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 || Links | ||
+ | |- | ||
+ | | 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) || 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 | + | | 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 | + | | 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 | + | | 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 | + | | 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" | ||
|- | |- | ||
− | + | ! Time !! Topic !! Presenter !! Links | |
|- | |- | ||
− | | 4: | + | | 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] |
|- | |- | ||
− | | | + | | 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: | + | | 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: | + | | 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: | + | | 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" | ||
|- | |- | ||
− | + | ! Time !! Topic !! Presenter !! Links | |
|- | |- | ||
− | | 10: | + | | 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]] |
|- | |- | ||
− | | | + | | 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: | + | | 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: | + | | 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] |
|- | |- | ||
− | | | + | | 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: | + | | 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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{| | {| | ||
− | |||
|- | |- | ||
− | + | ! 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: | + | | 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 - 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 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 || | ||
|- | |- | ||
− | | | + | |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 || |
|- | |- | ||
− | | | + | |10:00 - 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 || |
|- | |- | ||
− | | | + | |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= | + | |- |
− | | '''Wednesday January 14''' | + | |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] |
+ | |- | ||
+ | |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 || | ||
+ | |- | ||
+ | |10:00 - 11:30 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14525.html P1132]: Grass Genomes in Ensembl Plants || Paul Kersey || Poster session || | ||
+ | |- | ||
+ | | 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] | ||
+ | |- | ||
+ | |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 || | ||
+ | |- | ||
+ | | 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 || | ||
+ | |- | ||
+ | | 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] | ||
+ | |- | ||
+ | | 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 || | ||
+ | |- | ||
+ | | 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/Paper16344.html P267]: Discovering Novel Protein-Coding Genes and Long Non-Coding RNAs in ''Bos taurus'' || Darren Hagen || 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/Paper15302.html P737]: 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/Paper15992.html P697]: The Legume Information System (LegumeInfo.org) 2015 || Steven Cannon || 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 || | ||
+ | |- | ||
+ | | 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 || | ||
+ | |- | ||
+ | | 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]] | ||
+ | |- | ||
+ | | 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/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/Paper17285.html P839]: Accessing SGN Genomes through Tools || Susan Strickler || 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 || | ||
+ | |- | ||
+ | ! colspan=5 style="background-color: #ccc;" | <span id="Tuesday">'''Tuesday January 13'''</span> | ||
+ | |- | ||
+ | | 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]] | ||
+ | |- | ||
+ | | 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] | ||
+ | |- | ||
+ | | 11:15 - 11:35 || [https://pag.confex.com/pag/xxiii/webprogram/Paper14181.html W725]: Accessing SGN Genomes through Tools || Susan Strickler || Towne || | ||
+ | |- | ||
+ | | 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 || | ||
+ | |- | ||
+ | | 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 || | ||
+ | |- | ||
+ | | 12:30 - 12:45 || [https://pag.confex.com/pag/xxiii/webprogram/Paper16135.html C23]: Using the Arabidopsis Information Portal || Jason Miller || California || | ||
+ | |- | ||
+ | | 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] | ||
+ | |- | ||
+ | | 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 ||[https://wiki.galaxyproject.org/Documents/Presentations?action=AttachFile&do=view&target=2015_PAG_Variant.pdf Slides] | ||
+ | |- | ||
+ | ! colspan=5 style="background-color: #ccc;" | <span id="Wednesday">'''Wednesday January 14'''</span> | ||
|- | |- | ||
− | | 10:30 - 2:30|| [[#GMOD Workshop|GMOD Workshop]] || 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
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.
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 |