GMOD
PAG 2015
There is plenty of GMOD content at the Plant and Animal Genomes (PAG) conference in January
- There is a dedicated GMOD Workshop and also posters and presentations from many GMOD users, as well as from developers of GMOD tools.
Contents
- 1 Core GMOD Content
- 2 Tripal Database Network and Initiatives Workshop
- 3 GMOD Workshop
- 4 GMOD Consumers and Providers
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 |