GMOD

PAG 2015

(Redirected from PAG

Plant and Animal Genomes 2015 (PAG XXIII

There is plenty of GMOD content at the Plant and Animal Genomes (PAG) conference in January

  1. There is a dedicated GMOD Workshop and also posters and presentations from many GMOD users, as well as from developers of GMOD tools.

Contents

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 |

Category:

Documentation

Community

Tools