Difference between revisions of "PAG 2015"

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m (GMOD Consumers and Providers: Finished JBrowse)
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| 10:30 - 11:00 || [https://pag.confex.com/pag/xxiii/webprogram/Session2627.html W238]: Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines) || Dave Micklos || California Room
 
| 10:30 - 11:00 || [https://pag.confex.com/pag/xxiii/webprogram/Session2627.html W238]: Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines) || Dave Micklos || California Room
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| 10:30 - 11:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15662.html W571]: GenSAS || Dorrie Main || Pacific Salon 6-7
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| 12:00 - 12:40 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14925.html W159]: Management and Visualization of Ianimal Quantitative Data Using iPlant and EPIC-CoGe || Sabarinath Subramaniam || San Diego
 
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| 2:10 - 2:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16326.html W162]: Citrus Genome DB Updates || Sook Jung || Pacific Salon 6-7
 
| 2:10 - 2:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16326.html W162]: Citrus Genome DB Updates || Sook Jung || Pacific Salon 6-7
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| 2:10 - 2:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15396.html C3]: GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence || Jodi Humann || California Room
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| 4:00 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Session2856.html W377]: Genome management and analysis with CoGe || Haibao Tang and Eric Lyons || California Room
 
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| colspan=3 | '''Sunday January 11'''
 
| colspan=3 | '''Sunday January 11'''
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| 2:30- 2:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16049.html W421]: Overview of the GnpIS Grape Genomics and Genetic Integrative Resource for Diversity Studies || Nacer Mohellibi || Pacific Salon 6-7
 
| 2:30- 2:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16049.html W421]: Overview of the GnpIS Grape Genomics and Genetic Integrative Resource for Diversity Studies || Nacer Mohellibi || Pacific Salon 6-7
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| 2:45 - 3:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15761.html C14]: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research || Jing Yu || California Room
 
 
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| colspan=3  | '''Monday January 12'''
 
| colspan=3  | '''Monday January 12'''
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| EVEN
 
| EVEN
 
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|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16367.html P268]: New Data Mining Interfaces at the Bovine Genome Database || Colin Diesh || Poster session
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| 10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16367.html P268]: New Data Mining Interfaces at the Bovine Genome Database || Colin Diesh || Poster session
 
|-
 
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|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15302.html P346]: PeanutBase: A Resource for Peanut Genetic, Genomic, and Trait Information || Ethalinda Cannon || Poster session
 
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15302.html P346]: PeanutBase: A Resource for Peanut Genetic, Genomic, and Trait Information || Ethalinda Cannon || Poster session
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|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16655.html P1010]: The i5k Workspace@NAL - Enabling Genomic Data Access, Visualization, and Curation of Arthropod Genomes || Monica Poelchau || Poster session
 
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16655.html P1010]: The i5k Workspace@NAL - Enabling Genomic Data Access, Visualization, and Curation of Arthropod Genomes || Monica Poelchau || Poster session
 
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|10:00 - 11:30 || [ P]:  || || Poster session
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|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15952.html P778]:  || CicArVarDB: Chickpea Variation Database || Poster session
 
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|10:00 - 11:30 || [ P]:  ||  || Poster session
 
|10:00 - 11:30 || [ P]:  ||  || Poster session
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| 2:30-2:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15573.html C13]: How to Use GDR, the Genome Database for Rosaceae || Sook Joon || California Room
 
| 2:30-2:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15573.html C13]: How to Use GDR, the Genome Database for Rosaceae || Sook Joon || California Room
 +
|-
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| 2:45 - 3:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15761.html C14]: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research || Jing Yu || California Room
 
|-
 
|-
 
| ODD  
 
| ODD  
 
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| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14878.html P101]: High-Throughput SNP Genotyping for Crop Improvement || Michael J. Thomson || Poster session
 
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14878.html P101]: High-Throughput SNP Genotyping for Crop Improvement || Michael J. Thomson || Poster session
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|-
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| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16344.html P0267]: Discovering Novel Protein-Coding Genes and Long Non-Coding RNAs in ''Bos taurus'' || Darren Hagen || Poster Session
 
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| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16477.html P301]: Tools for Phylogenomic Exploration within and Among Clade-Oriented Databases || Alan Cleary || Poster session
 
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16477.html P301]: Tools for Phylogenomic Exploration within and Among Clade-Oriented Databases || Alan Cleary || Poster session
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| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16382.html P1117]: An Integrated Annotation Data Warehouse at the Hymenoptera Genome Database || Aditi Tayal || Poster session
 
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16382.html P1117]: An Integrated Annotation Data Warehouse at the Hymenoptera Genome Database || Aditi Tayal || Poster session
 
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|-
| 3:00 - 4:30 || [ P]: || || Poster session
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| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15379.html P1153]: GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence || Jodi Humann || Poster session
 
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|-
| 3:00 - 4:30 || [ P]: || || Poster session
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| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17285.html P839]: Accessing SGN Genomes through Tools || Susan Strickler || Poster session
 
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| 3:00 - 4:30 || [ P]:  || || Poster session
 
| 3:00 - 4:30 || [ P]:  || || Poster session
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| 11:00 - 11:15 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14431.html C17]: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B || Thomas Letellier || California Room
 
| 11:00 - 11:15 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14431.html C17]: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B || Thomas Letellier || California Room
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| 11:15 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16265.html C18]: Using the Wheat Tilling Database to Search Mutants of Interest || Hans Vasquez-Gross || California Room
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| 11:15 - 11:35 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14181.html W725]: Accessing SGN Genomes through Tools || Susan Strickler || Towne
 
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| 11:30 - 11:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16566.html C19]: TreeGenes and CartograTree: Tools for Forest Tree Genomics || Emily Grau || California Room  
 
| 11:30 - 11:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16566.html C19]: TreeGenes and CartograTree: Tools for Forest Tree Genomics || Emily Grau || California Room  
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| 12:10 - 12:40 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14861.html W074]: Updates on the ''Musa acuminata'' Reference Genome Sequence
 
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| 12:30 - 12:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16135.html C23]: Using the Arabidopsis Information Portal || Jason Miller || California Room  
 
| 12:30 - 12:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16135.html C23]: Using the Arabidopsis Information Portal || Jason Miller || California Room  

Revision as of 23:20, 18 December 2014

Plant and Animal Genomes 2015 (PAG XXIII

There is plenty of GMOD content at the Plant and Animal Genomes (PAG) conference in January 2015. There is a dedicated GMOD Workshop and also posters and presentations from many GMOD users, as well as from developers of GMOD tools.

Core GMOD Content

There are a number of items focussed on the tools and services that GMOD provides. These are:

Date Time Session Component(s) Presenter / Organizer Location
Jan. 11 (Sun) 1:30 - 3:10 W367: JBrowse Installation and Configuration (Tutorial page) JBrowse Scott Cain California Room
Jan. 11 (Sun) 4:30 - 6:10 Tripal Database Network and Initiatives Tripal Stephen Ficklin and Dorrie Main California Room
Jan 13. (Tue) 4:30 - 6:10 W354: Galaxy for SNP and Variant Data Analysis Galaxy Dave Clements California Room
Jan. 14 (Wed) 10:30 - 2:30 GMOD Workshop GMOD Scott Cain California Room

Tripal Database Network and Initiatives Workshop

The Tripal Database Network and Initiatives Workshop will be held, Sunday, January 11, in the California Room.

4:00-4:30 W872: Tripal Overview & Future Developments Stephen Ficklin
4:30 - 5:00 W873: Extending Tripal for Specialized Display and Management of Diversity and Breeding Data Lacey-Anne Sanderson
5:00 - 5:15 W874: GDR/CottonGen: Converting Legacy Sites to Tripal Sook Jung
5:15 - 5:30 W875: The i5k Workspace@Nal - a Tripal Based Arthropod Genome Portal Christopher Childers
5:30 - 5:45 W876: Tripal within the Arabidopsis Information Portal (AIP) Vivek Krishnakumar
5:45 - 6:00 W977: Tripal within the Legumes Genomics Community Ethalinda Cannon
6:00 - 6:10 W878: The Hardwood Genomics Database: Current Status and Future Directions after Four Years of Development Margaret Staton


GMOD Workshop

The GMOD workshop on Wednesday January 14th will be held in the Golden West room. The schedule is:

10:30 - 10:50 W407 - The Future of GMOD and Chado Scott Cain
10:50 - 11:10 W408 - KnowPulse: A Breeder-Focused Web Portal That Integrates Genetics and Genomics of Pulse Crops with Model Genomes Lacey-Anne Sanderson
11:10 - 11:30 W409 - Phytozome Population Diversity Visualization in JBrowse: A very large Dataset Case Study Richard Hayes
11:30 - 11:50 W410 - JBrowse within the Arabidopsis Information Portal (AIP) Project Vivek Krishnakumar
11:50 - 12:10 W411 - Apollo + i5K: Collaborative Curation and Interactive Analysis of Genomes Monica Munoz-Torres
12:10 - 12:30 W412 - The Teosinte (Zea mays ssp. parviglumis) de novo Genome Assembly Arun S. Seetharam
12:30 - 1:30 Lunch Break
1:30 Panel Discussion TBD

GMOD Consumers and Providers

There are also many groups who use GMOD components showing posters, and giving presentations and workshops; here is a small selection:

Time Title Presenter Location
Saturday January 10
9:35 - 9:55 W068: Progress on the I5K Pilot at the Baylor College of Medicine Human Genome Sequencing Center Kim Worley Esquire
10:30 - 11:00 W238: Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines) Dave Micklos California Room
10:30 - 11:00 W571: GenSAS Dorrie Main Pacific Salon 6-7
12:00 - 12:40 W159: Management and Visualization of Ianimal Quantitative Data Using iPlant and EPIC-CoGe Sabarinath Subramaniam San Diego
2:10 - 2:30 W162: Citrus Genome DB Updates Sook Jung Pacific Salon 6-7
2:10 - 2:30 C3: GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence Jodi Humann California Room
4:00 - 6:10 W377: Genome management and analysis with CoGe Haibao Tang and Eric Lyons California Room
Sunday January 11
9:00 - 9:20 W695: Introducing Undergraduate Students to Gene and Genome Structure through Gene Annotation Brent Buckner Towne
1:30 - 1:50 W311: TreeGenes: A Comprehensive Resource for Forest Tree Genomics Emily Grau Sunrise
2:30- 2:50 W421: Overview of the GnpIS Grape Genomics and Genetic Integrative Resource for Diversity Studies Nacer Mohellibi Pacific Salon 6-7
Monday January 12
EVEN
10:00 - 11:30 P268: New Data Mining Interfaces at the Bovine Genome Database Colin Diesh Poster session
10:00 - 11:30 P346: PeanutBase: A Resource for Peanut Genetic, Genomic, and Trait Information Ethalinda Cannon Poster session
10:00 - 11:30 P654: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B Thomas Letellier Poster session
10:00 - 11:30 P790: Data Integration for the Plant Research Community: The Arabidopsis Information Portal Chia-Yi Cheng Poster session
10:00 - 11:30 P792: Developing Content for the Arabidopsis Information Portal Matt Vaughn Poster session
10:00 - 11:30 P852: TOMATOMICS: An Integrated Database for Omics Information in Tomato Soichi Ozaki Poster session
10:00 - 11:30 P1010: The i5k Workspace@NAL - Enabling Genomic Data Access, Visualization, and Curation of Arthropod Genomes Monica Poelchau Poster session
10:00 - 11:30 P778: CicArVarDB: Chickpea Variation Database Poster session
10:00 - 11:30 [ P]: Poster session
10:00 - 11:30 [ P]: Poster session
2:30-2:45 C13: How to Use GDR, the Genome Database for Rosaceae Sook Joon California Room
2:45 - 3:00 C14: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research Jing Yu California Room
ODD
3:00 - 4:30 P101: High-Throughput SNP Genotyping for Crop Improvement Michael J. Thomson Poster session
3:00 - 4:30 P0267: Discovering Novel Protein-Coding Genes and Long Non-Coding RNAs in Bos taurus Darren Hagen Poster Session
3:00 - 4:30 P301: Tools for Phylogenomic Exploration within and Among Clade-Oriented Databases Alan Cleary Poster session
3:00 - 4:30 P953: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research Jing Yu Poster session
3:00 - 4:30 P1029: The Construction of Genome Annotation Database for Liverwort Hideki Nagasaki Poster session
3:00 - 4:30 P1117: An Integrated Annotation Data Warehouse at the Hymenoptera Genome Database Aditi Tayal Poster session
3:00 - 4:30 P1153: GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence Jodi Humann Poster session
3:00 - 4:30 P839: Accessing SGN Genomes through Tools Susan Strickler Poster session
3:00 - 4:30 [ P]: Poster session
Tuesday January 13
11:00 - 11:15 C17: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B Thomas Letellier California Room
11:15 - 11:30 C18: Using the Wheat Tilling Database to Search Mutants of Interest Hans Vasquez-Gross California Room
11:15 - 11:35 W725: Accessing SGN Genomes through Tools Susan Strickler Towne
11:30 - 11:45 C19: TreeGenes and CartograTree: Tools for Forest Tree Genomics Emily Grau California Room
12:10 - 12:40 W074: Updates on the Musa acuminata Reference Genome Sequence
12:30 - 12:45 C23: Using the Arabidopsis Information Portal Jason Miller California Room
4:00 - 6:10 W354: Galaxy for SNP and Variant Data Analysis Dave Clements California Room
Wednesday January 14
10:30 - 2:30 GMOD Workshop Scott Cain and the GMOD Community Golden West