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Bio

Prospecting for Proposals for GSoC 2021

GMOD News - Tue, 02/16/2021 - 15:21
GoogleSummer 2016logo.jpg

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

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 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 robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2021/02/16
Categories: Bio

News/Prospecting for Proposals for GSoC 2021

GMOD.org recent changes - Tue, 02/16/2021 - 15:21

Created page with "link=GSoC The Genome Informatics group and GMOD will be submitting an application for [https://summerofcode.withgoogle.com/ Goo..."

New page

[[File:GoogleSummer_2016logo.jpg|272px|right|link=GSoC]]

The Genome Informatics group and GMOD will be submitting an application for [https://summerofcode.withgoogle.com/ Google Summer of Code (GSoC)] this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

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|GSoC wiki page]] 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 [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] [mailto:help@gmod.org help@gmod.org].

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email [mailto:robin.haw@oicr.on.ca robin.haw@oicr.on.ca] and [mailto:help@gmod.org help@gmod.org] for advice!

{{NewsItem|2021/02/16}} Scott
Categories: Bio

Codefest 2020

GMOD News - Tue, 02/16/2021 - 15:18
Palms.jpg


Handlery Hotel in the Balboa room
(down the street from the Town and Country Hotel)
San Diego, California
January 9-10, 2020

Immediately before Plant and Animal Genome XXVIII (PAG 2020)

Participant list now available


There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to

GMOD Hackathon

We already know that there will be Tripal, Chado, Apollo and JBrowse developers present.

Agenda

Thursday:

9:00-10:00 Introduction and working group organization 10:00-12:00 Working groups 12:00-1:30 Lunch (on your own) 1:30-4:00 Working groups 4:00-5:00 Report on progress

Friday:

9:00-12:00 Working groups 12:00-1:30 Lunch (on your own) 1:30-3:00 Working groups 3:00-3:45 Report on progress
  • Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery.


Posted to the GMOD News on 2020/01/08
Categories: Bio

Codefest 2020

GMOD.org recent changes - Tue, 02/16/2021 - 15:18

← Older revision Revision as of 20:18, 16 February 2021 Line 1: Line 1: −   [[File:palms.jpg|center]] [[File:palms.jpg|center]]    Line 69: Line 68:     *Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery. *Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery.  +  +{{NewsItem|2020/01/08}} Scott
Categories: Bio

Main Page

GMOD.org recent changes - Tue, 02/16/2021 - 15:17

← Older revision Revision as of 20:17, 16 February 2021 Line 17: Line 17:  Keep up with GMOD papers and contribute your own in the '''[http://mnd.ly/WwRe8F GMOD group on Mendeley]''' Keep up with GMOD papers and contribute your own in the '''[http://mnd.ly/WwRe8F GMOD group on Mendeley]'''  </div> </div> −<div class="compBoxHdr">[[GMOD News]][[File:RSSIcon16x16.gif|right|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]]<div style="float: right; padding-right: 0.5em; font-size: 80%">[[GMOD News#Adding a News Item|Add]]</div></div>+<div class="compBoxHdr">[[GMOD News]][[File:RSSIcon16x16.gif|right|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]]<div style="float: right; padding-right: 0.5em; font-size: 80%">[[GMOD News#Adding a News Item|Add]]</div></div><rss time="1800" number="10" desc="off" title="off">http://gmod.org/wiki?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss> −'''[[Codefest 2020]]'''+ −<rss time="1800" number="10" desc="off" title="off">http://gmod.org/wiki?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>+  <!-- <rss max="10">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>--> <!-- <rss max="10">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss>-->  <!-- <div class="compBoxHdr">[[Special:Recentchanges|New &amp; Revised Pages]][[File:RSSIcon16x16.gif|right|link=http://gmod.org/mediawiki/index.php?title=Special:Recentchanges&feed=rss|All recent changes feed]]</div> <!-- <div class="compBoxHdr">[[Special:Recentchanges|New &amp; Revised Pages]][[File:RSSIcon16x16.gif|right|link=http://gmod.org/mediawiki/index.php?title=Special:Recentchanges&feed=rss|All recent changes feed]]</div> Scott
Categories: Bio

Codefest 2020

GMOD.org recent changes - Tue, 02/16/2021 - 15:15

← Older revision Revision as of 20:15, 16 February 2021 Line 1: Line 1:  +  [[File:palms.jpg|center]] [[File:palms.jpg|center]]    Scott
Categories: Bio

Tripal 3.5 Released

GMOD.org recent changes - Tue, 02/16/2021 - 14:57

Created page with "This [http://tripal.info Tripal] release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedure..."

New page

This [http://tripal.info Tripal] release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedures to update.
Changes in this version:

# Performance improvements to the Cross References, Relationships, and References.
# A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
# A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
# Updates to the online documentation
# Bug fixes in web services
# Bug fixes in the OBO loader for ontologies that won't import.

{{NewsItem|2021/02/08}} Scott
Categories: Bio

Tripal 3.5 Released

GMOD News - Tue, 02/16/2021 - 14:57

This Tripal release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedures to update. Changes in this version:

  1. Performance improvements to the Cross References, Relationships, and References.
  2. A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
  3. A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
  4. Updates to the online documentation
  5. Bug fixes in web services
  6. Bug fixes in the OBO loader for ontologies that won't import.


Posted to the GMOD News on 2021/02/08
Categories: Bio

News/BBOP Job Openings

GMOD.org recent changes - Tue, 02/16/2021 - 14:51

remove news tag

← Older revision Revision as of 19:51, 16 February 2021 Line 103: Line 103:     This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Lab in Berkeley, CA. This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Lab in Berkeley, CA. −  −{{NewsItem|2014/06/27}}  Scott
Categories: Bio

News/Now Hiring JBrowse Lead Developer

GMOD.org recent changes - Tue, 02/16/2021 - 14:51

remove news tag

← Older revision Revision as of 19:51, 16 February 2021 Line 42: Line 42:     Apply at [http://jobs.berkeley.edu jobs.berkeley.edu], job id# 18514. Apply at [http://jobs.berkeley.edu jobs.berkeley.edu], job id# 18514. −  −{{NewsItem|2014/08/26}}  Scott
Categories: Bio

News/Now Hiring CTO Phoenix Bioinfo

GMOD.org recent changes - Tue, 02/16/2021 - 14:50

remove news tag

← Older revision Revision as of 19:50, 16 February 2021 Line 2: Line 2:     Please see this [[Media:phoenix.pdf|job announcement]] for Phoenix Bioinformatics (home of [http://arabidopsis.org TAIR]).  Phoenix is a non-profit data publishing company. Please see this [[Media:phoenix.pdf|job announcement]] for Phoenix Bioinformatics (home of [http://arabidopsis.org TAIR]).  Phoenix is a non-profit data publishing company. −  −{{NewsItem|2016/11/01}}      [[Category:News_Items]] [[Category:News_Items]] Scott
Categories: Bio

News/Computational Biologist GrainGenes

GMOD.org recent changes - Tue, 02/16/2021 - 14:49

remove news tag

← Older revision Revision as of 19:49, 16 February 2021 Line 10: Line 10:  * Serves as an informational resource on genomics database code and hardware, and provides guidance and assistance on the proper use and application of a biological database digital platform to users, team members, and researchers. * Serves as an informational resource on genomics database code and hardware, and provides guidance and assistance on the proper use and application of a biological database digital platform to users, team members, and researchers.  * Guides researchers, technicians, and others on sequence data quality assurance, storage, and extraction. * Guides researchers, technicians, and others on sequence data quality assurance, storage, and extraction. −  −{{NewsItem|2016/11/28}}      [[Category:News_Items]] [[Category:News_Items]] Scott
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Tue, 02/16/2021 - 13:37

← Older revision Revision as of 18:37, 16 February 2021 (One intermediate revision by the same user not shown)Line 1: Line 1: −'''Got an idea for [[GSoC|GSOC 2020]]?'''+'''Got an idea for [[GSoC|GSOC 2021]]?'''     Then please post it.  You can either   Then please post it.  You can either   Line 10: Line 10:       −= Proposed project ideas for 2020 =+= Proposed project ideas for 2021 =     ''Be the first to add a project idea.'' ''Be the first to add a project idea.'' Robin.haw
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Tue, 02/16/2021 - 13:36

Created page with "'''Got an idea for GSOC 2020?''' Then please post it. You can either # Add it here, by directly editing this page. Just copy, paste and update the #Template|tem..."

New page

'''Got an idea for [[GSoC|GSOC 2020]]?'''

Then please post it. You can either

# Add it here, by directly editing this page. Just copy, paste and update the [[#Template|template]] below. This requires that you have or create a GMOD.org login.

Projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms.

Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route. As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open-source programmers.


= Proposed project ideas for 2020 =

''Be the first to add a project idea.''

== Template ==

*'''Project Idea Name (Project Name/Lab Name)'''
**''Brief explanation:'' Brief description of the idea, including any relevant links, etc.
**''Expected results:'' describe the outcome of the project idea.
**''Project Home Page URL:'' if there is one.
**''Project paper reference and URL:'' Is there a paper about the project this effort will be a part of?
**''Knowledge prerequisites:'' programming language(s) to be used, plus any other particular computer science skills needed.
**''Skill level:'' Basic, Medium or Advanced.
**''Mentors:'' name + contact details of the lead mentor, name + contact details of 1 or 2 backup mentors. Robin.haw
Categories: Bio

GSoC

GMOD.org recent changes - Tue, 02/16/2021 - 13:27

← Older revision Revision as of 18:27, 16 February 2021 Line 1: Line 1:  [[File:GoogleSummer_2016logo.jpg|373px|right|link=GSoC]] [[File:GoogleSummer_2016logo.jpg|373px|right|link=GSoC]]    −== Google Summer of Code 2020 @ Open Genome Informatics ==+== Google Summer of Code 2021 @ Open Genome Informatics ==     '''[https://summerofcode.withgoogle.com/ Google Summer of Code]''' is a global program that offers student developers stipends to write code for various open-source software projects. We work with many open-source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception fifteen years ago, the program has brought together over 15,000 successful student participants from 109 countries, 686 open-source organizations, and has generated over 36 million lines of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all. (''Excerpt from the [https://summerofcode.withgoogle.com/ Google Summer of Code website]'') '''[https://summerofcode.withgoogle.com/ Google Summer of Code]''' is a global program that offers student developers stipends to write code for various open-source software projects. We work with many open-source, free software, and technology-related groups to identify and fund projects over a three month period. Since its inception fifteen years ago, the program has brought together over 15,000 successful student participants from 109 countries, 686 open-source organizations, and has generated over 36 million lines of code. Through Google Summer of Code, accepted student applicants are paired with a mentor or mentors from the participating projects, thus gaining exposure to real-world software development scenarios and the opportunity for employment in areas related to their academic pursuits. In turn, the participating projects are able to more easily identify and bring in new developers. Best of all, more source code is created and released for the use and benefit of all. (''Excerpt from the [https://summerofcode.withgoogle.com/ Google Summer of Code website]'') Line 18: Line 18:  * Students and Mentors can email both [[User:Robin.haw|Robin]] and [[User:Scott|Scott]] to get more information about the program. * Students and Mentors can email both [[User:Robin.haw|Robin]] and [[User:Scott|Scott]] to get more information about the program.    −== [[GSOC_Project_Ideas_2020 | Project Ideas]] ==+== [[GSOC_Project_Ideas_2021 | Project Ideas]] ==    −'''Got an idea for a GSOC project? [[GSOC_Project_Ideas_2020 |Add it here]].'''  Ideas will be included in the proposal we send to GSOC, and great ideas make for a great proposal, so please add yours now.+'''Got an idea for a GSOC project? [[GSOC_Project_Ideas_2021 |Add it here]].'''  Ideas will be included in the proposal we send to GSOC, and great ideas make for a great proposal, so please add yours now.           These projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration, and algorithms. Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! <br> These projects can use a broad set of skills, technologies, and domains, such as GUIs, database integration, and algorithms. Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! <br>  '''Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route.''' As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open-source programmers. '''Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route.''' As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open-source programmers.    −== Preparing for GSoC 2020 ==+== Preparing for GSoC 2021 == −Right now it is the organization application process for GSoC - we won't know if Open Genome Informatics has been accepted as a GSOC 2020 mentoring organization until [https://developers.google.com/open-source/gsoc/timeline February 5th]. Nevertheless, it is a perfect time if students would like to talk to mentors about project ideas. If you are interested in mentoring, please check the Mentors section below, and contact the organization admin.+Right now it is the organization application process for GSoC - we won't know if Open Genome Informatics has been accepted as a GSOC 2021 mentoring organization until [https://developers.google.com/open-source/gsoc/timeline February 5th]. Nevertheless, it is a perfect time if students would like to talk to mentors about project ideas. If you are interested in mentoring, please check the Mentors section below, and contact the organization admin.     ===Students=== ===Students=== Robin.haw
Categories: Bio

gmod.org is OK,

GMOD.org status - Mon, 01/25/2021 - 13:36
Categories: Bio

gmod.org is DOWN, 1611590881

GMOD.org status - Mon, 01/25/2021 - 11:36
Categories: Bio

gmod.org is DOWN, 1611583681

GMOD.org status - Mon, 01/25/2021 - 09:36
Categories: Bio

AGR GFF

AGR GFF uploads - Thu, 12/10/2020 - 06:06
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Database"},"stableURL":"https://fms.alliancegenome.org/download/GFF_RGD.gff","stableGzipURL":"https://fms.alliancegenome.org/download/GFF_RGD.gff.gz","s3Url":"https://download.alliancegenome.org/3.2.0/GFF/RGD/GFF_RGD_4.gff.gz"},{"id":70318,"s3Path":"3.2.0/GFF/HUMAN/GFF_HUMAN_4.gff.gz","md5Sum":"6c7aa169c96a28d8e513a407e2b8708a","valid":true,"uploadDate":"2020-10-22T14:46:05.644+0000","releaseVersions":[{"id":66180,"releaseVersion":"4.0.0"},{"id":15546,"releaseVersion":"3.2.0","releaseDate":"2020-10-19T00:00:00.000+0000"}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":43,"name":"HUMAN","description":"Human"},"stableURL":"https://fms.alliancegenome.org/download/GFF_HUMAN.gff","stableGzipURL":"https://fms.alliancegenome.org/download/GFF_HUMAN.gff.gz","s3Url":"https://download.alliancegenome.org/3.2.0/GFF/HUMAN/GFF_HUMAN_4.gff.gz"},{"id":61000,"s3Path":"3.2.0/GFF/ZFIN/GFF_ZFIN_2.gff","md5Sum":"96158209680d20f631fe6525b5716af7","valid":true,"uploadDate":"2020-09-02T14:36:14.278+0000","releaseVersions":[{"id":66180,"releaseVersion":"4.0.0"},{"id":15546,"releaseVersion":"3.2.0","releaseDate":"2020-10-19T00:00:00.000+0000"}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":46,"name":"ZFIN","description":"Zebrafish Information Network"},"stableURL":"https://fms.alliancegenome.org/download/GFF_ZFIN.gff","stableGzipURL":"https://fms.alliancegenome.org/download/GFF_ZFIN.gff.gz","s3Url":"https://download.alliancegenome.org/3.2.0/GFF/ZFIN/GFF_ZFIN_2.gff"},{"id":77133,"s3Path":"3.2.0/GFF/SGD/GFF_SGD_3.gff.gz","md5Sum":"db2b6f5c2f12ded3fba416b8647c51d6","valid":true,"uploadDate":"2020-12-04T17:46:07.028+0000","releaseVersions":[{"id":15546,"releaseVersion":"3.2.0","releaseDate":"2020-10-19T00:00:00.000+0000"}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":48,"name":"SGD","description":"Saccharomyces Genome Database"},"stableURL":"https://fms.alliancegenome.org/download/GFF_SGD.gff","stableGzipURL":"https://fms.alliancegenome.org/download/GFF_SGD.gff.gz","s3Url":"https://download.alliancegenome.org/3.2.0/GFF/SGD/GFF_SGD_3.gff.gz"}]
Categories: Bio

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