Difference between revisions of "PAG 2015"

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There are also many groups who use GMOD components showing posters, and giving presentations and workshops; here is a small selection:
 
There are also many groups who use GMOD components showing posters, and giving presentations and workshops; here is a small selection:
  
{|
+
{| class="wikitable"
!Time !! Title !! Presenter !! Location
+
 
|-  
 
|-  
| colspan=3 | '''Saturday January 10'''
+
! colspan=4 | '''Saturday January 10'''
 +
|-
 +
!Time !! Title !! Presenter !! Location
 
|-
 
|-
 
| 9:00 - 9:30 || [https://pag.confex.com/pag/xxiii/webprogram/Session2680.html W569]: Sugar Pine Annotation || Jill Wegrzyn || Pacific Salon 6-7
 
| 9:00 - 9:30 || [https://pag.confex.com/pag/xxiii/webprogram/Session2680.html W569]: Sugar Pine Annotation || Jill Wegrzyn || Pacific Salon 6-7
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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
 
| 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
 
|-
 
|-
| colspan=3 | '''Sunday January 11'''
+
! colspan=4 | '''Sunday January 11'''
 
|-
 
|-
 
| 8:15 - 9:15 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14232.html W369]: Browsing Genes and Genomes with Ensembl and Ensembl Genomes || Emily Perry || California Room
 
| 8:15 - 9:15 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14232.html W369]: Browsing Genes and Genomes with Ensembl and Ensembl Genomes || Emily Perry || California Room
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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
 
|-
 
|-
| colspan=3 | '''Monday January 12'''
+
! colspan=4 | '''Monday January 12'''
|-
+
| EVEN
+
 
|-
 
|-
 
| 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
 
| 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/Paper16166.html P1168]: Improving Maker Gene Annotations in Grasses through the Use of GC Specific Hidden Markov Models || Kevin Childs || Poster session
 
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16166.html P1168]: Improving Maker Gene Annotations in Grasses through the Use of GC Specific Hidden Markov Models || Kevin Childs || Poster session
|-
 
|10:00 - 11:30 || [ P]:  ||  || Poster session
 
 
|-
 
|-
 
| 1:50 - 2:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15999.html C11]: Methods for Collecting, Integrating, and Displaying Complex Genetic Data, Using the Legume Information System and PeanutBase || Andrew Farmer || California Room
 
| 1:50 - 2:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15999.html C11]: Methods for Collecting, Integrating, and Displaying Complex Genetic Data, Using the Legume Information System and PeanutBase || Andrew Farmer || 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
 
| 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
 
 
|-
 
|-
 
| 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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|-
 
|-
 
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17285.html P839]: Accessing SGN Genomes through Tools || Susan Strickler || Poster session
 
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17285.html P839]: Accessing SGN Genomes through Tools || Susan Strickler || Poster session
|-
 
| 3:00 - 4:30 || [ P]:  || || Poster session
 
 
|-
 
|-
 
| 6:35 - 6:40 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17298.html W481]: Flash Demo: Annotating genomes with MAKER-P and the iPlant Discovery Environment || Sabarinath Subramaniam || California Room
 
| 6:35 - 6:40 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17298.html W481]: Flash Demo: Annotating genomes with MAKER-P and the iPlant Discovery Environment || Sabarinath Subramaniam || California Room
 
|-
 
|-
| colspan=3 | '''Tuesday January 13'''
+
! colspan=4 | '''Tuesday January 13'''
 
|-
 
|-
 
| 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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| 4:00 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Session2641.html W354]: [[Galaxy]] for SNP and Variant Data Analysis || [[User:Clements|Dave Clements]] || California Room
 
| 4:00 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Session2641.html W354]: [[Galaxy]] for SNP and Variant Data Analysis || [[User:Clements|Dave Clements]] || California Room
 
|-  
 
|-  
| colspan=3 | '''Wednesday January 14'''
+
! colspan=4 | '''Wednesday January 14'''
 
|-
 
|-
 
| 10:30 - 2:30|| [[#GMOD Workshop|GMOD Workshop]] || [[User:Scott|Scott Cain]] and the GMOD Community || Golden West
 
| 10:30 - 2:30|| [[#GMOD Workshop|GMOD Workshop]] || [[User:Scott|Scott Cain]] and the GMOD Community || Golden West

Revision as of 18:11, 19 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:

Saturday January 10
Time Title Presenter Location
9:00 - 9:30 W569: Sugar Pine Annotation Jill Wegrzyn Pacific Salon 6-7
9:35 - 9:55 W68: Progress on the I5K Pilot at the Baylor College of Medicine Human Genome Sequencing Center Kim Worley Esquire
10:30 - 11:00 W258: 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
8:15 - 9:15 W369: Browsing Genes and Genomes with Ensembl and Ensembl Genomes Emily Perry California Room
8:54 - 9:12 W611: QTL Data Standards at PeanutBase and LegumeInfo Ethalinda Cannon Pacific Salon 3
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
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 P778: CicArVarDB: Chickpea Variation Database Valentin Guignon 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 P852: Managing Banana Genetic Resources and Genomic Information with the Triplet Drupal/Tripal/Chado Valentin Guignon Poster session
10:00 - 11:30 P988: Genome Annotation and Repeat Sequence Characterization in Sugar Pine (Pinus lambertiana) Robin Paul Poster session
10:00 - 11:30 P1002: The Ensembl Farm: All You Need Is Livestock Thibaut Hourlier 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 P1118: The i5k Workspace@NAL - Enabling Genomic Data Access, Visualization, and Curation of Arthropod Monica Poelchau Poster session
10:00 - 11:30 P1124: Deploying and Maintaining Large Intermine Implementations: Phytomine at Phytozome Joseph Carlson Poster session
10:00 - 11:30 P1132: Grass Genomes in Ensembl Plants Paul Kersey Poster session
10:00 - 11:30 P1168: Improving Maker Gene Annotations in Grasses through the Use of GC Specific Hidden Markov Models Kevin Childs Poster session
1:50 - 2:10 C11: Methods for Collecting, Integrating, and Displaying Complex Genetic Data, Using the Legume Information System and PeanutBase Andrew Farmer California Room
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
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 P737: PeanutBase: A Resource for Peanut Genetic, Genomic, and Trait Information Ethalinda Cannon Poster session
3:00 - 4:30 P697: The Legume Information System (LegumeInfo.org) 2015 Steven Cannon 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 P1119: Browsing and Comparing Genomes Using the Gramene/Ensembl Plants Browser Joshua Stein 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
6:35 - 6:40 W481: Flash Demo: Annotating genomes with MAKER-P and the iPlant Discovery Environment Sabarinath Subramaniam California Room
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
11:50 - 12:06 W838: VitisCyc: A Metabolic Pathway Knowledgebase for Grape (Vitis vinifera) Sushma Naithani Pacific Salon 1
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
1:30 - 1:50 W413: Browsing and Comparing Genomes Using the Gramene/Ensembl Plants Browser Joshua Stein Poster session
1:50 - 2:10 Programmatic Interfaces to Plant Genomic Data Paul Kersey 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