Difference between revisions of "ASPB 2010 Workshop"

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==Phenote==
 
==Phenote==
Phenote is developed by the Berkeley Bioinformatics Open-Source Projects [http://www.berkeleybop.org/(BBOP)]. We greatly acknowledge the contribution made by the BBOP developers Nomi Harris begin_of_the_skype_highlighting     end_of_the_skype_highlighting and Chris Mungall for their help in customizing the Phenote tool for use in this workshop.  
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Phenote is developed by the Berkeley Bioinformatics Open-Source Projects [http://www.berkeleybop.org/(BBOP)]. We greatly acknowledge the contribution made by the BBOP developers Nomi Harris and Chris Mungall for their help in customizing the Phenote tool for use in this workshop.
 +
 
 
==Ontologies/datasets==
 
==Ontologies/datasets==
 
Several projects contributed data sets that are linked to the auto complete features in the Plant specific Phenote configuration. They include
 
Several projects contributed data sets that are linked to the auto complete features in the Plant specific Phenote configuration. They include

Revision as of 17:24, 29 July 2010

Plant Ontology and Gramene's Gene Annotation Workshop Plant Biology 2010 LINK

Saturday July 31, 8:00 am - 12:00 pm

Workshop Agenda

Venue

Room 512 a,b,e,f

Palais des congrès (the Montrèal convention centre)

Schedule (Tentative)

  July 31, 2010
  
   8:00 -  8.10 am --  Workshop goals and introduction [Pankaj Jaiswal]
   8.10 -  8.30 am --  What is annotation and why we need it. [Pankaj Jaiswal]
   8.30 -  8.50*am --  TAIR by Kate Dreher
   8.50 -  9.20#am --  Annotation Part-1: Phenote use and practice
   9.20 -  9.30 am --  Break
   9.30 - 10.00#am --  Annotation Part-2  Three papers. Everyone annotates all three
  10.00 - 10.20 am --  MaizeGDB by Jack Gardiner
  10.20 - 10.40*am --  Gramene
  10.40 - 11.20#am --  Annotation Part-3: Gene/Library annotation set (TBA)
                   --  Annotate your own data
  11.20 - 11.40*am --  BAR by Rohan Patel
  11.40 - 12.00 pm --  DISCUSSION and collect the annotations
  
  IMPORTANT: PLEASE READ
  * Talks : (15 min talk 5 min Q&A)
  $ Arrive 15 min early 
  # Actual hands on training sessions. 
    # Bring your own notebook/laptop computers
    # Wireless internet access will be provided.

About the workshop

As more plant species are sequenced and large-scale phenotyping screens are created, we see a diversity of annotation types and descriptors being used in these experiments. Having a new genome and large data sets is an excellent way to learn about plant development and behavior; however, in doing so we also realize that many of the descriptors are very species-specific may not meet the community standards of functional characterization as they fail to employ various controlled vocabularies (ontologies) such as Gene Ontology and Plant Ontologies. In addition to that, not every plant community has sufficient personnel, computational, or monetary resources to manage the annotation of its genome. Therefore, these communities depend heavily on the high-quality annotations of the model and reference plants.

To create gold-standard data sets that can be used in annotations, we want to train the current and future plant biologists with emphasis on young investigators, students, postdocs and especially those representing the minority and underrepresented institutions to help us foster good practices and build a community of curators who will undertake the task of creating accurate and reliable data sets for plant biologists.

Workshop material

Please read these important instructions

Computers

Though this is a hands on training workshop with lectures, and we will provide few on-site computers. Therefore it is necessary for you to BRING YOUR LAPTOP/NOTEBOOK in order to learn the process and work with the software we will use. Those computers we provide will most likely run Windows OS, but you will be able to perform the exercises on Mac, Linux and other platforms as well. See more details about the software requirements.

  • RECOMMENDATIONS
    • OS: Windows, Mac, Linux
    • You should have administrative rights and/or access to the ROOT for installing the software
    • INSTALL the PHENOTE software available from the links provided in the "Software" section below

Internet Access

We will provide FREE WIRELESS INTERNET for the duration of the workshop to first 100 connections. If you already have access to Internet through another arrangement, please feel free to use that; however, we will not reimburse you for buying access to the Internet.

  • RECOMMENDATION: Make sure the computer you are bringing has a wireless network card

Software

For the actual hands on training sessions #1, 2 and 3, we will use the software called PHENOTE.

Annotation Exercises

Exercise #1

TBA


Exercise #2

TBA

Exercise #3

TBA

Questions?

Contact Us

Participants

There are about 70 registered participants in this workshop. We will provide the list later.

Travel Awards

A limited number of travel felowships were awarded to support US residents affiliated with a US institution.

  Awardees         Institution name
  
  Andreas Madlung    --  University of Puget Sound
  Arijit Mukherjee   --  University of Wisconsin, Madison
  Dazhong Zhao       --  University of Wisconsin-Milwaukee
  Fuyu Xu            --  University of Maine
  Jeonghwa Lee       --  University of Massachusetts-Amherst
  Jian Zhao          --  The Samuel Roberts Noble Foundation
  Lei Zhu            --  University of California, Riverside
  Michelle Facette   --  University of California, San Diego
  Peter Lundquist    --  Cornell University
  Manoj Kumar        --  University of Louisiana at Lafayette
  Surinder Chopra    --  Pennsylvania State University
  Tanya Falbel       --  University of Wisconsin - Madison
  Veronica Justen *  --  University of Wisconsin-River Falls 
  Songqing Ye        --  University of Minnesota
  
  * DECLINED


Acknowledgments

NSF Plant Genome Program funded projects on the Plant Ontology and the Gramene database projects on comparative plant genomics and genetics.

Phenote

Phenote is developed by the Berkeley Bioinformatics Open-Source Projects [1]. We greatly acknowledge the contribution made by the BBOP developers Nomi Harris and Chris Mungall for their help in customizing the Phenote tool for use in this workshop.

Ontologies/datasets

Several projects contributed data sets that are linked to the auto complete features in the Plant specific Phenote configuration. They include