PAG 2015

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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