Difference between revisions of "PAG 2015"

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There are a number of items focussed on the tools and services that GMOD provides. These are:
 
There are a number of items focussed on the tools and services that GMOD provides. These are:
  
{| class="wikitable"
+
{| class="wikitable sortable"
 
|-
 
|-
! Date !! Time !! Session !! Component(s) !! Presenter / Organizer !! Location
+
! Date !! Time !! Session !! Component(s) !! Presenter / Organizer !! Location || Links
 
|-
 
|-
| Jan. 11 (Sun) || 1:30 - 3:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17123.html W367]: [[JBrowse]] Installation and Configuration ([[JBrowse_Tutorial_PAG_2015|Tutorial page]]) || [[JBrowse]] || [[User:Scott|Scott Cain]] || California Room
+
| Jan 10 (Sat) || 1:50 - 2:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14951.html Web Apollo 2.0: A Scalable, Distributed Sequence Annotation Editor] || [[WebApollo]] || Nathan Dunn || California Room || [http://genomearchitect.org/pag-2015 Poster]
 
|-
 
|-
| Jan. 11 (Sun) || 4:30 - 6:10 || [[#Tripal Database Network and Initiatives Workshop|Tripal Database Network and Initiatives]] || [[Tripal]] || Stephen Ficklin and Dorrie Main || California Room
+
| Jan 11 (Sun) || 1:30 - 3:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17123.html W367]: [[JBrowse]] Installation and Configuration  || [[JBrowse]] || [[User:Scott|Scott Cain]] || California Room || [[JBrowse_Tutorial_PAG_2015|Tutorial page]]
 
|-
 
|-
| Jan 13. (Tue) || 4:30 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Session2641.html W354]: [[Galaxy]] for SNP and Variant Data Analysis || [[Galaxy]] || [[User:Clements|Dave Clements]] || California Room
+
| Jan 12 (Mon) || 10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14964.html P1154: WebApollo 2.0: A Scalable, Distributed Sequence Annotation Editor for Multiple Genomes] || [[WebApollo]] || Nathan Dunn || Poster Session || [http://genomearchitect.org/pag-2015 Poster]
 
|-
 
|-
| Jan. 14 (Wed) || 10:30 - 2:30 || [[#GMOD Workshop|GMOD Workshop]] || GMOD || [[User:Scott|Scott Cain]] || California Room
+
| Jan 11 (Sun) || 4:00 - 6:10 || [[#Tripal Database Network and Initiatives Workshop|Tripal Database Network and Initiatives]] || [[Tripal]] || Stephen Ficklin and Dorrie Main || California Room || [[#Tripal Database Network and Initiatives Workshop|See below]]
 +
|-
 +
| Jan 13 (Tue) || 4:00 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Session2641.html W354]: [[Galaxy]] for SNP and Variant Data Analysis || [[Galaxy]] || [[User:Clements|Dave Clements]] || California Room || [https://wiki.galaxyproject.org/Documents/Presentations?action=AttachFile&do=view&target=2015_PAG_Variant.pdf Slides]
 +
|-
 +
| Jan 14 (Wed) || 10:30 - 2:30 || [[#GMOD Workshop|GMOD Workshop]] || GMOD || [[User:Scott|Scott Cain]] || California Room || [[#GMOD Workshop|See below]]
 
|}
 
|}
  
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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
| 4:00-4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14953.html W872]: [[Tripal]] Overview & Future Developments || Stephen Ficklin
+
! Time !! Topic !! Presenter !! Links
 
|-
 
|-
| 4:30 - 5:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14948.html W873]: Extending [[Tripal]] for Specialized Display and Management of Diversity and Breeding Data || Lacey-Anne Sanderson
+
| 4:00-4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14953.html W872]: [[Tripal]] Overview & Future Developments || Stephen Ficklin || [http://www.rosaceae.org/sites/default/files/files/Tripal_Workshop_PAG2015.pdf Slides]
 
|-
 
|-
| 5:00 - 5:15 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14947.html W874]: GDR/CottonGen: Converting Legacy Sites to [[Tripal]] || Sook Jung
+
| 4:30 - 5:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14948.html W873]: Extending [[Tripal]] for Specialized Display and Management of Diversity and Breeding Data || Lacey-Anne Sanderson ||
 
|-
 
|-
| 5:15 - 5:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14955.html W875]: The i5k Workspace@Nal - a Tripal Based Arthropod Genome Portal || Christopher Childers
+
| 5:00 - 5:15 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14947.html W874]: GDR/CottonGen: Converting Legacy Sites to [[Tripal]] || Sook Jung || [http://www.rosaceae.org/sites/default/files/files/Tripal_GDR_2015.ppsx Slides]
 
|-
 
|-
| 5:30 - 5:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15710.html W876]: Tripal within the Arabidopsis Information Portal (AIP) || Vivek Krishnakumar
+
| 5:15 - 5:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14955.html W875]: The i5k Workspace@Nal - a Tripal Based Arthropod Genome Portal || Christopher Childers || [https://i5k.nal.usda.gov/sites/default/files/childers_PAG_2015_Tripal.pptx Slides]
 
|-
 
|-
| 5:45 - 6:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14952.html W977]: Tripal within the Legumes Genomics Community || Ethalinda Cannon
+
| 5:30 - 5:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15710.html W876]: Tripal within the Arabidopsis Information Portal (AIP) || Vivek Krishnakumar || [http://www.slideshare.net/vivekkrish/w876-tripalaraportpag2015 Slides]
 
|-
 
|-
| 6:00 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14949.html W878]: The Hardwood Genomics Database: Current Status and Future Directions after Four Years of Development || Margaret Staton  
+
| 5:45 - 6:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14952.html W977]: Tripal within the Legumes Genomics Community || Ethalinda Cannon || [[Media:CannonTripalLegumes_PAG2015.pptx|Slides]]
 +
|-
 +
| 6:00 - 6:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14949.html W878]: The Hardwood Genomics Database: Current Status and Future Directions after Four Years of Development || Margaret Staton || [http://www.slideshare.net/mestato/staton-pag-tripal2015?related=1 Slides]
 
|}
 
|}
 
  
 
== GMOD Workshop ==
 
== GMOD Workshop ==
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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
| 10:30 - 10:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17188.html  W407] - The Future of GMOD and [[Chado]] || [[User:Scott|Scott Cain]]
+
! Time !! Topic !! Presenter !! Links
 
|-
 
|-
| 10:50 - 11:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17190.html W408] - KnowPulse: A Breeder-Focused Web Portal That Integrates Genetics and Genomics of Pulse Crops with Model Genomes  || Lacey-Anne Sanderson
+
| 10:30 - 10:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17188.html W407] - The Future of GMOD and [[Chado]] || [[User:Scott|Scott Cain]] || [[Media:The future of GMOD and Chado.pdf|Slides]]
 
|-
 
|-
| 11:10 - 11:30  || [https://pag.confex.com/pag/xxiii/webprogram/Paper17187.html W409] - Phytozome Population Diversity Visualization in [[JBrowse]]: A very large Dataset Case Study || Richard Hayes
+
| 10:50 - 11:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17190.html W408] - KnowPulse: A Breeder-Focused Web Portal That Integrates Genetics and Genomics of Pulse Crops with Model Genomes  || Lacey-Anne Sanderson ||  
 
|-
 
|-
| 11:30  - 11:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17189.html W410] - [[JBrowse]] within the Arabidopsis Information Portal (AIP) Project  || Vivek Krishnakumar
+
| 11:10 - 11:30  || [https://pag.confex.com/pag/xxiii/webprogram/Paper17187.html W409] - Phytozome Population Diversity Visualization in [[JBrowse]]: A very large Dataset Case Study || Richard Hayes ||
 
|-
 
|-
| 11:50 - 12:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17193.html W411] - [[Apollo]] + i5K: Collaborative Curation and Interactive Analysis of Genomes || Monica Munoz-Torres
+
| 11:30  - 11:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17189.html W410] - [[JBrowse]] within the Arabidopsis Information Portal (AIP) Project  || Vivek Krishnakumar || [http://www.slideshare.net/vivekkrish/jbrowse-within-the-arabidopsis-information-portal Slides]
 
|-
 
|-
| 12:10 - 12:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17385.html W412] - The Teosinte (''Zea mays'' ssp. ''parviglumis) de novo'' Genome Assembly || Arun S. Seetharam
+
| 11:50 - 12:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17193.html W411] - [[Apollo]] + i5K: Collaborative Curation and Interactive Analysis of Genomes || [https://www.linkedin.com/in/monimunozto Monica Munoz-Torres] || [http://genomearchitect.org/pag-2015 Slides]
 
|-
 
|-
| 12:30 - 1:30 ||colspan="2" | Lunch Break
+
| 12:10 - 12:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17385.html W412] - The Teosinte (''Zea mays'' ssp. ''parviglumis) de novo'' Genome Assembly || Arun S. Seetharam ||
 
|-
 
|-
| 1:30  || Panel Discussion  || TBD
+
| 12:30 - 1:30 ||colspan="3" | Lunch Break
 +
|-
 +
| 1:30  || Panel Discussion  || TBD ||
 
|}
 
|}
  
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{|
 
{|
!Time !! Title !! Presenter !! Location
 
 
|-  
 
|-  
| colspan=3 | '''Saturday January 10'''
+
! colspan=5 style="background-color: #ccc;" | <span id="Saturday">'''Saturday January 10'''</span>
 +
|-
 +
!Time !! Title !! Presenter !! Location !! Links
 +
|-
 +
| 9:00 - 9:30 || [https://pag.confex.com/pag/xxiii/webprogram/Session2680.html W569]: Sugar Pine Annotation || Jill Wegrzyn || Pacific Salon 6-7 ||
 +
|-
 +
| 9:35 - 9:55 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17320.html W68]: Progress on the I5K Pilot at the Baylor College of Medicine Human Genome Sequencing Center  || Kim Worley || Esquire ||
 +
|-
 +
| 10:30&nbsp;-&nbsp;11:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17295.html W258]: Simplifying Genome Annotation and Examples of Large-Scale Projects in DNA Barcoding (Red and Blue Lines) || Dave Micklos || California ||
 +
|-
 +
| 10:30 - 11:00 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15662.html W571]: GenSAS || Dorrie Main || Pacific Salon 6-7 || [http://www.rosaceae.org/sites/default/files/files/GenSAS_Pine_Workshop_Final_PAG2015.pdf Slides]
 +
|-
 +
| 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 ||
 +
|-
 +
| 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/Paper15396.html C3]: GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence || Jodi Humann || California || [http://www.rosaceae.org/sites/default/files/files/GenSAS_PAG2015_demo_010815.ppsx Slides]
 +
|-
 +
| 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 || [https://genomevolution.org/wiki/index.php/2015_PAG_Computer_Demo Slides, instructions, manual]
 +
|-
 +
! colspan=5 style="background-color: #ccc;" | <span id="Sunday">'''Sunday January 11'''</span>
 +
|-
 +
| 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 || [http://www.ebi.ac.uk/~emily/Workshops/2015/PAG/ensembl_presentation.pdf Slides] ([[BioMart]] slides 24-29), [http://www.ebi.ac.uk/~emily/Workshops/2015/PAG/ensembl_full_coursebook.pdf Handouts] ([[BioMart]]: pages 33-39)
 +
|-
 +
| 8:54 - 9:12 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16060.html W611]: QTL Data Standards at PeanutBase and LegumeInfo || Ethalinda Cannon || Pacific Salon 3 || [[Media:CannonPhenotypeQTL_PAG2015.pptx|Slides]]
 +
|-
 +
| 9:00 - 9:20 || [https://pag.confex.com/pag/xxiii/webprogram/Session2852.html W695]: Introducing Undergraduate Students to Gene and Genome Structure through Gene Annotation || Brent Buckner || Towne ||
 +
|-
 +
| 1:30 - 1:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14647.html W311]:  TreeGenes: A Comprehensive Resource for Forest Tree Genomics || Emily Grau || Sunrise  || [http://loblolly.ucdavis.edu/bipod/ftp/Presentations/PAG2015/W311_TreeGenes_2015.pdf Slides]
 +
|-
 +
| 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 || [[Media:MohellibiGrapevine_PAG2015.pdf|Slides]]
 +
|-
 +
! colspan=5 style="background-color: #ccc;" | <span id="Monday">'''Monday January 12'''</span>
 +
|-
 +
| 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&nbsp;session || [[Media:BovineMine_PAG2015.pdf|Poster]]
 +
|-
 +
|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 || [[Media:PeanutBase_PAG2015_Poster.pdf|Poster]]
 +
|-
 +
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17569.html P432]: Apollo + i5K: Collaborative Curation and Interactive Analysis of Genomes || Monica Munoz-Torres || Poster session || [[Media:PAG2015-Web-Apollo_Munoz-Torres.pdf|Poster]]
 +
|-
 +
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14696.html P654]: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B || Thomas Letellier  || Poster session || [[Media:Wheat3bMinePoster_PAG2015.pdf|Poster]]
 +
|-
 +
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15952.html P778]: CicArVarDB: Chickpea Variation Database || Valentin Guignon || Poster session ||
 +
|-
 +
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16112.html P790]: Data Integration for the Plant Research Community: The Arabidopsis Information Portal || Chia-Yi Cheng || Poster session ||
 +
|-
 +
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16142.html P792]: Developing Content for the Arabidopsis Information Portal || Matt Vaughn || Poster session ||
 +
|-
 +
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15461.html P852]: TOMATOMICS: An Integrated Database for Omics Information in Tomato || Soichi Ozaki || Poster session ||
 
|-
 
|-
| 9:35 - 9:55 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17320.html W068]: Progress on the I5K Pilot at the Baylor College of Medicine Human Genome Sequencing Center  || Kim Worley || Esquire
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16068.html P944]: Managing Banana Genetic Resources and Genomic Information with the Triplet Drupal/Tripal/Chado || Valentin Guignon || Poster session ||
 
|-
 
|-
| 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
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16259.html P988]: Genome Annotation and Repeat Sequence Characterization in Sugar Pine ''(Pinus lambertiana)'' || Robin Paul || Poster session ||
 
|-
 
|-
| 2:10 - 2:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16326.html W162]: Citrus Genome DB Updates || Sook Jung || Pacific Salon 6-7
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16165.html P1002]: The Ensembl Farm: All You Need Is Livestock || Thibaut Hourlier || Poster session ||
 
|-
 
|-
| colspan=3 | '''Sunday January 11'''
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16655.html P1118]: The i5k Workspace@NAL - Enabling Genomic Data Access, Visualization, and Curation of Arthropod  || Monica Poelchau || Poster session || [https://i5k.nal.usda.gov/sites/default/files/PAG_2015-2.pdf Poster]
 
|-
 
|-
| 9:00 - 9:20 || [https://pag.confex.com/pag/xxiii/webprogram/Session2852.html W695]: Introducing Undergraduate Students to Gene and Genome Structure through Gene Annotation || Brent Buckner || Towne
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16440.html P1124]: Deploying and Maintaining Large Intermine Implementations: Phytomine at Phytozome || Joseph Carlson || Poster session ||
 
|-
 
|-
| 1:30 - 1:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14647.html W311]:  TreeGenes: A Comprehensive Resource for Forest Tree Genomics || Emily Grau || Sunrise
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14525.html P1132]: Grass Genomes in Ensembl Plants || Paul Kersey || Poster session ||
 
|-
 
|-
| 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
+
| 10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14964.html P1154]: [[WebApollo]] 2.0: A Scalable, Distributed Sequence Annotation Editor for Multiple Genomes] || Nathan Dunn || Poster Session || [http://genomearchitect.org/pag-2015 Poster]
 
|-
 
|-
| 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
+
|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 ||
 
|-
 
|-
| colspan=3  | '''Monday January 12'''
+
| 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 ||
 
|-
 
|-
| EVEN
+
| 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 || [http://www.rosaceae.org/sites/default/files/files/GDRdemo_PAG2015.ppsx Slides]
 
|-
 
|-
|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
+
| 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 ||
 
|-
 
|-
|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
+
| 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 ||
-
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14696.html P654]: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B || Thomas Letellier  || Poster session
+
 
|-
 
|-
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16112.html P790]: Data Integration for the Plant Research Community: The Arabidopsis Information Portal || Chia-Yi Cheng || Poster session
+
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16344.html P267]: Discovering Novel Protein-Coding Genes and Long Non-Coding RNAs in ''Bos taurus'' || Darren Hagen || Poster session ||
 
|-
 
|-
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16142.html P792]: Developing Content for the Arabidopsis Information Portal || Matt Vaughn || 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 ||
||-
+
|10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15461.html P852]: TOMATOMICS: An Integrated Database for Omics Information in Tomato || Soichi Ozaki || 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
+
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15302.html P737]: PeanutBase: A Resource for Peanut Genetic, Genomic, and Trait Information || Ethalinda Cannon || Poster session ||
 
|-
 
|-
|10:00 - 11:30 || [ P]: || || Poster session
+
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15992.html P697]: The Legume Information System (LegumeInfo.org) 2015 || Steven Cannon || Poster session ||
 
|-
 
|-
|10:00 - 11:30 || [ P]:  || || Poster session
+
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15773.html P953]: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research || Jing Yu || Poster session ||
 
|-
 
|-
|10:00 - 11:30 || [ P]: || || Poster session
+
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15982.html P1029]: The Construction of Genome Annotation Database for Liverwort || Hideki Nagasaki || Poster session ||
 
|-
 
|-
| 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
+
| 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 || [[Media:HymenopteraMine_PAG2015.pdf|Poster]]
 
|-
 
|-
| ODD
+
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper17236.html P1119]: Browsing and Comparing Genomes Using the Gramene/Ensembl Plants Browser || Joshua Stein || Poster session || [http://de.iplantcollaborative.org/dl/d/5774899A-02E1-4075-91C2-9D7D8E30D42B/OGE_Gramene_poster_PAG2015.pdf Poster]
 
|-
 
|-
| 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/Paper15379.html P1153]: GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence || Jodi Humann || 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
+
| 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/Paper15773.html P953]: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research  || Jing Yu || 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  ||
 
|-
 
|-
| 3:00 - 4:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15982.html P1029]: The Construction of Genome Annotation Database for Liverwort || Hideki Nagasaki || Poster session
+
! colspan=5 style="background-color: #ccc;" | <span id="Tuesday">'''Tuesday January 13'''</span>
 
|-
 
|-
| 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
+
| 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 || [[Media:Wheat3bMineDemo_PAG2015.pdf|Slides]]
 
|-
 
|-
| 3:00 - 4:30 || [ P]: || || Poster session
+
| 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 || [http://dubcovskylab.ucdavis.edu/sites/default/files/hansvg/additional_files/computerdemo_pag2015v5.pdf Slides], [http://dubcovskylab.ucdavis.edu/wheat-tilling Wheat TILLING home page]
 
|-
 
|-
| 3:00 - 4:30 || [ P]: || || Poster session
+
| 11:15 - 11:35 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14181.html W725]: Accessing SGN Genomes through Tools || Susan Strickler || Towne ||
 
|-
 
|-
| 3:00 - 4:30 || [ P]: || || Poster session
+
| 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  || [http://loblolly.ucdavis.edu/bipod/ftp/Presentations/PAG2015/C19_TreeGenes_215.pdf Slides]
 
|-
 
|-
 +
| 11:50 - 12:06 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16825.html W838]: VitisCyc: A Metabolic Pathway Knowledgebase for Grape ''(Vitis vinifera)''  || Sushma Naithani || Pacific Salon 1 ||
 
|-
 
|-
| colspan=3 | '''Tuesday January 13'''
+
| 12:10 - 12:40 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14861.html W74]: Updates on the ''Musa acuminata'' Reference Genome Sequence || Angélique D'hont || Pacific Salon 6-7 ||
 
|-
 
|-
| 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
+
| 12:30 - 12:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16135.html C23]: Using the Arabidopsis Information Portal || Jason Miller || California ||
 
|-
 
|-
| 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
+
| 1:30 - 1:50 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15604.html W413]: Browsing and Comparing Genomes Using the Gramene/Ensembl Plants Browser || Joshua Stein || California || [http://de.iplantcollaborative.org/dl/d/9B849155-14AD-4B33-A339-7F6EEB496CED/steinj_Gramene_workshop_PAG2015.ppsx Slides]
 
|-
 
|-
| 12:30 - 12:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16135.html C23]: Using the Arabidopsis Information Portal || Jason Miller || California Room
+
| 1:50 - 2:10 || [https://pag.confex.com/pag/xxiii/webprogram/Paper15323.html Programmatic Interfaces to Plant Genomic Data] || Paul Kersey || California ||
 
|-
 
|-
| 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 ||[https://wiki.galaxyproject.org/Documents/Presentations?action=AttachFile&do=view&target=2015_PAG_Variant.pdf Slides]
 
|-  
 
|-  
| colspan=3 | '''Wednesday January 14'''
+
! colspan=5 style="background-color: #ccc;" | <span id="Wednesday">'''Wednesday January 14'''</span>
 
|-
 
|-
| 10:30 - 2:30|| [[#GMOD Workshop|GMOD Workshop]] || [[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 || [[#GMOD Workshop|See above]]
 
|}
 
|}
  
 
[[Category:Conferences]]
 
[[Category:Conferences]]

Latest revision as of 18:29, 31 March 2015

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 Links
Jan 10 (Sat) 1:50 - 2:10 Web Apollo 2.0: A Scalable, Distributed Sequence Annotation Editor WebApollo Nathan Dunn California Room Poster
Jan 11 (Sun) 1:30 - 3:10 W367: JBrowse Installation and Configuration JBrowse Scott Cain California Room Tutorial page
Jan 12 (Mon) 10:00 - 11:30 P1154: WebApollo 2.0: A Scalable, Distributed Sequence Annotation Editor for Multiple Genomes WebApollo Nathan Dunn Poster Session Poster
Jan 11 (Sun) 4:00 - 6:10 Tripal Database Network and Initiatives Tripal Stephen Ficklin and Dorrie Main California Room See below
Jan 13 (Tue) 4:00 - 6:10 W354: Galaxy for SNP and Variant Data Analysis Galaxy Dave Clements California Room Slides
Jan 14 (Wed) 10:30 - 2:30 GMOD Workshop GMOD Scott Cain California Room See below

Tripal Database Network and Initiatives Workshop

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

Time Topic Presenter Links
4:00-4:30 W872: Tripal Overview & Future Developments Stephen Ficklin Slides
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 Slides
5:15 - 5:30 W875: The i5k Workspace@Nal - a Tripal Based Arthropod Genome Portal Christopher Childers Slides
5:30 - 5:45 W876: Tripal within the Arabidopsis Information Portal (AIP) Vivek Krishnakumar Slides
5:45 - 6:00 W977: Tripal within the Legumes Genomics Community Ethalinda Cannon Slides
6:00 - 6:10 W878: The Hardwood Genomics Database: Current Status and Future Directions after Four Years of Development Margaret Staton Slides

GMOD Workshop

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

Time Topic Presenter Links
10:30 - 10:50 W407 - The Future of GMOD and Chado Scott Cain Slides
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 Slides
11:50 - 12:10 W411 - Apollo + i5K: Collaborative Curation and Interactive Analysis of Genomes Monica Munoz-Torres Slides
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 Links
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
10:30 - 11:00 W571: GenSAS Dorrie Main Pacific Salon 6-7 Slides
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 Slides
4:00 - 6:10 W377: Genome management and analysis with CoGe Haibao Tang and Eric Lyons California Slides, instructions, manual
Sunday January 11
8:15 - 9:15 W369: Browsing Genes and Genomes with Ensembl and Ensembl Genomes Emily Perry California Slides (BioMart slides 24-29), Handouts (BioMart: pages 33-39)
8:54 - 9:12 W611: QTL Data Standards at PeanutBase and LegumeInfo Ethalinda Cannon Pacific Salon 3 Slides
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 Slides
2:30- 2:50 W421: Overview of the GnpIS Grape Genomics and Genetic Integrative Resource for Diversity Studies Nacer Mohellibi Pacific Salon 6-7 Slides
Monday January 12
10:00 - 11:30 P268: New Data Mining Interfaces at the Bovine Genome Database Colin Diesh Poster session Poster
10:00 - 11:30 P346: PeanutBase: A Resource for Peanut Genetic, Genomic, and Trait Information Ethalinda Cannon Poster session Poster
10:00 - 11:30 P432: Apollo + i5K: Collaborative Curation and Interactive Analysis of Genomes Monica Munoz-Torres Poster session Poster
10:00 - 11:30 P654: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B Thomas Letellier Poster session Poster
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 P944: 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 P1118: The i5k Workspace@NAL - Enabling Genomic Data Access, Visualization, and Curation of Arthropod Monica Poelchau Poster session Poster
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 P1154: WebApollo 2.0: A Scalable, Distributed Sequence Annotation Editor for Multiple Genomes] Nathan Dunn Poster Session Poster
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
2:30-2:45 C13: How to Use GDR, the Genome Database for Rosaceae Sook Joon California Slides
2:45 - 3:00 C14: CottonGen: The Community Database for Cotton Genomics, Genetics and Breeding Research Jing Yu California
3:00 - 4:30 P101: High-Throughput SNP Genotyping for Crop Improvement Michael J. Thomson Poster session
3:00 - 4:30 P267: 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 Poster
3:00 - 4:30 P1119: Browsing and Comparing Genomes Using the Gramene/Ensembl Plants Browser Joshua Stein Poster session Poster
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
Tuesday January 13
11:00 - 11:15 C17: Wheat3BMine, a Data Warehouse Dedicated to Wheat Chromosome 3B Thomas Letellier California Slides
11:15 - 11:30 C18: Using the Wheat Tilling Database to Search Mutants of Interest Hans Vasquez-Gross California Slides, Wheat TILLING home page
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 Slides
11:50 - 12:06 W838: VitisCyc: A Metabolic Pathway Knowledgebase for Grape (Vitis vinifera) Sushma Naithani Pacific Salon 1
12:10 - 12:40 W74: Updates on the Musa acuminata Reference Genome Sequence Angélique D'hont Pacific Salon 6-7
12:30 - 12:45 C23: Using the Arabidopsis Information Portal Jason Miller California
1:30 - 1:50 W413: Browsing and Comparing Genomes Using the Gramene/Ensembl Plants Browser Joshua Stein California Slides
1:50 - 2:10 Programmatic Interfaces to Plant Genomic Data Paul Kersey California
4:00 - 6:10 W354: Galaxy for SNP and Variant Data Analysis Dave Clements California Slides
Wednesday January 14
10:30 - 2:30 GMOD Workshop Scott Cain and the GMOD Community Golden West See above