Gramene Technical Improvements

Slides:

Advertisements

Similar presentations

Working Group Meeting 2013 Objective 3: Deploy tools to increase user-specified flexible queries.

Advertisements

Gramene Scientific Advisory Board Meeting September 2003.

Stein Lab In-House Symposium The Plan  Overview of my lab’s activities  Detailed look at the Gramene Database  Run out of time  Talk really.

Gramene: A Resource for Comparative Grass Genomics RiceCAP Workshop DNA MARKERS, MAPPING, AND BEYOND 6/8/06.

Gramene Scientific Advisory Board Meeting January 2005.

Gramene Comparative & Phylogenomics Resources for Plants Joshua C. Stein 1, William Spooner 1, Sharon Wei 1, Liya Ren 1, Doreen Ware 1,2 1 Cold Spring.

The design, construction and use of software tools to generate, store, annotate, access and analyse data and information relating to Molecular Biology.

Creating An Allele Index For NPGS: Bioinformatic Issues Edward Buckler USDA-ARS at Cornell University, Ithaca, NY.

Bootcamp: Data Resources1 Paul Bain Reference and Education Services Librarian Countway Library of Medicine Countway.

We are developing a web database for plant comparative genomics, named Phytome, that, when complete, will integrate organismal phylogenies, genetic maps.

Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.

Data retrieval BioMart Data sets on ftp site MySQL queries of databases Perl API access to databases Export View.

DEMO CSE fall. What is GeneMANIA GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional.

Genome database & information system for Daphnia Don Gilbert, October 2002 Talk doc at

Aequatus Browser, an open-source web-based tool developed at TGAC to visualise homologous gene structures among differing species or subtypes of a common.

1 Welcome to the Quantitative Trait Loci (QTL) Tutorial This tutorial will describe how to navigate the section of Gramene that provides information on.

A Comparative Mapping Resource for Grains Gramene Outreach Summary 2005 Claire Hebbard Presented to the Gramene SAB January 13, 2006.

Gramene Objectives Develop a database and tools to store, visualize and analyze data on genetics, genomics, proteomics, and biochemistry of grass plants.

Maps and Markers Gramene SAB Report Jan CMap Improvements Expanded, reorganized and hidden menus New map glyphs –Number of features –Crop map –Magnify.

Rice Sequence and Map Analysis Leonid Teytelman. Rice Genome Annotation Sequence Alignments Automation Comparative Maps Genetic Marker Correspondences.

Comparative Genomics Tools in GMOD GMOD.org Dave Clements 1, Sheldon McKay 2, Ken Youns-Clark 2, Ben Faga 3, Scott Cain 4, and the GMOD Consortium 1 National.

A Comparative mapping resource GRAMENE Doreen Ware USDA ARS Cold Spring Harbor Laboratory

1 Welcome to the GrameneMart Tutorial A tool for batch data sequence retrieval 1.Select a Gramene dataset to search against. 2.Add filters to the dataset.

Using Gramene: A genomics and genetics resource for rice and other grasses. PAG XIV Jan 15, 2006 Immanuel (Noel) Yap Claire Hebbard.

Copyright OpenHelix. No use or reproduction without express written consent 2 Overview of Genome Browsers Materials prepared by Warren C. Lathe, Ph.D.

Use cases for Tools at the Bovine Genome Database Apollo and Bovine QTL viewer.

A Comparative Genomics Resource for Grains. Tutorial Tips If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the left.

A comparative mapping resource for the grasses Gramene Plant Biology July 25, 2004 Molly Fogleman Doreen Ware Pankaj Jaiswal.

GMOD: Managing Genomic Data from Emerging Model Organisms Dave Clements 1, Hilmar Lapp 1, Brian Osborne 2, Todd J. Vision 1 1 National Evolutionary Synthesis.

Diversity Bioinformatics Terry Casstevens Institute for Genomic Diversity, Cornell University GMOD Meeting at NESCent Durham, NC – June 29-30, 2006.

1 of 38 Data Mining in Ensembl with BioMart. 2 of 38 Simple Text-based Search Engine.

Got genom e? Community Meetings GMOD.org The GMOD community meets semi- annually to discuss GMOD components, best practices,

Introduction to the Gramene Genetic Diversity module 5/2010 Build #31.

A Comparative Genomic Mapping Resource for Grains.

Gramene Objectives Provide researchers working on grasses and plants in general with a bird’s eye view of the grass genomes and their organization. Work.

Gramene: Interactions with NSF Project on Molecular and Functional Diversity in the Maize Genome Maize PIs (Doebley, Buckler, Fulton, Gaut, Goodman, Holland,

The Public Face of TAIR User Interface Design Responsiveness to User Input.

GBrowse Population Display and CMap SMBE 2009 Ben Faga.

Building WormBase database(s). SAB 2008 Wellcome Trust Sanger Insitute Cold Spring Harbor Laboratory California Institute of Technology ● RNAi ● Microarray.

TRPGR Gramene: A Platform for Comparative Plant Genomics Doreen Ware USDA ARS Cold Spring Harbor Laboratory Pankaj Jaiswal Oregon State University Joshua.

A Comparative Genomics Resource for Grains V26. Tutorial Tips If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the.

Data Mining in Ensembl with BioMart Giulietta Spudich.

Exploring Rice Phenotypes Using Gramene Molly Fogleman – Outreach coordinator A Comparative Mapping Resource GRAMENE.

Exploring Rice Phenotypes Using Gramene A Comparative Mapping Resource GRAMENE.

Phenotype Curation Susan R. McCouch Department of Plant Breeding Cornell University.

Maize Genome Project Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego, CA Shiran Pasternak January 13, 2006 Gramene SAB Meeting San Diego,

Hands-On Exercise: Grain Yield after Milling RiceCAPS Gramene Workshop 6/8/06.

What do we already know ? The rice disease resistance gene Pi-ta Genetically mapped to chromosome 12 Rybka et al. (1997). It has also been sequenced Bryan.

Welcome to Gramene’s RiceCyc (Pathways) Tutorial RiceCyc allows biochemical pathways to be analyzed and visualized. This tutorial has been developed for.

Genome Database Comparative Genomics Phylogenomics Variation GrameneMart (BioMart) Discovery Environment Josh Stein Cold Spring Harbor Laboratory 1.

IMDB: A Generic Insertional Mutagenesis Database Xiaokang Pan and Lincoln Stein Cold Spring Harbor Laboratory.

Tools in Bioinformatics Genome Browsers. Retrieving genomic information Previous lesson(s): annotation-based perspective of search/data Today: genomic-based.

Welcome to the combined BLAST and Genome Browser Tutorial.

Welcome to the GrameneMart Tutorial A tool for batch data sequence retrieval 1.Select a Gramene dataset to search against. 2.Add filters to the dataset.

Dan Born, Peter Bradbury, Ed Buckler Payan Canaran, Terry Casstevens, Dallas Kroon, Dave Matthews, Susan McCouch, Junjian Ni, Isaak Yosief Tecle, Doreen.

The Bovine Genome Database Abstract The Bovine Genome Database (BGD, facilitates the integration of bovine genomic data. BGD is.

A Comparative Genomic Mapping Resource for Grains.

UK CropNet Software Development. UK CropNet Software Development Goals z Improve user access to data via user- friendly graphical displays. z Development.

Networks and Interactions

Behavior and Phenotype in GMOD Natural Diversity in GMOD

Data Mining with BioMart

Sequence based searches:

Welcome to the Gene and Allele Database Tutorial

got genome? Community Meetings Databases Training GMOD.org

Plant and Animal Genome XIX

TAMU Bovine QTL db and viewer

for the Cotton Community

CottonGen: Enabling Cotton Research through Big-Data Analysis and Integration Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Katheryn Buble, Ping Zheng,

Part II SeqViewer AraCyc Help

Tutorial for: Gramene Website Navigation

Presentation transcript:

Gramene Technical Improvements http://www.gramene.org Gramene Technical Improvements Chengzhi Liang

Goals Support Complex Queries Better Genome Annotation Diversity Visualization Biochemical Pathways Better Comparative Views

Complex Query Examples Find all rice genes/QTL that control a trait, eg, height Find all rice genes in the syntenic region of a Maize QTL

Complex Data View Primary Evolution Protein Family Gene Ontology Reference Tool Chromosome Clone (BAC) Synteny Marker Chromosome Marker Locus Allele Gene/QTL Diversity Trait Trait Option

Current Gramene Schema Portable, modular, etc, many advantages, but not well-suitable for complex queries The previous query examples need to access to multiple modules, including QTL, Genome Browser, CMap, Ontology Several ways, but usually 10-15 steps To do it better, we will use…

BioMart Data warehousing technology for complex queries Well developed, part of GMOD Simple, query optimized, generic schema Portable, easily integrated with Gramene

New Personnel Will Spooner Former Ensembl employee BioMart Developer Many years of experience in developing/deploying/using those programs

Better Genome Annotation Need consistent, reproducible gene predictions across the cereal genomes Software that is being used…

BioPipe Portable Easy to grasp -- close cousin to Ensembl technolgy Simple to use – works with Ensembl schema Data consistency -- using for Gramene alignment annotation

Portable, Standalone tools To search Interpro Go annotation Trans-membrane Prediction Sequence mapping

New Personnel Kiran Kumar Payan Canaran From Biopipe project From Merck’s pipeline project

Diversity Visualization For fast-accumulating diversity data Dr. Ed Buckler will discuss this in details

Biochemical Pathways To fully utilizing data of Trait Diversity Expression Make static data dynamic (both spatial and temporal)

Pathway Tools From Peter Karp, eg, EcoCyc Well developed/supported

To Be Released Liya Ren attended the Cyc short course, and is setting it up for rice and other cereals. Expected date: Fall 2005

Better Comparative Viewer Many web UI improvements to CMap (Ken Clark & Ben Faga) Multiple Genomes in Ensembl via Compara (Will Spooner)

Graphical Summary Web Web Web Web Raw Ensembl CMap BioMart DAS Data Objects API Objects API Objects API Objects API Raw Ensembl CMap BioMart DAS Diversity Data Gramene Dump