Difference between revisions of "PAG 2010"

From GMOD
Jump to: navigation, search
m
m (removing #icon)
 
(93 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
{{ImageLeft|Paglogo.gif|PAG 2010 Conference||http://www.intl-pag.org/}}
+
[[File:Paglogo.gif|link=http://www.intl-pag.org/|right|PAG 2010 Conference]]
−
{{ImageRight|Jan2009MtgLogoNoText.png|January 2010 GMOD Meeting|160|January 2010 GMOD Meeting}}
+
GMOD once again had a strong presence at the [http://www.intl-pag.org/ Plant and Animal Genome Conference (PAG XVIII)]. There were many workshops, computer demos, and posters, either about GMOD and  [[GMOD Components]], or using GMOD components.  This page lists the subset that mentioned GMOD or GMOD components in the abstract.
  
−
GMOD once again had a strong presence at the [http://www.intl-pag.org/ Plant and Animal Genome Conference (PAG 2010)].
 
  
−
There will be many workshops, computer demos, and posters, either about or using [[GMOD Components]].  This page will list items as they are listed on the [http://www.intl-pag.org/ PAG website].
+
== About GMOD Components ==
  
 +
[[File:PAG2010MAKERSession.jpg|thumb|300px|[[User:Carsonholt|Carson Holt]] presenting the [[MAKER]] genome annotation pipeline at PAG.]]
  
−
'''If you are attending PAG then please consider also attending the [[January 2010 GMOD Meeting]] that will be held in San Diego immediately after the PAG conference.'''
+
There were a record nine talks and workshops either entirely or partially about [[GMOD Components]].  It was the first time [[:Image:PAG2010Galaxy.pdf|Galaxy]], [[MAKER PAG 2010 Workshop|MAKER]], and [[:Image:PAG2010JBrowse.pdf|JBrowse]] were presented at PAG.  We also gave our first [[:Image:PAG2010GMODProjectUpdate.pdf|GMOD overview talk]] at PAG. There was a great dead of interest in GMOD and ll of the talks were well attended, with several of them being standing room only.
−
 
+
−
 
+
−
== About GMOD Components ==
+
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 19: Line 16:
 
! Components
 
! Components
 
|-
 
|-
−
! rowspan="1" | Saturday<br />Jan 9
+
! rowspan="2" | Saturday<br />Jan 9
−
! Computer & Training Workshop
+
! rowspan="2" | Computer & Training Workshop
 +
! 1:30-2:30
 +
! [[:Image:PAG2010Galaxy.pdf|Animal Genomics with Galaxy: Analyze, Publish, and Visualize]], [[User:DanB|Dan Blankenberg]]
 +
| [[Galaxy]]
 +
|-
 
! 3:50-6:00
 
! 3:50-6:00
 
! [[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]], [[User:Carsonholt|Carson Holt]]
 
! [[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]], [[User:Carsonholt|Carson Holt]]
 
| [[MAKER]]
 
| [[MAKER]]
 
|-
 
|-
−
! rowspan="1" | Sunday<br />Jan 10
+
! rowspan="2" | Sunday<br />Jan 10
−
! Computer & Training Workshop
+
! rowspan="2" | Computer & Training Workshop
−
! 1:15-3:25
+
! 8:15-9:15
 +
! [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI: Ensembl And Ensembl Genomes - Access To Genome-Scale Data Across The Taxonomic Space], Bert Overduin
 +
| [[BioMart]]
 +
|-
 +
! 1:30-3:40
 
! [[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse]], [[User:Scott|Scott Cain]]
 
! [[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse]], [[User:Scott|Scott Cain]]
 
| [[GBrowse]]
 
| [[GBrowse]]
 +
|-
 +
! rowspan="2" | Monday<br />Jan 11
 +
! rowspan="2" | Computer & Training Workshop
 +
! rowspan="1" | 12:50-1:10
 +
! [[:Image:PAG2010GMODProjectUpdate.pdf|GMOD Project Update]], [[User:Clements|Dave Clements]], [[User:Scott|Scott Cain]]
 +
| [[GMOD Components]]
 +
|-
 +
! 1:10-1:30
 +
! [[:Image:PAG2010JBrowse.pdf|Using the JBrowse Genome Browser with Large Amounts of Data]], [[User:MitchSkinner|Mitch Skinner]]
 +
| [[JBrowse]]
 
|-
 
|-
 
! rowspan="1" | Tuesday<br />Jan 12
 
! rowspan="1" | Tuesday<br />Jan 12
 
! Computer & Training Workshop
 
! Computer & Training Workshop
 
! 3:50-6:00
 
! 3:50-6:00
−
! [http://www.intl-pag.org/18/18-gramene.html Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses], Immanuel Yap
+
! [http://www.intl-pag.org/18/18-gramene.html Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses], Ken Youens-Clark
 
| [[CMap]]
 
| [[CMap]]
 
|-
 
|-
−
! rowspan="1" | Wednesday<br />Jan 13
+
! rowspan="2" | Wednesday<br />Jan 13
−
! Computer & Training Workshop
+
! rowspan="2" | Computer & Training Workshop
 
! 10:20-12:30
 
! 10:20-12:30
−
! [[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn: Visualizing your comparative genomics data with GBrowse_syn]], [[User:Mckays|Sheldon McKay]]
+
! [[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn: Visualizing your comparative genomics data with the Generic Synteny Browser]], [[User:Mckays|Sheldon McKay]]
 
| [[GBrowse_syn]]
 
| [[GBrowse_syn]]
−
<!--
 
 
|-
 
|-
−
! rowspan="3" | Monday<br />Jan 12
+
! 2:30-2:50
−
! EVEN Numbered Poster Session
+
! [[Media:PAG2010Tripal.pdf|Tripal: a Construction Toolkit for Online Genomic Databases]], [[User:Sficklin|Stephen Ficklin]]
−
! 10:00-11:30
+
| [[Tripal]], [[Chado]]
−
| [[#Posters|See below]] for a list of relevant posters.
+
−
|
+
−
|-
+
−
! [http://www.intl-pag.org/17/17-demos.html Computer Demo]
+
−
! 1:10-1:30
+
−
| [http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki EcoliWiki] and [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS]: Wiki-Based Systems for Community Annotation, [[User:JimHu|Jim Hu]], ''et al.''
+
−
| [[Table Editor]]
+
−
|-
+
−
! ODD Numbered Poster Session
+
−
!  | 3:00-4:30
+
−
| [[#Posters|See below]] for a list of relevant posters.
+
−
|
+
−
-->
+
 
|}
 
|}
  
Line 70: Line 71:
 
! Title & Author
 
! Title & Author
 
! Components
 
! Components
−
<!--
 
 
|-
 
|-
−
! rowspan="2" | Saturday<br />Jan 10
+
! rowspan="3" | Saturday<br>Jan 9
−
! [http://www.intl-pag.org/17/17-brassicas.html Brassicas Workshop]
+
! rowspan="3" | Workshop
−
! 11:20-11:40
+
! 8:45-9:05
−
| [http://www.intl-pag.org/17/abstracts/W10_Workshop_077.html Annotation And Data Mining For The ''Brassica rapa'' Genome Sequencing Project], Martin Trick, ''et al.''
+
! [http://www.intl-pag.org/18/abstracts/W32_PAGXVIII_249.html Full Genome Sequencing Of The Woodland Strawberry, ''Fragaria vesca''], Vladimir Shulaev
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
! [http://www.intl-pag.org/17/17-aqua.html Aquaculture Workshop]
+
! 11:40-12:00
−
! 4:20-4:40
+
! [[Media:PAG2010CMap3D.pdf|Development Of Tools For The Analysis And Visualisation Of Second Generation Sequencing Data For ''Brassica'' Species]], Chris Duran
−
| [http://www.intl-pag.org/17/abstracts/W04_Workshop_025.html A Review Of The Marine Genomics Project, A Web-Based Genomic And Transcriptional Database], Stephen P Ficklin, ''et al.''
+
| [[CMap]] ([[CMap3D]])
−
| [[Chado]], [[GBrowse]]
+
 
|-
 
|-
−
! rowspan="3" | Sunday<br />Jan 11
 
−
! [http://www.intl-pag.org/17/17-large-insert.html Large Insert DNA Libraries Workshop]
 
−
! 8:25-8:45
 
−
| [http://www.intl-pag.org/17/abstracts/W39_Workshop_294.html Use Of The Soybean Physical Map Derived Minimum Tile For BIBAC Plant Transformations Encompassing The Entire Genome], David A Lightfoot
 
−
| [[GBrowse]]
 
 
|-
 
|-
−
! [http://www.intl-pag.org/17/17-foresttree.html Forest Trees workshop]
+
! 4:10-4:30
−
! 2:15-2:30
+
! [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_914.html The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation], Takeshi Itoh
−
| [http://www.intl-pag.org/17/abstracts/W24_Workshop_190.html Genomic Tool Development For The Fagaceae], Margaret E. Staton, ''et al.''
+
| [[GBrowse_syn]]
−
| [[Chado]]
+
 
|-
 
|-
−
! [http://www.intl-pag.org/17/17-demos.html Computer Demo]
+
! rowspan="10" | Sunday<br />Jan 10
−
! 4:50-5:10
+
! rowspan="4" | Workshop
−
| The [http://rapdb.dna.affrc.go.jp/ Rice Annotation Project Database (RAP-DB)]: Introduction to the Comparative Analysis between Rice and Other Plant Species, [mailto:hirsakai@affrc.go.jp Hiroaki Sakai], ''et al''.
+
! 8:20-8:40
 +
! [http://www.intl-pag.org/18/abstracts/W31_PAGXVIII_228.html Epigenomic Analysis Of Populus trichocarpa Tissues From Differing Developmental Stages], Kelly J. Vining
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
! rowspan="8" | Monday<br />Jan 12
+
! 11:30-12:00
−
! rowspan="1" | EVEN Numbered Poster Session
+
! [http://www.intl-pag.org/18/abstracts/W17_PAGXVIII_138.html The Bovine Gene Atlas], Tad Sonstegard
−
! rowspan="1" | 10:00-11:30
+
| [[GBrowse]]
−
| [[#Posters|See below]] for a list of relevant posters.
+
−
|
+
 
|-
 
|-
−
! rowspan="5" | [http://www.intl-pag.org/17/17-demos.html Computer Demo]
+
! 2:15-2:30
−
! 1:30-1:50
+
! [http://www.intl-pag.org/18/abstracts/W31_PAGXVIII_243.html ConiferGDB: Current Status And Future Direction], Chun Liang
−
| [http://www.cottondb.org CottonDB]: A Resource for Cotton Genome Research, [mailto:jingyu@tamu.edu Jing Yu], ''et al''.
+
 
| [[CMap]]
 
| [[CMap]]
 
|-
 
|-
−
! 1:50-2:10
+
! 3:50-6:00
−
| Updates to [http://soybeangenome.siu.edu/ SoyGD]: Genome Sequence Search Tools and a Predicted Interactome, [mailto:ga4082@siu.edu David Lightfoot], ''et al''.
+
! [[:Category:TAIR|TAIR]] Workshop, Eva Huala
−
| [[GBrowse]]
+
| [[GBrowse]], [[GBrowse_syn]]
 
|-
 
|-
−
! 2:10-2:30
+
! rowspan="6" | Computer Demo
−
| [http://www.comparative-legumes.org/ The Legume Information System (LIS)]: An Integrated, Dynamic Comparative Legume Information Resource, [mailto:gdm@ncgr.org Gregory May] ''et al''.
+
! rowspan="1" | 4:10-4:30
−
| [[CMap]]
+
! MaizeGDB: Tools and Resources, Carson Andorf
 +
| [[CMap]], [[GBrowse]]
 
|-
 
|-
−
! 2:10-2:30
+
! 4:30-4:50
−
| The [http://www.maizegdb.org/ MaizeGDB] Genome Browser, [mailto:taner.sen@ars.usda.gov Taner Sen] ''et al''.
+
! [http://www.intl-pag.org/18/abstracts/C02_PAGXVIII_937.html How to Use MetaCyc, a Reference Database for Metabolism, and SolCyc, a Collection of Pathway Databases for the ''Solanaceae'', on the Web and Using Pathway Tools], Lukas Mueller
−
| [[GBrowse]]
+
| [[Pathway Tools]]
 
|-
 
|-
−
! 2:30-2:50
+
! 4:50-5:10
−
| [http://dendrome.ucdavis.edu/treegenes/ TreeGenes]: A Forest Tree Genome Database, [mailto:jlwegrzyn@ucdavis.edu Jill Wegrzyn] ''et al.''
+
! [[:Image:PAG2010GDRinDrupal.pdf|GDR in Drupal: Facilitating Community Building and Efficient Maintenance]], Sook Jung
−
| [[CMap]]
+
| [[Chado]], [[Tripal]]
 
|-
 
|-
−
! [http://www.intl-pag.org/17/17-transgene.html Plant Transgene Genetics Workshop]
+
! 5:10-5:30
−
! 2:40-3:00
+
! The Soybean Genome Database (SoyGD) Genomic Interactome Viewer, David Lightfoot
−
| [http://www.intl-pag.org/17/abstracts/W55_Workshop_379.html Use Of pCLD04541 Large Insert Clones And A Minimum Tile Path For Plant Transformations Encompassing The Entire Soybean Genome], David A Lightfoot, Hidayat Ullah
+
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
! rowspan="1" | ODD Numbered Poster Session
+
! 5:30-5:50
−
! rowspan="1" | 3:00-4:30
+
! [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_917.html PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism], Dawei Lin
−
| [[#Posters|See below]] for a list of relevant posters.
+
| [[CMap]], [[GBrowse]]
−
|
+
 
|-
 
|-
−
! Tuesday<br />Jan 13
+
! 5:50-6:10
−
! Computer & Training Workshop
+
! Community Curation Software at the [[:Category:SGN|Sol Genomics Network]] ([http://solgenomics.net solgenomics.net]), Lukas Mueller
−
! 3:50-6:00
+
| [[Chado]]
−
| [http://www.intl-pag.org/17/17-gramene.html Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses.], [mailto:cer17@cornell.edu Claire Hebbard], and [mailto:ivy1@cornell.edu Immanuel Yap]
+
|-
 +
! rowspan="1" | Monday<br />Jan 11
 +
! rowspan="1" | Computer Demo
 +
! 1:50-2:10
 +
! [http://dendrome.ucdavis.edu/treegenes/ TreeGenes]: A Forest Tree Genome Database, Jill Wegrzyn
 
| [[CMap]]
 
| [[CMap]]
 
|-
 
|-
−
! rowspan="2" | Wednesday<br />Jan 14
+
! Tuesday<br />Jan 12
−
! rowspan="2" | [http://www.intl-pag.org/17/17-demos.html Computer Demo]
+
! Workshop
−
! 2:20-2:40
+
! 11:55-12:10
−
| Structural and Functional Annotation of Wheat and Barley Genome Sequences with [http://urgi.versailles.inra.fr/projects/TriAnnot/ TriAnnot Pipeline], [mailto:leroy@clermont.inra.fr Philippe Leroy] ''et al''.
+
! [http://www.intl-pag.org/18/abstracts/W10_PAGXVIII_076.html Towards A Bioinformatics Platform For The Musa Research Community], Mathieu Rouard
−
| [[Apollo]] (under consideration), [[GBrowse]]
+
| [[CMap]], [[GBrowse]]
−
|-
+
−
! 2:40-3:00
+
−
| [http://urgi.versailles.inra.fr/projects/Softwares/ GnpIS], The Plant Information System of INRA URGI Bioinformatic Platform,  [mailto:michael.alaux@versailles.inra.fr Michael Alaux], [mailto:delphine.steinbach@versailles.inra.fr Delphine Steinbach] ''et al''.
+
−
| [[Apollo]], [[BioMart]], [[Chado]], [[CMap]], [[GBrowse]]
+
−
-->
+
 
|}
 
|}
  
 
== Posters ==
 
== Posters ==
  
−
All poster sessions are on '''Monday, January 12'''.
+
Titles of sessions that are about [[GMOD Components]] are shown in '''bold'''.
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 163: Line 152:
 
! Title & Author
 
! Title & Author
 
! Components
 
! Components
−
<!--
 
−
|-
 
−
! rowspan="11" | EVEN Numbered Poster Session<br />Monday<br />Jan 12
 
−
! rowspan="11" | 10:00-11:30
 
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P02a_Poster_050.html P050: Use Of The Soybean Physical Map Derived Minimum Tile For BIBAC Plant Transformations Encompassing The Entire Genome], David A Lightfoot
+
! rowspan="8" valign="top" | EVEN Numbered Poster Session<br />Monday<br />Jan 11
 +
! rowspan="8" valign="top" | 10:00-11:30
 +
| [http://www.intl-pag.org/18/abstracts/P03b_PAGXVIII_150.html P150: The Use Of BES And Genome Sequence Derived Microsatellite Markers For QTL Discovery], Rabia Bashir, Samreen Kazi, David A Lightfoot
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P02d_Poster_092.html P092: Re-Annotation Of The Physical Map Of Glycine max For Polyploid-Like Regions By BAC End Sequence Driven Whole Genome Shotgun Read Assembly], Navinder Saini, Jeffry L Shultz, David A Lightfoot
+
| [http://www.intl-pag.org/18/abstracts/P07b_PAGXVIII_786.html P786: Bioinformatics Tools For Avian Genomics], Carl J Schmidt, Catalina O Tudor, li Jin, Keith S. Decker, Fiona McCarthy, Peter D'Eustachio, K-Vijay Shanker
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P05f_Poster_364.html P364: SoyBase And The Soybean Breeder’S Toolbox: Updated Features And New Data], David Grant, Rex T. Nelson, Steven B. Cannon, Randy C. Shoemaker
+
| [[:Image:PAG2010HymenopteraGenomeDatabse.pdf|P830: The ''Hymenoptera'' Genome Database]], Monica C. Munoz-Torres, Justin T. Reese, [[User:Childers|Christopher P. Childers]], Anna K. Bennet, Jaideep P. Sundaram, Donald C Vile, Christine G. Elsik
−
| [[CMap]], [[GBrowse]]
+
| [[Apollo]], [[Chado]], [[GBrowse]], [[GMODTools]]. [[XORT]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P05k_Poster_478.html P478: Identification Of Metabolic Gene Losses In The Cattle Genome], Seongwon Seo1, Harris A. Lewin
+
| [http://www.intl-pag.org/18/abstracts/P08a_PAGXVIII_832.html P832: Design And Implementation Of The Cacao Genome Database], Ping Zheng, Sook Jung, Margaret Staton, Randall Svancera, Taein Lee, [[User:Sficklin|Stephen Ficklin]], David N. Kuhn, Raymond J. Schnell, Juan Carlos Montamayor, Dorrie Main
−
| [[Pathway Tools]]
+
| [[Chado]], [[Tripal]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_782.html P782: Expanding The Utility Of Animal QTLdb], Zhi-Liang Hu, ''et al.''
+
| [[:Image:PAG2010BovineGenomeDatabaseInfra.pdf| P838: Bovine Genome Database Systems Infrastructure]], Jaideep P. Sundaram, Christopher P. Childers, Justin T. Reese, Donald C. Vile, Christine G. Elsik
−
| [[BioMart]], [[GBrowse]]
+
| [[Chado]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_788.html P788: MetaCyc: The Global Reference Database For Metabolic Information], Anuradha Pujar, ''et al.''
+
| [[:Image:PAG2010BovineGenomeDatabase.pdf|P842: The Bovine Genome Database]], [[User:Childers|Christopher P. Childers]], Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, Darren E. Hagen, Anna K. Bennett, Christine G. Elsik
−
| [[Pathway Tools]]
+
| [[Apollo]], [[Chado]], [[GBrowse]], [[GMODTools]], [[XORT]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_796.html P796: The Hymenoptera Genome Database], Justin T. Reese, ''et al.''
+
! [[Media:GBrowse_nextgen_poster.pdf|P858: GBrowse And Next Generation Sequencing Data]], [[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], [[User:Lstein|Lincoln Stein]], the GMOD Consortium
−
| [[Apollo]]
+
! [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08b_Poster_824.html P824: Comparative Genomics Software Packages At GMOD], [[User:Scott|Scott Cain]], [[User:Clements|David Clements]], The GMOD Consortium  ([[Media:Cain GI poster.pdf|PDF]])
+
| [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_914.html P914: The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation], Takeshi Itoh, Tsuyoshi Tanaka, Hiroaki Sakai, Hisataka Numa, Naoki Amano, Hiroshi Ikawa, Takashi Matsumoto
−
| [[Apollo]], [[CMap]], [[GBrowse_syn]], [[Sybil]], [[SynBrowse]], [[Synview]]
+
| [[GBrowse_syn]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08b_Poster_828.html P828: Managing Next Generation Sequence Data With GMOD], [[User:Clements|Dave Clements]], ''et al.'' ([[Media:PAG2009NextGenSeqPoster.pdf|PDF]])
+
! colspan="4" |
−
| [[Chado]], [[GBrowse]]
+
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/C01_PosterDemo_848.html P848: Structural and Functional Annotation of Wheat and Barley Genome Sequences with TriAnnot Pipeline], Philippe Leroy, ''et al''.
+
! Track
−
| [[Apollo]] (under consideration), [[GBrowse]]
+
! Time
 +
! Title & Author
 +
! Components
 
|-
 
|-
 +
! rowspan="15" valign="top" | ODD Numbered Poster Session<br>Monday<br />Jan 11
 +
! rowspan="15" valign="top" | 3:00-4:30
 +
| [http://www.intl-pag.org/18/abstracts/P01_PAGXVIII_016.html P016: Analysis Of Genomic Sequences From ''Lupinus luteus'' L.], Héctor A Urbina Saavedra, Marcos R Olivos Trujillo, Cristell S Navarro Navarro, Lorena B Parra González, Gabriela A Aravena Abarzúa, Joshua A Udall, Shannon C Straub, Haroldo E Salvo Garrido, Iván J Maureira Butler
 +
| [[GBrowse]]
 
|-
 
|-
−
! rowspan="9" | ODD Numbered Poster Session<br>Monday<br />Jan 12
+
| [http://www.intl-pag.org/18/abstracts/P05c_PAGXVIII_295.html P295: Wheat Genomic Data In GnpIS The URGI Information System] Michael Alaux, Daphné Verdelet, Aminah-Olivia Keliet, Erik Kimmel, Baptiste Brault, Nacer Mohellibi, Benoit Hilselberger, Sophie Durand, Isabelle Luyten, Sébastien Reboux, Delphine Steinbach
−
! rowspan="9" | 3:00-4:30
+
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P05f_Poster_371.html P371: Coupled QTL And Association Mapping Soybeans: Examples From Seed Protein And Oil Content And Disease Resistance], Ali Srour, ''et al.''
+
| [http://www.intl-pag.org/18/abstracts/P05j_PAGXVIII_513.html P513: ''Populus trichocarpa'' Epigenomics: Analysis Of The Developmental Poplar Methylome], Kelly J. Vining, Kyle R. Pomraning, Larry Wilhelm, Palitha D. Dharmawardhana, Henry D. Priest, Olga Shevchenko, Cathleen Ma, Ruoqing Zhu, Elizabeth Etherington, Todd Mockler, Michael Freitag, Steven Strauss
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_783.html P783: The Bovine Genome Database], Christopher P. Childers, ''et al.''
+
| [http://www.intl-pag.org/18/abstracts/P05k_PAGXVIII_537.html P537: QTL, Hypothalamic-Transcriptome, And Candidate Gene Query Suggest Bovine Chromosome 2 Influences Heifer Pregnancy], Milton G Thomas, Sunday O Peters, Kadir Kazilkaya, Dorian J Garrick, Rohan L Fernando, James M Reecy, Z-L Hu, Faye D Schilkey, Robert L Weaber, Gail A Silver
−
| [[Apollo]], [[chado]], [[GBrowse]]
+
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_785.html P785: The URGI Bioinformatics Platform: Focus On Genomic Annotation Databases And Tools], Michael Alaux, Joelle Amselem ''et al.'' ([[Media:PAG2009_poster_Michael_Alaux.pdf|PDF]])
+
| [http://www.intl-pag.org/18/abstracts/P05n_PAGXVIII_599.html P599: Segmental Duplications In Pig Genome], Zhi-Qiang Du , Danielle M. Gorbach , Zhiliang Hu , Max F. Rothschild
−
| [[Apollo]], [[Chado]], [[GBrowse]]
+
| [[BioMart]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_789.html P789: Integrated Genome Informatics - Current Approaches and Platforms in a Rapidly Changing Environment], [[User:Russellsmithies|Russell Smithies]]
+
| [http://www.intl-pag.org/18/abstracts/P08a_PAGXVIII_823.html P823: BRISKA: Brassica Seed Knowledge Base], Hugo Berube, Alain Tchagang, Yunli Wang, Ziying Liu, Sieu Phan, Fazel Famili, Youlian Pan
 +
| [[Chado]]
 +
|-
 +
| [http://www.intl-pag.org/18/abstracts/P08a_PAGXVIII_833.html P833: QTL Analysis, Visualization And The Link To Genomes At SGN Database], Isaak Y Tecle, Naama Menda, [[User:RobertBuels|Robert Buels]], Lukas Mueller
 
| [[GBrowse]]
 
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/P08a_Poster_805.html P805: AlliumMap: An Online Comparative Genomics Resource For Allium], John McCallum, ''et al.''
+
| [http://www.intl-pag.org/18/abstracts/P08a_PAGXVIII_839.html P839: How To Use The New Functionalities At MaizeGDB: Now Sequence-Centric!], Lisa C. Harper, Mary L. Schaeffer, Taner Z. Sen, Carson M. Andorf, Ethalinda Cannon, Darwin A. Campbell, Lawrence Carolyn J.
−
| [[CMap]]
+
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/C01_PosterDemo_845.html P845: EcoliWiki And GONUTS: Wiki-Based Systems For Community Annotation], Daniel Renfro ''et al.''
+
| [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_851.html P851: SNPlotz: A Genome Plot Tool For SNP Association Studies], Zhi-Liang Hu, Rex Fernando, Dorian Garrick, James M. Reecy
−
| [[Table Editor]]
+
| [[GBrowse]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/C01_PosterDemo_847.html P847: TreeGenes: A Forest Tree Genome Database], Jill Wegrzyn, ''et al.''
+
! [[Media:CMapGenomeInformatics2009.pdf|P859: Visualizing And Comparing Genomes]], Ken Youens-Clark, Immanual V. Yap, Doreen Ware
−
| [[CMap]]
+
! [[CMap]]
 
|-
 
|-
−
| [http://www.intl-pag.org/17/abstracts/C01_PosterDemo_849.html P849: GnpIS, The Plant Information System Of INRA URGI Bioinformatic Platform], Delphine Steinbach, Michael Alaux ''et al.'' ([[Media:PAG2009_poster_URGI_GnpIS.pdf|PDF]])
+
! [[:Media:PAG2010ComparativeGenomicsToolsInGMOD.pdf|P861: Comparative Genomics Tools In GMOD]], [[User:Clements|Dave Clements]], [[User:Mckays|Sheldon McKay]], Ken Youens-Clark, [[User:Faga|Ben Faga]], [[User:Scott|Scott Cain]]
−
| [[Apollo]], [[BioMart]], [[Chado]], [[CMap]], [[GBrowse]]
+
! [[CMap]], [[GBrowse_syn]], [[Sybil]], [[SynView]], [[Apollo]]
 
|-
 
|-
−
-->
+
| [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_915.html P915: GDR In Drupal: Facilitating Community Building And Efficient Maintenance], Sook Jung, Randall Svancara, Meg Staton, [[User:Sficklin|Stephen Ficklin]], Ping Zheng, Taein Lee, Dorrie Main
 +
| [[GBrowse]]
 +
|-
 +
| [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_917.html P917: PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism], Dawei Lin, Paul Gepts, Adam Schaal, Jose Boveda, JVG dos Santos, Joe Fass, Jim Kami, Nikhil Joshi, Monica Britton, Zhiwei Lu
 +
| [[CMap]], [[GBrowse]]
 +
|-
 +
! [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_919.html P919: Using The JBrowse Genome Browser With Large Amounts Of Data], [[User:MitchSkinner|Mitchell E Skinner]], Andrew V Uzilov, [[User:Lstein|Lincoln D Stein]], Christopher J Mungall, Ian H Holmes
 +
! [[JBrowse]]
 +
|-
 +
| [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_921.html P921: TreeGenes: A Forest Tree Genome Database], Jill L Wegrzyn, Ben Figueroa, Minyoung Choi, Elly Y Chen, David B Neale
 +
| [[CMap]]
 
|}
 
|}
 +
 +
== Flier ==
 +
* The [[:Image:GMODatPAG2010.pdf|GMOD @ PAG 2010 Flier]] highlights the presentations above, and was distributed at the conference.
  
 
== See Also ==
 
== See Also ==
  
−
* [[January 2010 GMOD Meeting]]
+
* [[PAG 2012]]
 +
* [[PAG 2011]]
 +
* The [[January 2010 GMOD Meeting]] immediately followed PAG 2010.
 
* [[PAG 2009]]
 
* [[PAG 2009]]
  
−
[[Category:Meetings]]
 
 
[[Category:Education and Outreach]]
 
[[Category:Education and Outreach]]
 +
[[Category:Conferences]]

Latest revision as of 18:17, 2 October 2012

PAG 2010 Conference

GMOD once again had a strong presence at the Plant and Animal Genome Conference (PAG XVIII). There were many workshops, computer demos, and posters, either about GMOD and GMOD Components, or using GMOD components. This page lists the subset that mentioned GMOD or GMOD components in the abstract.


About GMOD Components

Carson Holt presenting the MAKER genome annotation pipeline at PAG.

There were a record nine talks and workshops either entirely or partially about GMOD Components. It was the first time Galaxy, MAKER, and JBrowse were presented at PAG. We also gave our first GMOD overview talk at PAG. There was a great dead of interest in GMOD and ll of the talks were well attended, with several of them being standing room only.

Day Track Time Title & Presenter Components
Saturday
Jan 9 		Computer & Training Workshop 1:30-2:30 Animal Genomics with Galaxy: Analyze, Publish, and Visualize, Dan Blankenberg Galaxy
3:50-6:00 MAKER: An easy to use genome annotation pipeline, Carson Holt MAKER
Sunday
Jan 10 		Computer & Training Workshop 8:15-9:15 Database Resources at the EBI: Ensembl And Ensembl Genomes - Access To Genome-Scale Data Across The Taxonomic Space, Bert Overduin BioMart
1:30-3:40 The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse, Scott Cain GBrowse
Monday
Jan 11 		Computer & Training Workshop 12:50-1:10 GMOD Project Update, Dave Clements, Scott Cain GMOD Components
1:10-1:30 Using the JBrowse Genome Browser with Large Amounts of Data, Mitch Skinner JBrowse
Tuesday
Jan 12 		Computer & Training Workshop 3:50-6:00 Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses, Ken Youens-Clark CMap
Wednesday
Jan 13 		Computer & Training Workshop 10:20-12:30 Comparative Genomics with GBrowse_syn: Visualizing your comparative genomics data with the Generic Synteny Browser, Sheldon McKay GBrowse_syn
2:30-2:50 Tripal: a Construction Toolkit for Online Genomic Databases, Stephen Ficklin Tripal, Chado

Projects Using GMOD Components

Day Track Time Title & Author Components
Saturday
Jan 9 		Workshop 8:45-9:05 Full Genome Sequencing Of The Woodland Strawberry, Fragaria vesca, Vladimir Shulaev GBrowse
11:40-12:00 Development Of Tools For The Analysis And Visualisation Of Second Generation Sequencing Data For Brassica Species, Chris Duran CMap (CMap3D)
4:10-4:30 The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation, Takeshi Itoh GBrowse_syn
Sunday
Jan 10 		Workshop 8:20-8:40 Epigenomic Analysis Of Populus trichocarpa Tissues From Differing Developmental Stages, Kelly J. Vining GBrowse
11:30-12:00 The Bovine Gene Atlas, Tad Sonstegard GBrowse
2:15-2:30 ConiferGDB: Current Status And Future Direction, Chun Liang CMap
3:50-6:00 TAIR Workshop, Eva Huala GBrowse, GBrowse_syn
Computer Demo 4:10-4:30 MaizeGDB: Tools and Resources, Carson Andorf CMap, GBrowse
4:30-4:50 How to Use MetaCyc, a Reference Database for Metabolism, and SolCyc, a Collection of Pathway Databases for the Solanaceae, on the Web and Using Pathway Tools, Lukas Mueller Pathway Tools
4:50-5:10 GDR in Drupal: Facilitating Community Building and Efficient Maintenance, Sook Jung Chado, Tripal
5:10-5:30 The Soybean Genome Database (SoyGD) Genomic Interactome Viewer, David Lightfoot GBrowse
5:30-5:50 PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism, Dawei Lin CMap, GBrowse
5:50-6:10 Community Curation Software at the Sol Genomics Network (solgenomics.net), Lukas Mueller Chado
Monday
Jan 11 		Computer Demo 1:50-2:10 TreeGenes: A Forest Tree Genome Database, Jill Wegrzyn CMap
Tuesday
Jan 12 		Workshop 11:55-12:10 Towards A Bioinformatics Platform For The Musa Research Community, Mathieu Rouard CMap, GBrowse

Posters

Titles of sessions that are about GMOD Components are shown in bold.

Track Time Title & Author Components
EVEN Numbered Poster Session
Monday
Jan 11 		10:00-11:30 P150: The Use Of BES And Genome Sequence Derived Microsatellite Markers For QTL Discovery, Rabia Bashir, Samreen Kazi, David A Lightfoot GBrowse
P786: Bioinformatics Tools For Avian Genomics, Carl J Schmidt, Catalina O Tudor, li Jin, Keith S. Decker, Fiona McCarthy, Peter D'Eustachio, K-Vijay Shanker GBrowse
P830: The Hymenoptera Genome Database, Monica C. Munoz-Torres, Justin T. Reese, Christopher P. Childers, Anna K. Bennet, Jaideep P. Sundaram, Donald C Vile, Christine G. Elsik Apollo, Chado, GBrowse, GMODTools. XORT
P832: Design And Implementation Of The Cacao Genome Database, Ping Zheng, Sook Jung, Margaret Staton, Randall Svancera, Taein Lee, Stephen Ficklin, David N. Kuhn, Raymond J. Schnell, Juan Carlos Montamayor, Dorrie Main Chado, Tripal
P838: Bovine Genome Database Systems Infrastructure, Jaideep P. Sundaram, Christopher P. Childers, Justin T. Reese, Donald C. Vile, Christine G. Elsik Chado
P842: The Bovine Genome Database, Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, Darren E. Hagen, Anna K. Bennett, Christine G. Elsik Apollo, Chado, GBrowse, GMODTools, XORT
P858: GBrowse And Next Generation Sequencing Data, Scott Cain, Dave Clements, Lincoln Stein, the GMOD Consortium GBrowse
P914: The Rice Annotation Project Database (RAP-DB): IRGSP/RAP Build 5 Annotation, Takeshi Itoh, Tsuyoshi Tanaka, Hiroaki Sakai, Hisataka Numa, Naoki Amano, Hiroshi Ikawa, Takashi Matsumoto GBrowse_syn
Track Time Title & Author Components
ODD Numbered Poster Session
Monday
Jan 11 		3:00-4:30 P016: Analysis Of Genomic Sequences From Lupinus luteus L., Héctor A Urbina Saavedra, Marcos R Olivos Trujillo, Cristell S Navarro Navarro, Lorena B Parra González, Gabriela A Aravena Abarzúa, Joshua A Udall, Shannon C Straub, Haroldo E Salvo Garrido, Iván J Maureira Butler GBrowse
P295: Wheat Genomic Data In GnpIS The URGI Information System Michael Alaux, Daphné Verdelet, Aminah-Olivia Keliet, Erik Kimmel, Baptiste Brault, Nacer Mohellibi, Benoit Hilselberger, Sophie Durand, Isabelle Luyten, Sébastien Reboux, Delphine Steinbach GBrowse
P513: Populus trichocarpa Epigenomics: Analysis Of The Developmental Poplar Methylome, Kelly J. Vining, Kyle R. Pomraning, Larry Wilhelm, Palitha D. Dharmawardhana, Henry D. Priest, Olga Shevchenko, Cathleen Ma, Ruoqing Zhu, Elizabeth Etherington, Todd Mockler, Michael Freitag, Steven Strauss GBrowse
P537: QTL, Hypothalamic-Transcriptome, And Candidate Gene Query Suggest Bovine Chromosome 2 Influences Heifer Pregnancy, Milton G Thomas, Sunday O Peters, Kadir Kazilkaya, Dorian J Garrick, Rohan L Fernando, James M Reecy, Z-L Hu, Faye D Schilkey, Robert L Weaber, Gail A Silver GBrowse
P599: Segmental Duplications In Pig Genome, Zhi-Qiang Du , Danielle M. Gorbach , Zhiliang Hu , Max F. Rothschild BioMart
P823: BRISKA: Brassica Seed Knowledge Base, Hugo Berube, Alain Tchagang, Yunli Wang, Ziying Liu, Sieu Phan, Fazel Famili, Youlian Pan Chado
P833: QTL Analysis, Visualization And The Link To Genomes At SGN Database, Isaak Y Tecle, Naama Menda, Robert Buels, Lukas Mueller GBrowse
P839: How To Use The New Functionalities At MaizeGDB: Now Sequence-Centric!, Lisa C. Harper, Mary L. Schaeffer, Taner Z. Sen, Carson M. Andorf, Ethalinda Cannon, Darwin A. Campbell, Lawrence Carolyn J. GBrowse
P851: SNPlotz: A Genome Plot Tool For SNP Association Studies, Zhi-Liang Hu, Rex Fernando, Dorian Garrick, James M. Reecy GBrowse
P859: Visualizing And Comparing Genomes, Ken Youens-Clark, Immanual V. Yap, Doreen Ware CMap
P861: Comparative Genomics Tools In GMOD, Dave Clements, Sheldon McKay, Ken Youens-Clark, Ben Faga, Scott Cain CMap, GBrowse_syn, Sybil, SynView, Apollo
P915: GDR In Drupal: Facilitating Community Building And Efficient Maintenance, Sook Jung, Randall Svancara, Meg Staton, Stephen Ficklin, Ping Zheng, Taein Lee, Dorrie Main GBrowse
P917: PhaseolusGenes: A Genomics Information Management And Marker Discovery Toolkit For A Non-Model Organism, Dawei Lin, Paul Gepts, Adam Schaal, Jose Boveda, JVG dos Santos, Joe Fass, Jim Kami, Nikhil Joshi, Monica Britton, Zhiwei Lu CMap, GBrowse
P919: Using The JBrowse Genome Browser With Large Amounts Of Data, Mitchell E Skinner, Andrew V Uzilov, Lincoln D Stein, Christopher J Mungall, Ian H Holmes JBrowse
P921: TreeGenes: A Forest Tree Genome Database, Jill L Wegrzyn, Ben Figueroa, Minyoung Choi, Elly Y Chen, David B Neale CMap

Flier

See Also

Retrieved from "http://gmod.org/mediawiki/index.php?title=PAG_2010&oldid=21790"