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

[Gmod-announce] Call for Abstracts for BOSC

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

Hi All,

I'm forwarding this call for abstracts for BOSC (Bioinformatics Open Source
Conference) this year in Orlando, Florida:

>From Peter Cock (p.j.a.cock at googlemail.com):

As BOSC co-chair I would like to encourage you all to think about
attending BOSC 2016, and if you are working on your own open
source software for bioinformatics please consider submitting an
abstract. See the email below and:

http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/

Also, as a member of the Open Bioinformatics Foundation (OBF)
Board of Directors, I am delighted to let you know about the new
OBF Travel Fellowship which could be used to attend BOSC:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

In case you missed the earlier announcement last year, we finally
got rid of the paper forms for OBF membership, see:

http://news.open-bio.org/2015/12/10/online-membership-form/

Thank you,

Peter

[Biopython developer, BOSC co-chair, OBF Secretary, etc.]


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

[Gmod-announce] GMOD in Google Summer of Code 2016

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

Hello,

Very good news!  GMOD (as part of the Open Genome Informatics group along
with Reactome) has been accepted into Google Summer of Code this year.  If
you are or know of a student that might like to participate, please take a
look at

  http://gmod.org/wiki/GSOC_Project_Ideas_2016

where there are several really interesting project ideas.  It is also
possible for students to suggest their own ideas and we will try hard to
find them a mentor.

Please let me know if you have any questions about GSoC.

Scott

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

[Gmod-announce] GMOD 2016 meeting

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

Hello all,

I am pleased to announce that details have been finalized for the 2016 GMOD
meeting.  It will take place immediately following the Galaxy Community
Conference at Indiana University in Bloomington, IN on June 30 and July 1.
We're still working on agenda details, so if you have suggestions or would
like to present, please let me know.

For registration information, please see:

  https://gmod2016.eventbrite.com

And for other information about the meeting, keep an eye on:

  http://gmod.org/wiki/Jun_2016_GMOD_Meeting

I look forward to seeing you there!
Scott


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

[Gmod-announce] Chado 1.31 released

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

Hello,

You have no idea how happy it makes me to announce the release of Chado
1.31:

https://sourceforge.net/projects/gmod/files/gmod/chado-1.31/

This release marks the first schema change in Chado in 5 years, and
incorporates several changes, including

* Converting all primary and foreign keys from integers to BigInts
* Converting feature.seqlen and featureloc.fmin and fmax from integers to
BigInts (darn pine trees!)
* Several added linking tables.
* Fixed gmod_bulk_load_gff3.pl to only warn when the "part_of" term is not
found (thanks Eric Rasche).
* Fixed the ncbi_taxonomy loader to load the entire NCBI taxonomy (thanks
Naama Menda).
* Fixed the "organism by data" functionality of gmod_bulk_load_gff3.pl
(thanks Alexie Papanicolaou).
* Removed much of the initialization data included with Chado that is
considered out of date.

For details on what changed in the schema, you can find the sql diff in
chado/schemas/1.23-1.31/diff.sql or at

https://raw.githubusercontent.com/GMOD/Chado/1.31/chado/schemas/1.23-1.31/diff.sql

(note that this file is fairly large, due to the large number of statements
required to convert all of the primary keys to BigInts.)

Note that if you are a Tripal user, you will want to wait until Tripal has
been updated to support the new schema.

Finally, I want to give a very big "THANK YOU!!" to Stephen Ficklin and
Lacey Sanderson, without whom I never would have gotten this release out.

Thanks,
Scott




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

Re: [Gmod-announce] Biocuration 2016 - Registration now open !

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

Hello all,

Registration for Biocuration 2016 is now open.

Dave C.

On Tue, Dec 1, 2015 at 6:25 AM, Pascale Gaudet <Pas...@is...>
wrote:

> Dear colleagues,
>
> We are pleased to announce that the registration for Biocuration 2016 is
> now open ! Visit the conference site here:
> http://www.isb-sib.ch/events/biocuration2016/
> or access directly the registration page at:
> http://www.isb-sib.ch/events/biocuration2016/registration
>
> The conference will be held on April 10-14th, 2016.
>
> Please note that the conference space is limited to 300 people, and some
> workshops/tutorials have limited space, so we encourage you to register
> early. Also, make sure to book your accommodation early to benefit from
> discounted rates. Suggestions for hotels can be found here:
> http://www.isb-sib.ch/events/biocuration2016/location-accommodation
>
> We are looking forward to seeing you in Geneva in 2016 !
>
> Sylvain and Pascale, on behalf of the Organizing Committee
>



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

[Gmod-announce] Apollo Developers Hackathon, Jan 2016, La Jolla, CA - Registration is now open!

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

*Berkeley Bioinformatics Open-Source Projects* <http://www.berkeleybop.org/>
and
*The Su Lab* <http://sulab.org/>

invite you to join us this January for the second Apollo Developers
Hackathon in La Jolla, California.

Registration is now open!
<https://www.eventbrite.com/e/apollo-developers-hackathon-tickets-19087864316>

For three days developers will work on new features of interest to their
research communities, will be able to improve on existent Apollo
<http://genomearchitect.org/> & JBrowse <http://jbrowse.org/> features, and
will collaborate in the development of features of interest to other
colleagues.

*Participants should: *
- be able to set up your own Apollo server before arriving to Berkeley;
including Postgres, Tomcat, etc.
- code comfortably in JavaScript (client) and Java (server).
- if you have great ideas for features even though you are not a developer,
please let us know. We will be sure to include your thoughts, and,
space-permitting, you may still be able to join us!

*What will we do during the hackathon?:*
The plan is still brewing, but we have a few ideas:
- Interactive tracks for visualization of aggregated variant data,
including background population statistics, which will enable researchers
to annotate the impact of variants including associations with human
disease phenotypes.
- Exploration of synergies with the myvariant.info tool: a BD2K-supported
software tool for aggregating annotations on human genetic variants from a
variety of databases (ClinVar, exac, dbsnp, dbnsfp, etc.)
- Visualization of protein modification data overlaid on gene models. Using
data available from http://www.ebi.ac.uk/pride/archive/ to understand the
impact of variants on these sites.
- Creating a plugin to design CRISPR experiments.
- *your ideas go here!*

*Please send your suggestions for feature development, your questions, and
any other comments to the Apollo Developers email* at: apollo-dev @
lists.lbl.gov

*When: *Thursday January 14 - Saturday January 16, 2016 (immediately after
PAG <http://www.intlpag.org/>).
*Where: *The Scripps Research Institute, Molecular and Experimental
Medicine Building, 3545 Cray Court, La Jolla, CA 92121. USA.
*Registration:* Tickets are required. The cost of your ticket will be used
to cover lunch, refreshments, prizes, and minor logistics charges. Visit
the registration page at http://tinyurl.com/apollo-2016-registration
*Getting there, accommodations:* Participants are responsible for arranging
travel and accommodations on their own. Some suggestions are available on
the hackathon page at http://tinyurl.com/apollo-2016

*See you in January!*

Berkeley Bioinformatics Open-Source Projects & The Su Lab
www.GenomeArchitect.org

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





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

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

[Gmod-announce] Time is short: GMOD related talks at PAG

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

Hi All,

I realize time is short for this: there is a hard deadline of November 6
for entering speakers for the Plant and Animal Genomes meeting in January
2016.  If you would like to give a talk in the GMOD section of the meeting,
please get me a title and brief description (an abstract would be good but
not required) by November 5.  The talk can take the form of a project
update, user "story" or interpretive dance.  Speakers get early
registration discount no matter when they register, so if you haven't
registered yet, it would be like getting $100 off.

Sorry for the short notice, and I look forward to seeing in San Diego!
Scott


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

[Gmod-announce] Fwd: Two more weeks to submit your manuscripts to the Biocuration 2016 Virtual Issue

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

Hi All,

Cross-posting from the ISB Mailing list.

Dave C


---------- Forwarded message ----------
From: Pascale Gaudet <Pas...@is...>
Date: Wed, Oct 14, 2015 at 3:57 PM
Subject: Two more weeks to submit your manuscripts to the Biocuration 2016
Virtual Issue
To: IS...@li...


Dear Colleagues,

The International Biocuration Conference is a unique event for curators and
developers of biological databases to discuss their work, promote
collaborations, and foster a sense of community in this very active and
growing area of research. For the 9th International Biocuration Conference
in Geneva, Switzerland, you are invited to submit your work for
publication. This call for papers is done in collaboration with DATABASE:
The Journal of Biological Databases and Curation and the International
Society for Biocuration. The DATABASE journal will publish an online
Virtual Issue of the accepted papers, see below for a link to last years
issue. This is a great occasion to enhance the recognition of your work and
of our profession by the greater biological research communities.

This year manuscripts are invited for the following topic areas:

- Functional Annotation
- Phenotypes, genotypes, and variants
- Clinical annotations, diseases, drugs
- Big data to knowledge
- Large scale and predictive annotation
- Data standards and ontologies
- Crowd/community curation
- Data integration, data visualization
- Curation standards and best practice; inference from evidence; data and
annotation quality
- Biocuration and the scholarly communication cycle; data publishing and
curation, data sharing


Papers on topics outside the above will also be considered for publication.

The manuscript review process will be expedited and we will thus need to be
firm on the submission deadline:

Submission deadline: October 30, 2015
First decisions: December 4, 2015
Deadline for revisions: January 22, 2015
Final decisions: February 26, 2016
Conference: April 10-14, 2016

Authors wishing to submit to DATABASE for the 2016 Biocuration Virtual
issue should go to the DATABASE home page (<
http://database.oxfordjournals.org/>) and click on the "submit now" after
having read the "Instructions to Authors". Authors should CLEARLY state
that they are submitting this manuscript for consideration for the
Biocuration 2016 conference so that the DATABASE staff will ensure
appropriate fast-track for inclusion in this meeting's proceedings. In
addition, in the database submission form, they should also select. The
proceedings of the past International Biocuration Conference, the
Biocuration Virtual Issue, are online at
<
http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html
>

Submitting a paper to DATABASE does not sign you up to give a talk or
poster, you must register your interest separately.
*To submit your abstract for presentation at the Biocuration 2016
Conference, follow the instructions here:
*<*http://www.isb-sib.ch/events/biocuration2016/submission
<http://www.isb-sib.ch/events/biocuration2016/submission>*>


We look forward to your participation at Biocuration 2016 the 9th
International Biocuration Conference.


Kind regards,

-Biocuration 2016 Organizing Committee



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

[Gmod-announce] Apollo Developers Hackathon, Jan 2016, La Jolla, CA - Save the Date!

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

*Save the Date!*

*Berkeley Bioinformatics Open-Source Projects <http://www.berkeleybop.org/>
at Lawrence Berkeley National Laboratory*
and
*The Su Lab <http://sulab.org/> at The Scripps Research Institute*

invite you to join us this winter for the second *Apollo Developers
Hackathon *in La Jolla, California.

For three days developers will work on new features of interest to their
research communities, will be able to improve on existent Apollo
<http://genomearchitect.org/> & JBrowse <http://jbrowse.org/> features, and
will collaborate in the development of features of interest to other
colleagues.

*Participants should: *
- be able to set up your own Apollo server before arriving to Berkeley;
including Postgres, Tomcat, etc.
- code comfortably in JavaScript (client) and Java (server).

*What will we do at the hackathon?:*
The plan is still brewing, but we have a few ideas:
- New tracks for visualization of variant data. We want interactive tracks,
and tracks that aggregate many data at once. Including exploration of
synergies with with the myvariant.info tool.
- Integration of JBrowse / Apollo with Gene-Wiki.
- Usage of EBI's protein modification data format (some examples of their
implementation at http://www.ebi.ac.uk/pride/archive/).
- Creating a plugin to design CRISPR experiments.
- *your ideas go here!*

Please send your suggestions for feature development, your questions, and
any additional comments to the Apollo Developers email at: apollo [dash]
dev [at] lists [dot] lbl [dot] gov

*When: *Thursday January 14 - Saturday January 16, 2016 (immediately after
PAG <http://www.intlpag.org/>).
*Where:* The Scripps Research Institute, Molecular and Experimental
Medicine Building, 3545 Cray Court, La Jolla, CA 92121. USA.
*Registration:* A nominal registration fee of $75 will be collected, to
cover the cost of refreshments, and minor logistics charges.* Registration
page coming soon!*
*Getting there, accommodations: *Participants are responsible for arranging
travel and accommodations on their own. *Details about hotel blocks and
directions coming soon!*

See you in January!

Berkeley Bioinformatics Open-Source Projects & The Su Lab
www.GenomeArchitect.org

[image: Inline image 2]

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


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

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

[Gmod-announce] 2015 Galaxy Community Conference, 4-8 July, Norwich UK

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

Hello all,

The 2015 Galaxy Community Conference (GCC2015, http://gcc2015.tsl.ac.uk/)
is being held at the Sainsbury Lab in Norwich, United Kingdom, 4-8 July.
GCC2015 is an opportunity to meet with 200+ others working at the forefront
data-intensive biomedical research.  The 2015 edition of GCC includes more
than ever before (http://gcc2015.tsl.ac.uk/programme/):

   - Coding and Data Wrangling Hackathons (and a colocated BioJS Hackathon
   too)
   - Two days of training offering 18 sessions on 15 topics in up to 5
   parallel tracks, covering topics ranging from analysis to administration to
   tool development.
   - A two day meeting featuring accepted talks, poster presentations,
   keynote talks, vendor exhibits, lightning talks, birds-of-a-feather
   meetups, and plenty of networking.

Early registration is now open (but closes Friday, 22 May, *which is this
Friday)*.  Registering early saves you 40%.  Registering now ensures you'll
get a spot in the hackathon and training sessions of your choice.

Finally, there are also many other events going on before and after
GCC2015, and GCC itself ends right before ISMB / ECCB starts in Dublin.
See https://wiki.galaxyproject.org/News/NearGCC2015 for a complete list.

Hope to see you in Norwich!

Dave Clements, on behalf of the GCC2015 Organising Committee

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

[Gmod-announce] LAST CALL! Re: GMOD user talks at PAG

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

Hi All,

Last call: does anybody else want to give a GMOD-related talk at PAG this
January?  We already have some good talk proposals, but we could use a few
more.

Scott


On Mon, Nov 10, 2014 at 3:04 PM, Scott Cain <sc...@sc...> wrote:

> Hello,
>
> I'm looking for some people to give talks about how you've used GMOD tools
> at your site at the Plant and Animal Genomes meeting in San Diego this
> January.  If you're already going to PAG, or are looking for an excuse to
> go to San Diego in January, I encourage you to send me a brief note with a
> title for your talk.  If you haven't registered for PAG but will give a
> talk, you can register at early bird pricing (a savings of $100 dollars I
> think).
>
> Unfortunately, I'm running a little late with this announcement, so if
> you'd like to give a talk, please get back to me by November 13 (Thursday).
>
> Thanks and I hope to see you in San Diego in a few months,
> Scott
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



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

[Gmod-announce] GMOD user talks at PAG

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

Hello,

I'm looking for some people to give talks about how you've used GMOD tools
at your site at the Plant and Animal Genomes meeting in San Diego this
January.  If you're already going to PAG, or are looking for an excuse to
go to San Diego in January, I encourage you to send me a brief note with a
title for your talk.  If you haven't registered for PAG but will give a
talk, you can register at early bird pricing (a savings of $100 dollars I
think).

Unfortunately, I'm running a little late with this announcement, so if
you'd like to give a talk, please get back to me by November 13 (Thursday).

Thanks and I hope to see you in San Diego in a few months,
Scott


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

[Gmod-announce] Fwd: [Gmod-ajax] JBrowse is hiring

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

---------- Forwarded message ----------
From: Ian Holmes <ihh...@gm...>
Date: Wed, Sep 24, 2014 at 1:57 PM
Subject: [Gmod-ajax] JBrowse is hiring
To: jbr...@li..., jbr...@li..., "
gmo...@li..." <gmo...@li...>,
apo...@li...


Description

The JBrowse project is recruiting a new lead developer. If you are excited
by the maturation of bioinformatics into a web-based, broad-utility
discipline, this is the job for you. Since 2007 JBrowse has been bringing a
modern dynamic HTML aesthetic to the “traditional” genome browser, being
the first mainstream web-based genome browser with live panning, zooming,
interactive track rearrangement and dynamic filtering of track lists. Since
2010, JBrowse has been the platform for Web Apollo, the first web-based
tool for truly collaborative genome annotation, offering live visual
feedback on gene model edits from non-local collaborators. In a sense, the
JBrowse project represents both the “Google Maps” and the “Google Docs” of
the genome browser space.

We have more exciting offshoots planned, from synthetic biology design aids
to genome-based social networking tools. These will demand the
visualization of more bioinformatic data types (e.g. gene ontology
annotations, phylogenetic trees, sequence alignments, synteny
relationships, gene pathways and networks) and integration of associated
computational analysis tools. The job requirements go far beyond that of a
“maintenance programmer” position, demanding a high level of knowledge of
bioinformatics practise, involvement in all aspects of the software life
cycle (initial R&D, prototyping, test development, devops deployment,
maintenance) as well as clear and effective communication with users and
stakeholders.

Your desk will be in the Holmes Lab on the UC Berkeley campus, co-located
with the Web Apollo team in Stanley Hall, right at the nexus of genome
engineering and applied bioinformatics in the SF Bay Area. This project has
a high-visibility, high-impact position at the leading edge of web-based
bioinformatics tool development. Previous incumbents of this position have
“graduated” to high-responsibility equity-holding positions at key
companies in the emerging computational genomics market, such as Foundation
Medicine (cancer therapeutics) and Counsyl (prenatal genetic counseling).

Responsibilities

The primary role will be JBrowse development. JBrowse primarily consists of
a JavaScript frontend supported by server-side Perl scripts. A one-year
goal is the release of JBrowse version 2, a refactoring-in-progress to
facilitate integration with other web services and data backends. In the
shorter term the role will also support of Web Apollo and various other
collaborating projects. The job will also involve a small and limited
amount of user support. Along the way there will be numerous opportunities
to prototype and develop new web-based technologies for the collaborative
analysis of genomic data.


Qualifications

Essential:

   -

   B.S. in Computer Engineering, Bioinformatics or a related field with a
   minimum of five years related experience, or an equivalent combination of
   education and experience. Advanced degree is preferred.
   -

   Experience in development with JavaScript in client contexts:
   -

      Experience in understanding and using a variety of libraries and
      resources in an application
      -

      Experience with class prototyping frameworks
      -

      Experience with graphics frameworks such as d3
      -

      Experience with client testing frameworks such as Selenium
      -

      Experience with user interface frameworks such as Dojo and jQuery UI
      -

      Experience with CSS and CSS3 (e.g. responsive layout, media queries)
      -

   Experience in development in UNIX server contexts:
   -

      JavaScript (NodeJS), Perl, and/or Ruby
      -

      Experience with server unit testing frameworks
      -

   Demonstrated experience in developing robust web-based user-facing
   software projects.
   -

   Familiarity with current issues in web development and design (e.g.
   HTML5, WebSockets, Web Workers, message queue frameworks).
   -

   Experience with a range of database technologies (e.g. relational,
   NoSQL, triplestores).
   -

   Excellent verbal and written communication skills.
   -

   Ability to perform research and make independent decisions about
   approaches and tools to reach specific goals.
   -

   Ability to apply analytical skills and creativity to solve complex
   software and data management problems.

Desirable:

   -

   Familiarity with genomic sequence data (next-gen sequencing, reads,
   assemblies)
   -

   Experience with ontologies for annotation of genomic data
   -

   Experience with collaborative coding and build tools and workflows
   (notably github)


Applications


Apply at jobs.berkeley.edu, job id# 18514.

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https://lists.sourceforge.net/lists/listinfo/gmod-ajax




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

[Gmod-announce] Both WebApollo and JBrowse are hiring

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

Both WebApollo and JBrowse are hiring developers in beautiful Berkeley.
 Both of these projects are high profile in the bioinformatics community
and make use of leading edge technologies.  If you or anyone you know would
be interested, please be take a look at these announcements:

WebApollo:
  http://gmod.org/wiki/News/BBOP_Job_Openings

JBrowse:
  http://gmod.org/wiki/News/Now_Hiring_JBrowse_Lead_Developer

Scott



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

[Gmod-announce] Bioinformatician position at the University of Calgary

[Kamran K. <kk...@uc...>]

Bioinformatician position at the University of Calgary.



Xenbase (www.xenbase.org<http://www.xenbase.org>) is a Model Organism Database (MOD) supporting biomedical research using the amphibian model system, Xenopus. Our content is complex and includes automatically harvested as well as curated data. We store, process and display many types of DNA, RNA and protein sequence data and also epigenomic data such as RNA-seq and ChIP-seq. Sequence content within Xenbase is used in BLAST queries, visualized via the Gbrowse genome browser, and used by many of the in-house data-processing pipelines.



We are seeking to hire a bioinformatician/genomics specialist. The bioinformatician will be responsible for our sequence based content and Perl based data pipelines.



The bioinformatician's responsibilities include:

*         Managing data pipelines that bring content into Xenbase and also export it for use by third parties

*         Managing our Gbrowse genome browser

*         Perform various bioinformatics processing tasks, report generation, and aiding researchers using Xenopus by providing content and in some cases scripting custom queries



Required qualifications:

*         Solid understanding of bioinformatics file formats and processing techniques

*         Solid Perl experience



Having one or more of the following qualifications would be beneficial:

*         Experience with GBrowse and JBrowse

*         Experience with processing raw data using the Galaxy platform, or tools such as Bowtie and Cufflinks

*         Working knowledge of Java, SQL, Javascript, and HTML

*         Web programing experience

*         Database programming experience





The position is available immediately and has a salary commensurate with experience on the Tech 2 scale (http://www.ucalgary.ca/HR). To apply please visit University of Calgary's careers page at http://www.ucalgary.ca/careersuofc/ and search for job number 6604. Please contact Kamran Karimi at kk...@uc...<mailto:kk...@uc...> for any further information.

[Gmod-announce] Galaxy Community Conference Registration ends this Friday, June 6

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

Hello all,

First, that's not true.  *Affordable* registration closes this Friday.
 After that late registration is still open, but that is hard to classify
as affordable.

So, if a conference that is all about high-throughput biology interests
you, then please take a look at GCC2014 (
https://wiki.galaxyproject.org/Events/GCC2014).  The full program is
posted, and includes

   - Training Day
   <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> - 15
   sessions on 12 topics in 5 parallel tracks with topics ranging from
*Visualizing
   NGS data *to* Galaxy installation and administration*
   - 26 talks
   <https://wiki.galaxyproject.org/Events/GCC2014/Program#Day_1:_Main_Meeting.2C_July_1>
including
   a keynote by Steven Salzberg, and 25 other talks by researchers and
   industry leaders
   - 25 Posters
   <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Poster_Abstracts> -
   and counting - we still have space for a few more
   <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Abstract_Submission>
   - Lightning Talks - Present your rsesarch in two fast paced sessions.
   - Birds-of-a-Feather <https://wiki.galaxyproject.org/Events/GCC2014/BoFs>
   - Gather with other researchers with common interests and
challenges (and propose
   one
   <https://wiki.galaxyproject.org/Events/GCC2014/BoFs#Want_to_plan_a_BoF.3F>
for
   your own area of interest)

Please do let me know if you have any questions.  We would love to see you
in Baltimore.

Thanks,

Dave C


On Wed, Feb 19, 2014 at 10:30 AM, Dave Clements <cle...@ga...>
wrote:

> *2014 Galaxy Community Conference (GCC2014)
> <http://galaxyproject.org/GCC2014>*
>     http://galaxyproject.org/GCC2014
>     June 30 - July 2, 2014
>     Homewood Campus
> <http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/>
>
>     Johns Hopkins University <http://jhu.edu/>
>     Baltimore, Maryland <http://visitors.baltimorecity.gov/>, United
> States
>
> ------
> The *2014 Galaxy Community Conference *(*GCC2014*,
> http://galaxyproject.org/GCC2014) features two full days of
> presentations, discussions, poster sessions, lightning talks and
> birds-of-a-feather, *all about data-intensive biology and the tools that
> support it*.  GCC2014 also includes a Training Day
> <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> for the third
> year in a row, this year with five concurrent tracks, and in-depth coverage
> of thirteen different topics.
>
> GCC2014 <http://galaxyproject.org/GCC2014> will be held at the Homewood
> Campus
> <http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/>
>  of Johns Hopkins University <http://jhu.edu/>, in Baltimore, Maryland
> <http://visitors.baltimorecity.gov/>, United States, from June 30 through
> July 2, 2014.
>
> Galaxy is an easily extensible data integration and analysis platform for
> life sciences research that supports hundreds of bioinformatics analysis
> tools. Galaxy is open-source and can be locally installed or run on the
> cloud.  There are hundreds of local installs, and over 50 publicly
> accessible servers around the world.
>
> *Early registration
> <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open.
> Early combined registration (Training Day
> <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main
> meeting) starts at $140 for post-docs and students. Registration is capped
> this year at 250 participants, *and we expect to hit that limit*.
> Registering early assures you a place at the conference and also a spot in
> the Training Day workshops you want to attend.
>
> You can also book affordable conference housing at the same time you
> register. See the conference Logistics page
> <https://wiki.galaxyproject.org/Events/GCC2014/Logistics> for details on
> this and other housing options.
>
> *Abstract submission
> <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral
> presentations and posters is also open.  Abstract submission for oral
> presentations closes April 4, and poster submission closes April 25.  The *GigaScience
> <http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and
> Reproducible Research <http://www.gigasciencejournal.com/series/Galaxy>"
> series (announced for GCC2013) *is continuing to take submissions for
> this year's meeting and beyond. * BGI is also continuing to cover the
> article processing charges until the end of the year, and for more
> information see their latest update
> <http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/>.
>  *Please consider presenting your work.*
>
> Thanks, and hope to see you in Baltimore!
>
> The GCC2014 Organizing Committee
> <https://wiki.galaxyproject.org/Events/GCC2014/Organizers>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> http://wiki.galaxyproject.org/
>



-- 
http://galaxyproject.org/GCC2014
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] Fwd: [apollo] Web Apollo Developers Hackathon at Berkeley.

[Amelia I. <ame...@gm...>]

from Monica Munoz-Torres <McM...@lb...>:


Dear colleagues,

Berkeley Bioinformatics Open-Source Projects (BBOP) invites you to join us
this summer for a Web Apollo Hackathon at Lawrence Berkeley National
Laboratory.

For five days developers will work on new features of interest to their
research communities, will be able to improve on existent features, and
will collaborate in the development of features of interest to other
colleagues.


*Participants should: *

   -
*be able to set up your own Web Apollo server before arriving to Berkeley;
   including Postgres, Tomcat, etc. *
   - *code comfortably in JavaScript (client) and Java (server).*


*When: *Monday, June 2 - 6, 2014

*Where: *Lawrence Berkeley National Laboratory. Building 74 (B74), Room 104.
 1 Cyclotron Rd, Berkeley, CA 94720 <http://goo.gl/aWV6v3>

* What will we do while we are there?: You tell us! *S
*end your suggestions for feature development, your questions, and any
additional comments to *apollo [dash] dev [at] lists [dot] lbl [dot] gov

* Registration: *registration is free of charge, but tickets are required.
Please register at http://goo.gl/WRfuai

*Getting there, accommodations: *Participants are responsible for arranging
travel and accommodations on their own. For details visit:
http://genomearchitect.org/developers_hackathon_2014


See you in June!

*Berkeley Bioinformatics Open-Source Projects*



-- 
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Lawrence Berkeley National Laboratory
Twitter @monimunozto | Google Scholar Profile: http://goo.gl/sXYTE

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631

[Gmod-announce] GMOD Online Training 2014

[Amelia I. <ame...@gm...>]

Greetings GMOD community!

Applications are now open for the 2014 GMOD online training course, to be
held from May 19th - 23rd 2014.

The course will cover the installation, configuration, and usage of core
GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal,
WebApollo, Canto, and the Chado database.

The course is taught by experienced instructors and developers with deep
knowledge of the tools. Although the course will be run online, students
will be able to interact with the tutors and fellow attendees, ask
questions, and so on.

For more information and to apply, please see
http://gmod.org/wiki/GMOD_Online_Training_2014

If you have any questions, please contact the GMOD help desk at
he...@gm....

Thanks!

-- 
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject

[Gmod-announce] 2014 Galaxy Community Conference (GCC2014) Talk Abstracts due April 4

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

Hello all,

This is a reminder that talk abstract submissions for the 2014 Galaxy
Community Conference *are due this Friday, April 4*.  See
http://bit.ly/gcc2014abs for details.  This is a great opportunity to share
your work in high-throughput biology.

Accepted abstracts will be considered for the *GigaScience
<http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and
Reproducible Research <http://www.gigasciencejournal.com/series/Galaxy>"
series (announced for GCC2013)*. * BGI is also continuing to cover the
article processing charges until the end of the year

Poster abstracts are being accepted until April 25.  Early registration
(save a bundle, really) is also open.

Thanks, and I do hope you'll join us in Baltimore,

Dave C

On Wed, Feb 19, 2014 at 10:30 AM, Dave Clements
<cle...@ga...>wrote:

> *2014 Galaxy Community Conference (GCC2014)
> <http://galaxyproject.org/GCC2014>*
>     http://galaxyproject.org/GCC2014
>     June 30 - July 2, 2014
>     Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/>
>
>     Johns Hopkins University <http://jhu.edu/>
>     Baltimore, Maryland <http://visitors.baltimorecity.gov/>, United
> States
>
> ------
> The *2014 Galaxy Community Conference *(*GCC2014*,
> http://galaxyproject.org/GCC2014) features two full days of
> presentations, discussions, poster sessions, lightning talks and
> birds-of-a-feather, *all about data-intensive biology and the tools that
> support it*.  GCC2014 also includes a Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> for
> the third year in a row, this year with five concurrent tracks, and
> in-depth coverage of thirteen different topics.
>
> GCC2014 <http://galaxyproject.org/GCC2014> will be held at the Homewood
> Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/>
>  of Johns Hopkins University <http://jhu.edu/>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>,
> United States, from June 30 through July 2, 2014.
>
> Galaxy is an easily extensible data integration and analysis platform for
> life sciences research that supports hundreds of bioinformatics analysis
> tools. Galaxy is open-source and can be locally installed or run on the
> cloud.  There are hundreds of local installs, and over 50 publicly
> accessible servers around the world.
>
> *Early registration
> <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open.
> Early combined registration (Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> +
> main meeting) starts at $140 for post-docs and students. Registration is
> capped this year at 250 participants, *and we expect to hit that limit*.
> Registering early assures you a place at the conference and also a spot in
> the Training Day workshops you want to attend.
>
> You can also book affordable conference housing at the same time you
> register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics> for
> details on this and other housing options.
>
> *Abstract submission
> <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral
> presentations and posters is also open.  Abstract submission for oral
> presentations closes April 4, and poster submission closes April 25.  The *GigaScience
> <http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and
> Reproducible Research <http://www.gigasciencejournal.com/series/Galaxy>"
> series (announced for GCC2013) *is continuing to take submissions for
> this year's meeting and beyond. * BGI is also continuing to cover the
> article processing charges until the end of the year, and for more
> information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/>.
>  *Please consider presenting your work.*
>
> Thanks, and hope to see you in Baltimore!
>
> The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> http://wiki.galaxyproject.org/
>



-- 
http://galaxyproject.org/GCC2014
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/

[Gmod-announce] BOSC 2014 Call for Abstracts

[Amelia I. <ame...@gm...>]

via Nomi Harris, nlh...@gm...

Call for Abstracts for the 15th Annual Bioinformatics Open Source
Conference (BOSC 2014)
A Special Interest Group (SIG) of ISMB 2014

Dates: July 11-12, 2014
Location: Boston, MA, USA
Web site: http://www.open-bio.org/wiki/BOSC_2014
Email: bo...@op...
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates:
March 24, 2014: Registration opens for ISMB and BOSC (
https://www.iscb.org/ismb2014-registration)
April 4, 2014: Deadline for submitting BOSC abstracts (
http://www.open-bio.org/wiki/BOSC_Abstract_Submission)
May 1, 204: Notification of accepted talk abstracts emailed to authors
July 9-10, 2014: Codefest 2014, Boston (
http://www.open-bio.org/wiki/Codefest_2014)
July 11-12, 2014: BOSC 2014, Boston (http://www.open-bio.org/wiki/BOSC_2014)
July 11-15, 2014: ISMB 2014, Boston

The Bioinformatics Open Source Conference (BOSC) covers the wide range of
open source bioinformatics software being developed, and encompasses the
growing movement of Open Science, with its focus on transparency,
reproducibility, and data provenance.  We welcome submissions relating to
all aspects of bioinformatics and open science software, including new
computational methods, reusable software components, visualization,
interoperability, and other approaches that help to advance research in the
biomolecular sciences. Two full days of talks, posters, panel discussions,
and informal discussion groups will enable BOSC attendees to interact with
other developers and share ideas and code, as well as learning about some
of the latest developments in the field of open source bioinformatics. BOSC
is sponsored by the Open Bioinformatics Foundation, a non-profit,
volunteer-run group dedicated to promoting the practice and philosophy of
Open Source software development and Open Science within the biological
research community.

We invite you to submit one-page abstracts for talks and posters.  This
year's session topics are:
- Open Science and Reproducible Research
- Software Interoperability
- Genome-scale Data and Beyond
- Visualization
- Translational Bioinformatics
- Bioinformatics Open Source Libraries and Projects

Once again we thank Eagle Genomics for sponsoring the BOSC Student Travel
Awards, and welcome the open access journal GigaScience as a new sponsor
for BOSC 2014.

BOSC 2014 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad
Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp







Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject

[Gmod-announce] Precompiled Ontologies in Chado available

[Amelia I. <ame...@gm...>]

Chado database dumps of precompiled ontologies are now publicly available
at https://cpt.tamu.edu/~docs/chado/ , courtesy of Eric Rasche and Center
for Phage Technology at Texas A&M University (https://cpt.tamu.edu/).

The ontologies are updated on a weekly basis, and will save Chado users the
time and trouble of downloading and compiling the ontologies themselves.

The ontologies currently compiled and included in the database dump are:

- Chado Feature Properties
- Gene Ontology
- Plant Ontology
- Relationship Ontology
- Sequence Ontology

More information is available on the GMOD wiki:

http://gmod.org/wiki/Precompiled_Chado_Databases

GMOD thanks Eric Rasche for kindly providing this resource for Chado users!

--
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject

[Gmod-announce] 2014 Galaxy Community Conference (GCC2014), Baltimore, June 30-July 2

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

*2014 Galaxy Community Conference (GCC2014)
<http://galaxyproject.org/GCC2014>*
    http://galaxyproject.org/GCC2014
    June 30 - July 2, 2014
    Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/>

    Johns Hopkins University <http://jhu.edu/>
    Baltimore, Maryland <http://visitors.baltimorecity.gov/>, United States

------
The *2014 Galaxy Community Conference *(*GCC2014*,
http://galaxyproject.org/GCC2014) features two full days of presentations,
discussions, poster sessions, lightning talks and birds-of-a-feather, *all
about data-intensive biology and the tools that support it*.  GCC2014 also
includes a Training
Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> for
the third year in a row, this year with five concurrent tracks, and
in-depth coverage of thirteen different topics.

GCC2014 <http://galaxyproject.org/GCC2014> will be held at the Homewood
Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/>
 of Johns Hopkins University <http://jhu.edu/>, in Baltimore,
Maryland<http://visitors.baltimorecity.gov/>,
United States, from June 30 through July 2, 2014.

Galaxy is an easily extensible data integration and analysis platform for
life sciences research that supports hundreds of bioinformatics analysis
tools. Galaxy is open-source and can be locally installed or run on the
cloud.  There are hundreds of local installs, and over 50 publicly
accessible servers around the world.

*Early registration
<https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open.
Early combined registration (Training
Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> +
main meeting) starts at $140 for post-docs and students. Registration is
capped this year at 250 participants, *and we expect to hit that limit*.
Registering early assures you a place at the conference and also a spot in
the Training Day workshops you want to attend.

You can also book affordable conference housing at the same time you
register. See the conference Logistics
page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics> for
details on this and other housing options.

*Abstract submission
<https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral
presentations and posters is also open.  Abstract submission for oral
presentations closes April 4, and poster submission closes April 25.
The *GigaScience
<http://www.gigasciencejournal.com/>* "Galaxy: Data Intensive and
Reproducible Research <http://www.gigasciencejournal.com/series/Galaxy>"
series (announced for GCC2013) *is continuing to take submissions for this
year's meeting and beyond. * BGI is also continuing to cover the article
processing charges until the end of the year, and for more information see
their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/>.
 *Please consider presenting your work.*

Thanks, and hope to see you in Baltimore!

The GCC2014 Organizing
Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers>

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

[Gmod-announce] Genome Annotation Library (Version 0.2.2)

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

Message forwarded from the Sequence Ontology list; this looks like an
excellent tool for anybody who works with GFF3.

Scott


---------- Forwarded message ----------
From: Barry Moore <bar...@gm...>
Date: Wed, Jan 29, 2014 at 7:58 PM
Subject: [maker-devel] Genome Annotation Library (Version 0.2.2)
To: SO developers <son...@li...>, la...@ya..., "
mak...@ya... List" <mak...@ya...>


The Sequence Ontology is please to announce the release of the Genome
Annotation Library (GAL) Version 0.2.2.  GAL is a library of Perl modules
that makes working with sequence features in GFF3/GVF files straight
forward and intuitive.  GAL also provides numerous parser classes for
converting other formats to GFF3 and makes writing new parsers easy. GAL
takes advantage of the ontology based relationships captured in SO-based
sequence feature data to allow users to easily traverse the relationships
between features in a GFF3 file.  In addition to the GAL programming
library many scripts utilizing the library are included as well as several
stand-alone scripts for working with GFF/GVF and other genomic dataset.

Updates in this version include:

-Adding bin/footprint script
-Adding gal_indexer script
-Adding bin/gene_CDS_footprint script
-New CPAN style html docs for GAL
-Updates to gtf2gff3
-Adding warnings when mrna.pm can not return CDS or protein sequence
-Added progress counter to Storage::SQLite::load_files
-Adding --template option to gff_tool
-Adding templates/gff_tool_gvf_example2.tt
-Adding gal_remove_transcripts and gal_gff_tool
-Adding fix_gvf function to bin/gff_tool
-Added --clean to gal_protein_genes
-Adding GAL::Base::open_file

For more information, to access the GAL docs and to download GAL code
please visit:

http://www.sequenceontology.org/software/GAL.html

Barry Moore
Research Scientist
Dept. of Human Genetics
Dept. of Biomedical Informatics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




_______________________________________________
maker-devel mailing list
mak...@bo...
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




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

[Gmod-announce] Biocuration 2014, Toronto, Canada, April 6-9

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

Forwarded from Robin Haw; Biocuration is a great conference for curators.
There will probably be one or two workshops for GMOD related software; the
possibilities include workshops for WebApollo and Canto.


See you there!

Scott



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

7th International Biocuration Conference

Biocuration 2014


Toronto, Canada


April 6-9, 2014


http://biocuration2014.events.oicr.on.ca/


Abstracts Due: February 10, 2014


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

Dear Colleagues,


On behalf of the Organizing Committee, I am pleased to invite you to the
7th International Biocuration Conference in Toronto, Canada. The conference
will will begin at 6pm on Sunday 6, April and run through to 5pm on
Wednesday 9, 2014. The conference will provide a forum for trainees,
biocurators, investigators, clinicians and developers of biological
databases to discuss their work, promote collaboration and foster a sense
of community in this very active and growing area of research. Participants
from academia, government and industry interested in the methods and tools
employed in curation of biological and medical data are encouraged to
attend. While a number of speakers have been invited, please note that the
majority of oral presentations will be drawn from openly submitted
abstracts.


VENUE:

The primary site for the conference is Hart House, considered the cultural
and ceremonial centre of the University of Toronto.


SCOPE:

The proposed 2014 conference sessions and workshops will address the
following challenges in biocuration:

Automated Function Prediction (workshop)

Big Data Curation: Dealing with supplementary data (workshop)

Biocreative Text Mining (workshop)

Biological and Clinical Ontologies (session)

Clinical Annotations (session)

Data Integration and Data Sharing (session)

Functional Annotations (session)

Microbial Informatics (session)

Phenotype (workshop)

Social Tools for publishing and curation (workshop)


INVITED SPEAKERS:

Dr. Tim Hubbard, King’s College London

Dr. Suzanna Lewis, Lawrence Berkeley National Laboratory

Dr. Patricia Babbitt, California Institute for Quantitative Biosciences
(QB3)

Dr. Lincoln Stein, Ontario Institute for Cancer Research


REGISTRATION:

The registration form can be found at:
http://biocuration2014.events.oicr.on.ca/biocuration-registration-and-abstract-submission


ABSTRACT SUBMISSION:

Submit your abstract for presentation (poster or talks only) via this link:
https://www.easychair.org/conferences/?conf=isb2014


KEY DATES:

Abstract submission deadline (poster or oral presentation): February 10,
2014

Fellowships Application deadline: February 10, 2014

Notification of decision for abstract submission: February 24, 2014

Fellowships Notification of acceptance: February 24, 2014

Online registration ends: March 24, 2014.


HOTEL ACCOMMODATIONS:

A limited number of rooms have been secured at the Holiday Inn, Courtyard
Marriott and Downtown Eaton Chelsea at a discounted rate:
http://biocuration2014.events.oicr.on.ca/biocuration-location-and-accommodation


Looking forward to seeing you at Biocuration 2014.

Sincerely,

Robin Haw


Organizing Committee

Robin Haw (Chair) Ontario Institute for Cancer Research, ON, Canada

Marc Gillespie (Co-chair) St John's University, NY, USA

Francis Ouellette (Co-chair) Ontario Institute for Cancer Research, ON,
Canada

Alex Bateman, European Bioinformatics Institute, UK

Michelle Brazas, Ontario Institute for Cancer Research, ON, Canada

Fiona Brinkman, Simon Fraser University, BC, Canada

Mike Cherry, Stanford University, CA, USA

Patricia Falzon, Ontario Institute for Cancer Research, ON, Canada

Nicole Gleed, Ontario Institute for Cancer Research, ON, Canada

Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland

Iddo Friedberg, Miami University, OH, USA

Todd Harris, Ontario Institute for Cancer Research, ON, Canada

Raja Mazumder, George Washington University, DC, USA

Dennis McCormac, Ontario Genomics Institute, ON, Canada

Ilene Mizrachi, National Center for Biotechnology Information, DC, USA

Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory, CA, USA

John Parkinson, The Hospital for Sick Children, ON, Canada

Paul Thomas, University of Southern California, CA, USA

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

[Gmod-announce] Google Summer of Code: we want your ideas!

[Amelia I. <ame...@gm...>]

Hello all,

GMOD is participating in Google Summer of Code (GSoC) again this year, and
we are soliciting project ideas from people and groups involved in the GMOD
project:

http://gmod.org/wiki/GSoC

GSoC is a global program run by Google to encourage students to get
real-world experience of participating in a software project; students work
on a project over the summer months and receive a stipend from Google for
participating. Thousands of organizations of many different sizes take part
in GSoC, with the common factor being that they must produce open-source
code.

Please take a look at the GSoC wiki page (http://gmod.org/wiki/GSoC) and
think about any projects that might work well for a GSoC student, and add
them to the wiki. If you are interested in being a mentor, please contact
us at he...@gm... .

If you have any questions--e.g. what constitutes an appropriate project;
whether your idea is sufficiently GMOD-related--please feel free to email
he...@gm... for advice!

Thanks!

-- 
Amelia Ireland
GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject