GeWorkbench Highlights caBIG ® Molecular Analysis Tools Knowledge Center AACR Annual Meeting, April 3, 2011.

Slides:

Advertisements

Similar presentations

GoMiner: (Zeeberg et al., Genome Biology, March 2003) For Tour of GoMiner: Advance using forward arrow.

Advertisements

The Maize Inflorescence Project Website Tutorial Nov 7, 2014.

Beyond PubMed and BLAST: Exploring NCBI tools and databases Kate Bronstad David Flynn Alumni Medical Library.

Genome databases and webtools for genome analysis Become familiar with microbial genome databases Use some of the tools useful for analyzing genome Visit.

Oncomine Database Lauren Smalls-Mantey Georgia Institute of Technology June 19, 2006 Note: This presentation contains animation.

Pathways analysis Iowa State Workshop 11 June 2009.

Gene Set Enrichment Analysis (GSEA)

Prof. Carolina Ruiz Computer Science Department Bioinformatics and Computational Biology Program WPI WELCOME TO BCB4003/CS4803 BCB503/CS583 BIOLOGICAL.

5 EBI is an Outstation of the European Molecular Biology Laboratory. Master title Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI.

The IntAct Database Sandra Orchard & Birgit Meldal.

5 EBI is an Outstation of the European Molecular Biology Laboratory. Master title Molecular Interactions – the IntAct Database Sandra Orchard EMBL-EBI.

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

GeWorkbench caGrid TeraGrid Integration Scott Oster Ohio State University – Dept. of Biomedical Informatics Christine Hung Columbia University – JCSB/C2B2.

Sequence Analysis MUPGRET June workshops. Today What can you do with the sequence? What can you do with the ESTs? The case of SNP and Indel.

Kate Milova MolGen retreat March 24, Microarray experiments: Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

341: Introduction to Bioinformatics Dr. Natasa Przulj Deaprtment of Computing Imperial College London

GeWorkbench Remote Access to caArray Data Fan Lin Ph.D. Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of MIT and.

>>> Korean BioInformation Center >>> KRIBB Korea Research institute of Bioscience and Biotechnology GS2PATH: Linking Gene Ontology and Pathways Jin Ok.

Genome Informatics 2005 ~ 220 participants 1 keynote speaker: David Haussler 47 talks 121 posters.

Ch10. Intermolecular Interactions and Biological Pathways

Cytoscape A powerful bioinformatic tool Mathieu Michaud

Cancer is heterogeneous disease! -> enabled characterization of new tumor subtypes for improving personalized treatment and ultimately achieving better.

Erice 2008 Introduction to PDB Workshop From Molecules to Medicine: Integrating Crystallography in Drug Discovery Erice, 29 May - 8 June Peter Rose

1 geWorkbench Hands-On Training Session Date: Session Length: Target Audience: Trainer: Developer Subject Matter Expert:

EGAN: Exploratory Gene Association Networks by Jesse Paquette Biostatistics and Computational Biology Core Helen Diller Family Comprehensive Cancer Center.

Networks and Interactions Boo Virk v1.0.

Intralab Workshop - Reactome CMAP Chang-Feng Quo June 29 th, 2006.

GENOME-CENTRIC DATABASES Daniel Svozil. NCBI Gene Search for DUT gene in human.

GenePattern Overview for MAGE-TAB Workshop Ted Liefeld January 24, 2007.

Taverna Workflow. A suite of tools for bioinformatics Fully featured, extensible and scalable scientific workflow management system – Workbench, server,

BioHealthBase: A Web-based Database and Analysis Resource for Francisella Shubhada Godbole 1, Jyothi Noronha 1, Burke Squires 1, Victoria Hunt 1, Ed Klem.

Tutorial session 2 Network annotation Exploring PPI networks using Cytoscape EMBO Practical Course Session 8 Nadezhda Doncheva and Piet Molenaar.

Using geWorkbench: Hierarchical & SOM Clustering Fan Lin, Ph. D Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of.

Building and Running caGrid Workflows in Taverna 1 Computation Institute, University of Chicago and Argonne National Laboratory, Chicago, IL, USA 2 Mathematics.

EADGENE and SABRE Post-Analyses Workshop 12-14th November 2008, Lelystad, Netherlands 1 François Moreews SIGENAE, INRA, Rennes Cytoscape.

Phase II Additions to LSG Search capability to Gene Browser –Though GUI in Gene Browser BLAST plugin that invokes remote EBI BLAST service Working set.

Introduction to caArray caBIG ® Molecular Analysis Tools Knowledge Center April 3, 2011.

Gene expression analysis

Browsing the Genome Using Genome Browsers to Visualize and Mine Data.

Tutorial session 3 Network analysis Exploring PPI networks using Cytoscape EMBO Practical Course Session 8 Nadezhda Doncheva and Piet Molenaar.

Tutorial 7 Gene expression analysis 1. Expression data –GEO –UCSC –ArrayExpress General clustering methods –Unsupervised Clustering Hierarchical clustering.

Analysis of GEO datasets using GEO2R Parthav Jailwala CCR Collaborative Bioinformatics Resource CCR/NCI/NIH.

Gene Expression and Networks. 2 Microarray Analysis Supervised Methods -Analysis of variance -Discriminate analysis -Support Vector Machine (SVM) Unsupervised.

NCBI Genome Workbench Chuong Huynh NIH/NLM/NCBI Sao Paulo, Brasil July 15, 2004 Slides from Michael Dicuccio’s Genome Workbench.

Gene Expression Omnibus (GEO)

Biological Networks & Systems Anne R. Haake Rhys Price Jones.

2009 IADR, MIAMI, FL, USA Hands-on Experience for using the Human Oral Microbiome Database (HOMD) 2009 IADR Workshop, Miami, FL, USA Tsute (George) Chen.

BBN Technologies Copyright 2009 Slide 1 The S*QL Plugin for Cytoscape Visual Analytics on the Web of Linked Data Rusty (Robert J.) Bobrow Jeff Berliner,

Clustering Algorithms to make sense of Microarray data: Systems Analyses in Biology Doug Welsh and Brian Davis BioQuest Workshop Beloit Wisconsin, June.

GeWorkbench John Watkinson Columbia University. geWorkbench The bioinformatics platform of the National Center for the Multi-scale Analysis of Genomic.

An overview of Bioinformatics. Cell and Central Dogma.

A collaborative tool for sequence annotation. Contact:

Introduction to caIntegrator caBIG ® Molecular Analysis Tools Knowledge Center April 3, 2011.

Cool BaRC Web Tools Prat Thiru. BaRC Web Tools We have.

ARGOS (A Replicable Genome InfOrmation System) for FlyBase and wFleaBase Don Gilbert, Hardik Sheth, Vasanth Singan { gilbertd, hsheth, vsingan

Using geWorkbench: Working with Sets of Data Fan Lin, Ph. D. Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of MIT.

GeWorkbench Overview Support Team Molecular Analysis Tools Knowledge Center Columbia University and The Broad Institute of MIT and Harvard.

Tutorial 8 Gene expression analysis 1. How to interpret an expression matrix Expression data DBs - GEO Clustering –Hierarchical clustering –K-means clustering.

CaGrid Workflow Examples Wei Tan, Ravi Madduri University of Chicago {wtan,

NCBI: something old, something new. What is NCBI? Create automated systems for knowledge about molecular biology, biochemistry, and genetics. Perform.

Bioinformatics Shared Resource Introduction to Gene Expression Omnibus (GEO) bsrweb.sanfordburnham.org

Lab Interactions and Ontologies LAB CBW Bioinformatics Workshop February 23 th 2006, Toronto Christopher Hogue Blueprint Initiative.

ARCH/VCDE F2F BoF And the Presentation Subtitle Goes Here Ravi Madduri December 2008.

Networks and Interactions

Using ArrayExpress.

Genome Annotation Continued

INFORMATION FLOW AARTHI & NEHA.

Overview Gene Ontology Introduction Biological network data

Network biology An introduction to STRING and Cytoscape

Presentation transcript:

geWorkbench Highlights caBIG ® Molecular Analysis Tools Knowledge Center AACR Annual Meeting, April 3, 2011

Customizable Load needed modules on demand.

Visualize microarray data Available viewers include tabular, expression profile, color mosaic and scatter plot components.

Differential Expression

Hierarchical Clustering – Dendrogram heatmap display with subtree selection

Query interactomes in the Cellular Network Knowledge Base…

…and visualize molecular interaction networks using the Cytoscape plugin

Gene Ontology Enrichment Analysis Enrichment calculations performed using Ontologizer2.0

BioCarta Pathway Diagrams BioCarta diagrams are supplied by the NCI’s caBIO service.

Cancer Gene Index Query for curated cancer-related literature references including context sentence and Pubmed links. Data via NCI’s caBIO data service.

Retreive genomic and protein sequences

Scan sequence with promoter motifs

Full NCBI BLAST interface with integrated result browser

Retrieve data from caArray Direct download of data from the NCI’s caArray microarray data repository

View molecular structures in Jmol 1e09.pdb - Major Cherry Allergen PRU AV 1

Invoke GenePattern Analytical Routines…

…then test and apply generated classifiers Test the classifier via cross-validation Apply the classifier to a test set of arrays

Query SkyBase Homology Models Finds pre-built NESG homology models with similarity to a sequence supplied by the user.

Homology Modeling using Pudge Pudge integrates numerous model building and evaluation methods.

Protein Structure Functional Annotation using MarkUs Calculates and displays electrostatic, cavity, conservation, and many other properties

Online Resources for geWorkbench Molecular Analysis Tools Knowledge Center kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench geWorkbench User Forum kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3 Tool Landing Pagehttps://cabig.nci.nih.gov/tools/geWorkbench geWorkbench Project and Documentation Site NCICB Applications Support Phone: Toll-free: Web: