taking a look at and giving a test drive to the site (create pages and the like) to see if it seems to you like it's working the way it should be?
>>> 
>>> http://54.209.91.209/wiki/Main_Page
>>> 
>>> I'll probably leave that machine up for a few days, so have at it.
>>> 
>>> Thanks,
>>> Scott
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> ------------------------------------------------------------------------------
>>> Transform Data into Opportunity.
>>> Accelerate data analysis in your applications with
>>> Intel Data Analytics Acceleration Library.
>>> Click to learn more.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
>>> _______________________________________________
>>> Gmod-devel mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
> _______________________________________________
> Gmod-devel mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

Re: [GMOD-devel] Testing a migration of gmod.org

[Hilmar L. <hl...@dr...>]

There are other processes running as well, but the wikis are the primary workload.

-hilmar

Sent from away

> On Mar 16, 2016, at 9:50 AM, Scott Cain <sc...@sc...> wrote:
> 
> Is the only thing running on the OBF machine the wikis for the various projects or are there other processes as well?