Pathways Database System: An Integrated System For Biological Pathways L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan.

Slides:

Advertisements

Similar presentations

Martin John Bishop UK HGMP Resource Centre Hinxton Cambridge CB10 1 SB

Advertisements

SRI International Bioinformatics Comparative Analysis Q

MitoInteractome : Mitochondrial Protein Interactome Database Rohit Reja Korean Bioinformation Center, Daejeon, Korea.

SRI International Bioinformatics 1 The consistency Checker, or Overhauling a PGDB By Ron Caspi.

BIOINFORMATICS Ency Lee.

Bioinformatics for biomedicine Summary and conclusions. Further analysis of a favorite gene Lecture 8, Per Kraulis

Interoperation of Molecular Biology Databases Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International Menlo Park, CA

Systems Biology Existing and future genome sequencing projects and the follow-on structural and functional analysis of complete genomes will produce an.

KEGG: Kyoto Encyclopedia of Genes and Genomes Susan Seo Intro to Bioinformatics Fall 2004.

Introduction to Bioinformatics Spring 2008 Yana Kortsarts, Computer Science Department Bob Morris, Biology Department.

Introduction to Bioinformatics - Tutorial no. 13 Probe Design Gene Networks.

Bioinformatics: a Multidisciplinary Challenge Ron Y. Pinter Dept. of Computer Science Technion March 12, 2003.

Data-intensive Computing: Case Study Area 1: Bioinformatics B. Ramamurthy 6/17/20151.

ONCOMINE: A Bioinformatics Infrastructure for Cancer Genomics

Use of Ontologies in the Life Sciences: BioPax Graciela Gonzalez, PhD (some slides adapted from presentations available at

Pathways Analysis using Protein Expression Data Venkatesh Jitender Dr. Vanathi Gopalakrishnan Center for Biomedical Informatics, UPMC.

Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.

Algorithm Animation for Bioinformatics Algorithms.

Bioinformatics Original definition (1979 by Paulien Hogeweg): “application of information technology and computer science to the field of molecular biology”

Modeling Functional Genomics Datasets CVM Lessons 4&5 10 July 2007Bindu Nanduri.

From T. MADHAVAN, & K.Chandrasekaran Lecturers in Zoology.. EXIT.

Ch10. Intermolecular Interactions and Biological Pathways

Cytoscape A powerful bioinformatic tool Mathieu Michaud

Review of Ondex Bernice Rogowitz G2P Visualization and Visual Analytics Team March 18, 2010.

Bioinformatics.

Synthetic biology: New engineering rules for emerging discipline Andrianantoandro E; Basu S; Karig D K; Weiss R. Molecular Systems Biology 2006.

Biological Databases By : Lim Yun Ping E mail :

Introduction to Bioinformatics Spring 2002 Adapted from Irit Orr Course at WIS.

Tutorial on Current Biochemical Pathway Visualization Tools By Rana Khartabil.

What is Genetic Research?. Genetic Research Deals with Inherited Traits DNA Isolation Use bioinformatics to Research differences in DNA Genetic researchers.

Network & Systems Modeling 29 June 2009 NCSU GO Workshop.

AP Biology DNA Study Guide. Chapter 16 Molecular Basis of Heredity The structure of DNA The major steps to replication The difference between replication,

Bioinformatics for Human Biologists Rasmus Wernersson, Associate Professor Center for Biological Sequence Analysis, DTU [ -

Workshop Aims NMSU GO Workshop 20 May Aims of this Workshop  WIIFM? modeling examples background information about GO modeling  Strategies for.

Predicting protein degradation rates Karen Page. The central dogma DNA RNA protein Transcription Translation The expression of genetic information stored.

Jianlin Cheng Institute for Genomics and Bioinformatics School of Information and Computer Science University of California Irvine Sigmoid: A Systems Biology.

Supporting Scientific Collaboration Online SCOPE Workshop at San Diego Supercomputer Center March 19-22, 2008.

WMU CS 6260 Parallel Computations II Spring 2013 Presentation #1 about Semester Project Feb/18/2013 Professor: Dr. de Doncker Name: Sandino Vargas Xuanyu.

Jobs, Careers, Internships, Senior Projects and Research Computer Application Development K-12 education Industrial Training Bioinformatics Validation.

A collaborative tool for sequence annotation. Contact:

Introduction to biological molecular networks

1 From Mendel to Genomics Historically –Identify or create mutations, follow inheritance –Determine linkage, create maps Now: Genomics –Not just a gene,

GO based data analysis Iowa State Workshop 11 June 2009.

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

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

Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.

Bioinformatics Dipl. Ing. (FH) Patrick Grossmann

Gene_identifier color_no gtm1_mouse 2 gtm2_mouse 2 >fasta_format_description_line >GTM1_HUMAN GLUTATHIONE S-TRANSFERASE MU 1 (GSTM1-1) PMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKI.

The Central Dogma of Molecular Biology DNA  RNA  Protein  Trait.

High throughput biology data management and data intensive computing drivers George Michaels.

RDF based on Integration of Pathway Database and Gene Ontology SNU OOPSLA LAB DongHyuk Im.

 What is MSA (Multiple Sequence Alignment)? What is it good for? How do I use it?  Software and algorithms The programs How they work? Which to use?

1 Survey of Biodata Analysis from a Data Mining Perspective Peter Bajcsy Jiawei Han Lei Liu Jiong Yang.

Lecture 1.01 Developing the Tools Montreal 2004 Course Introduction John J. Salama.

SC.912.L.16.3 DNA Replication. – During DNA replication, a double-stranded DNA molecule divides into two single strands. New nucleotides bond to each.

Bioinformatics Overview

Data-intensive Computing: Case Study Area 1: Bioinformatics

The Pathway Tools Schema

Bioinformatics Madina Bazarova. What is Bioinformatics? Bioinformatics is marriage between biology and computer. It is the use of computers for the acquisition,

Introduction to bioinformatics

Bioinformatics Capstone Project

“Proteomics is a science that focuses on the study of proteins: their roles, their structures, their localization, their interactions, and other factors.”

Relationship between Genotype and Phenotype

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

LESSON 1 INTNRODUCTION HYE-JOO KWON, Ph.D /

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Introduction to Bioinformatics

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Presentation transcript:

Pathways Database System: An Integrated System For Biological Pathways L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan and W. Xu Bioinformatics Vol. 19 no Pages Presented by Mohamed Uduman Bioinformatics Computing II Spring 043

Outline Background Pathways Database System Architecture of the system Data model Tools of the Pathways Database System Other pathway tools Future Developments Conclusion Questions

Background Genome sequencing – what to do with data? DNA sequence good for analyzing  Organization  Evolution  Mutation Biological Pathways “Pathways are the sequential and cumulative action of genetically distinct but functionally related molecules.”

Background Biological Pathways  Metabolic & biochemical  Transcription & protein synthesis  Signal Transduction

Pathways Database System Genomic pathway information:  Store / manage  Analyze  Visualize  Query Features  GUI tools  Multiple abstraction levels for viewing information  XML output

Architecture Pathways Browser Browser Tool Visualization Tool Querying Tool Services Data Extraction Querying Services Relational Database Pathways DB HTTPSOAP

Pathways Data Model Molecular entity Basic molecules (protein, enzyme, gene, amino acid, substrate, co-factors etc...) Process Reaction between molecular entities Pathways Interconnection of processes

Pathways Browser Tree pane Query result pane Visualization pane

Browser Tool

Visualization Tool

Querying Tool

Querying Service (QRS) Query functions submit predefined queries Results passed as XML Supports SOAP / HTTP protocols

Query Functions Basic query Statistical query Neighborhood query Path-finding query

Other Pathway Tools Biocarta ExPASy Biochemical pathways Signaling Pathway database PathDB Gene Ontology

Future Developments Ability to add new pathways Ability to modify views Incorporating GO Enhance the visualization tool

Conclusion Pathways Database System is an integrated system for storing, analyzing and visualizing biology pathways. Biological pathways show the “bigger picture”

Questions or Comments ? Presented by Mohamed Uduman Bioinformatics Computing II Spring 043