Reinventing MaizeGDB
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Reinventing MaizeGDB Abstract The Maize Database (MaizeDB -> MaizeGDB) turns 20 this year, and such a significant milestone must be celebrated! With the release of the B73 reference sequence and more sequenced genomes on the way, the maize community needs to address various opportunities and challenges. MaizeGDB, the community’s Model Organism Database is in an excellent position to address evolving needs by deploying tools that will allow researchers to make use of multiple genome sequences as well as large-scale phenotypic associations. To prepare for both current and future needs of the community, the MaizeGDB team is planning a complete interface redesign to keep the resource relevant and to allow for expansion in desired directions while continuing to update the data as usual over time. The redesign will be both cosmetic and functional. The overall goal of the redesign is to create a clean modern interface with improved user interaction while expanding the overall functionality of MaizeGDB. Cosmetically, we will modernize the appearance and simplify page organization and navigation. Functionally, we will put particular emphasis on ways to view and compare multiple maize genomes, billions of SNPs, and new ways to search and browse phenotypes, gel images, QTLs, and other data types. A key component to the redesign will be community involvement. To insure that the new interface is useful, guidance and beta testing groups will be created and consulted. Here we report our anticipated timelines and focus on initial concepts and designs, new features to be deployed (data, tools, and resources), and outline how you can be involved in changing MaizeGDB to better meet your needs. Timeline Diversity Collaboration New Interface Acknowledgment Direct Contributors: Carson Andorf Sanford Baran Mary Berlyn Scott Birkett Bremen Braun Volker Brendel Lou Butler Pat Byrne Darwin Campbell Ethalinda Cannon Ed Coe Georgia Davis Qunfeng Dong Zhiwei Fang Christiane Fauron Arturo Garcia Jack Gardiner Denis Hancock Lisa Harper Davendra Jayasingam Shirley Kowalewski Heike Kross Carolyn Lawrence Stan Letovsky Mike McMullen Gerry Neuffer Steve Rodermel Marty Sachs Hector Sanchez-Villeda Mary (Polacco) Schaeffer Steve Schroeder Trent Seigfried Taner Sen Brian Smith-White Chris Steele Jordan Thistle Leszek Vincent Allison Weidemeier Carolyn Wetzel “Recommendations” Committee, 1990: Ben Burr Don Duvick Tim Helentjaris Dave Hoisington Ron Phillips Paul Sisco Advisory, 1991: Bill Beavis Mary Berlyn Doug Bigwood Ben Burr Peter Bretting Vicki Chandler Neil Cowen Larry Darrah Denis Hancock Tim Helentjaris Dave Hoisington Kendall Lamkey Oliver Nelson Robert Robbins Jean Romero-Severson Margaret Smith Charles Stuber Scott Tingey Other Resource Persons, 1990: Bill Beavis Jack Beckett Lawrence Bogorad Shiaoman Chao Karen Cone Jim Coors Neil Cowen Larry Darrah Christiane Fauron Nina Fedoroff David Grant Sarah Hake Arnel Hallauer R.G. Herrmann Jerry Kermicle Eric Lander Brian Larkins John Laughnan Sam Levings Michael Murray Oliver Nelson Gerry Neuffer Kathy Newton Earl Patterson Tom Peterson Scott Poethig Daryl Pring Don Robertson Marty Sachs Bill Sheridan David Skibbe Charlie Stuber Scott Tingey Virginia Walbot David Weber Edward Weck Sue Wessler Allen Wright Steering Committees &Working Groups, 2002-Present: Alice Barkan Volker BrendelEd Buckler Vicki ChandlerKaren Cone- Mike Freeling Sarah Hake Owen Hoekenga Anne-Francoise Lamblin Thomas Lubberstedt Eric Lyons Karen McGinnis Lukas Mueller Mihai Pop Marty Sachs Mary (Polacco) Schaeffer Pat Schnable Tom Slezak Cari Soderlund Lincoln Stein Anne Sylvester Doreen Ware Instrumental at the Funding Agencies: Peter Bretting Leland Ellis Jerry Miksche Diane Okamuro Jack Okamuro Jane Silverthorne Kay Simmons Judy St. John Editorial Board 2005-Present: Mario Arteaga-Vazquez Peter Balint-Kurti Patrick Brown Tom Brutnell Ed Buckler Surinder Chopra Kelly Dawe Brian Dilkes Hugo Dooner Jane Dorweiler Erich Grotewold Lisa Harper Jim Holland Guri Johal Mike Kolomiets Damon Lisch Karen McGinnis Michael Muszynski Wojtek Pawlowski Gael Pressoir Mike Scanlon Paul Scott Moira Sheehan Richard Keith Slotkin Nathan Springer Erik Vollbrecht Cliff Weil Clinton Whipple Randall Wisser Jianming Yu Genome Browser Guidance Group, 2007: Peter Balint-Kurti Sarah Hake Damon Lisch Michael Muszynski Virginia Walbot Genome Browser Beta Testers, 2007: Alain Charcosset Olivier Dugas James Estill David Hessel Damon Lisch Michael Muszynski Paul Scott Virginia Walbot Rachel Wang Cesar Alvarez-Mejia Outside Funds: Volker Brendel Guy Davenport Erik Grotewold Shawn Kaeppler Jonathan Lynch Don McCarty Dan Rokhsar Pat Schnable Graphic Design: Destri Andorf Why Now? Biological Tools: • Diversity • Multiple Fully Sequenced Genomes • Orthology Computational Access: • Portal • Serve & Consume Remote Data Technology Upgrade MaizeGDB Team Stay Connected to MaizeGDB! 2011 Maize Meeting Program and Abstracts Carson Andorf 1 , Ethy Cannon 2 , Bremen Braun 1 , Scott Birkett 2 , Lisa Harper 3 , Mary Schaeffer 4 , Jack Gardiner 2,5 , Davendra Jayasingam 2,6 , Darwin Campbell 1 , Taner Sen 1,2 , Carolyn Lawrence 1,2 1 USDA-ARS Corn Insects and Crop Genetics Unit, Iowa State University, Ames, Iowa 50011-3260. 2 Department of Genetics Development & Cell Biology, Iowa State University, Ames, Iowa 50011-3260. 3 USDA-ARS Plant Gene Expression Center, Albany, CA 94710, and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720. 4 USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, University of Missouri, Columbia, MO 65211. 5 School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036. 6 Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011-3260 We want to hear from you! We want to make the new MaizeGDB as useful as possible. Please let us know what you would like to be able to do, or do better at MaizeGDB. Send us your feedback: 1. Fill out the survey here at the meeting, and also future surveys that will be coming by email 2. Use the feedback button at the bottom of every page 3. Discuss MaizeGDB at your lab meeting- write up a report and email it to us! 4. Talk to any member of our group- in person or on the phone or by email.
Transcript of Reinventing MaizeGDB
Reinventing MaizeGDB
AbstractThe Maize Database (MaizeDB -> MaizeGDB) turns 20 this year, and such a significant milestone must be celebrated!
With the release of the B73 reference sequence and more sequenced genomes on the way, the maize community needs to address various opportunities and challenges.
MaizeGDB, the community’s Model Organism Database is in an excellent position to address evolving needs by deploying tools that will allow researchers to make use of multiple genome sequences as well as large-scale phenotypic associations. To prepare for both current and future needs of the community, the MaizeGDB team is planning a complete interface redesign to keep the resource relevant and to allow for expansion in desired directions while continuing to update the data as usual over time. The redesign will be both cosmetic and functional.
The overall goal of the redesign is to create a clean modern interface with improved user interaction while expanding the overall functionality of MaizeGDB. Cosmetically, we will modernize the appearance and simplify page organization and navigation. Functionally, we will put particular emphasis on ways to view and compare multiple maize genomes, billions of SNPs, and new ways to search and browse phenotypes, gel images, QTLs, and other data types. A key component to the redesign will be community involvement. To insure that the new interface is useful, guidance and beta testing groups will be created and consulted. Here we report our anticipated timelines and focus on initial concepts and designs, new features to be deployed (data, tools, and resources), and outline how you can be involved in changing MaizeGDB to better meet your needs.
Timeline
Diversity Collaboration New Interface
AcknowledgmentDirect Contributors:Carson Andorf Sanford BaranMary BerlynScott BirkettBremen BraunVolker BrendelLou ButlerPat ByrneDarwin CampbellEthalinda CannonEd CoeGeorgia DavisQunfeng DongZhiwei FangChristiane FauronArturo GarciaJack GardinerDenis HancockLisa HarperDavendra JayasingamShirley KowalewskiHeike Kross Carolyn LawrenceStan LetovskyMike McMullen Gerry NeufferSteve RodermelMarty SachsHector Sanchez-VilledaMary (Polacco) SchaefferSteve SchroederTrent SeigfriedTaner SenBrian Smith-WhiteChris SteeleJordan ThistleLeszek Vincent Allison WeidemeierCarolyn Wetzel
“Recommendations”Committee, 1990:Ben BurrDon DuvickTim HelentjarisDave HoisingtonRon PhillipsPaul Sisco
Advisory, 1991:Bill BeavisMary BerlynDoug BigwoodBen BurrPeter BrettingVicki ChandlerNeil CowenLarry DarrahDenis HancockTim HelentjarisDave HoisingtonKendall LamkeyOliver NelsonRobert RobbinsJean Romero-SeversonMargaret SmithCharles StuberScott Tingey
Other ResourcePersons, 1990:Bill BeavisJack BeckettLawrence BogoradShiaoman ChaoKaren ConeJim CoorsNeil CowenLarry DarrahChristiane FauronNina FedoroffDavid GrantSarah HakeArnel HallauerR.G. HerrmannJerry KermicleEric LanderBrian LarkinsJohn LaughnanSam LevingsMichael MurrayOliver NelsonGerry NeufferKathy NewtonEarl PattersonTom PetersonScott PoethigDaryl PringDon RobertsonMarty SachsBill SheridanDavid SkibbeCharlie StuberScott TingeyVirginia WalbotDavid WeberEdward WeckSue WesslerAllen Wright
Steering Committees &Working Groups, 2002-Present:Alice BarkanVolker BrendelEd BucklerVicki ChandlerKaren Cone-Mike FreelingSarah HakeOwen HoekengaAnne-Francoise LamblinThomas LubberstedtEric LyonsKaren McGinnisLukas MuellerMihai PopMarty SachsMary (Polacco) SchaefferPat SchnableTom Slezak Cari SoderlundLincoln SteinAnne SylvesterDoreen Ware
Instrumental at the Funding Agencies:Peter BrettingLeland EllisJerry MikscheDiane OkamuroJack OkamuroJane SilverthorneKay SimmonsJudy St. John
Editorial Board2005-Present:Mario Arteaga-Vazquez Peter Balint-KurtiPatrick BrownTom BrutnellEd BucklerSurinder ChopraKelly DaweBrian Dilkes Hugo DoonerJane DorweilerErich GrotewoldLisa HarperJim HollandGuri JohalMike KolomietsDamon LischKaren McGinnisMichael MuszynskiWojtek PawlowskiGael Pressoir Mike ScanlonPaul ScottMoira SheehanRichard Keith SlotkinNathan SpringerErik VollbrechtCliff WeilClinton WhippleRandall WisserJianming Yu
Genome BrowserGuidance Group, 2007:Peter Balint-Kurti Sarah Hake Damon Lisch Michael Muszynski Virginia Walbot
Genome BrowserBeta Testers, 2007:Alain Charcosset Olivier Dugas James Estill David Hessel Damon Lisch Michael Muszynski Paul Scott Virginia Walbot Rachel Wang Cesar Alvarez-Mejia
Outside Funds:Volker BrendelGuy DavenportErik GrotewoldShawn KaepplerJonathan LynchDon McCartyDan RokhsarPat Schnable
Graphic Design:Destri Andorf
Why Now?
Biological Tools:• Diversity
• Multiple Fully Sequenced Genomes
• Orthology
Computational Access:• Portal
• Serve & Consume Remote Data
Technology Upgrade MaizeGDB Team
Stay Connected to MaizeGDB!2011 Maize MeetingProgram and Abstracts
Carson Andorf1, Ethy Cannon2, Bremen Braun1, Scott Birkett2, Lisa Harper3, Mary Schaeffer4, Jack Gardiner2,5, Davendra Jayasingam2,6, Darwin Campbell1, Taner Sen1,2, Carolyn Lawrence1,2
1 USDA-ARS Corn Insects and Crop Genetics Unit, Iowa State University, Ames, Iowa 50011-3260. 2 Department of Genetics Development & Cell Biology, Iowa State University, Ames, Iowa 50011-3260. 3 USDA-ARS Plant Gene Expression Center, Albany, CA 94710, and Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720. 4 USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, University of Missouri, Columbia, MO 65211. 5 School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036. 6 Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011-3260
We want to hear from you!We want to make the new MaizeGDB as useful as possible. Please let us know what you would like to be able to do, or do better at MaizeGDB. Send us your feedback:
1. Fill out the survey here at the meeting, and also future surveys that will be coming by email2. Use the feedback button at the bottom of every page3. Discuss MaizeGDB at your lab meeting- write up a report and email it to us! 4. Talk to any member of our group- in person or on the phone or by email.
