Developing the Tools Montreal 2004

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Developing the ToolsMontreal 2004

• Course Introduction
• John J. Salama

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Todays Talk

• Course Introduction
• Bioinformatics Introduction
• Data Introduction
• Applications Introduction

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COURSE INTRODUCTION
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Introductions

• What is your work experience?
• How will bioinformatics help you in your work?
• What do you hope to learn from this course?

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Canadian Bioinformatics Workshops
Bioinformatics
Proteomics
Genomics
Developing the Tools
www.bioinformatics.ca
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Course Objectives

• Data modeling
• Using existing open source bioinformatics
  packages
• Using and creating databases
• Algorithms and data mining
• Web application design
• Foundations of software architecture

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Detailed Schedule
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Assignments Marking Scheme
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Administration

• Login / Password
• Will be given to you in the first lab
• After First Login
• cbw.setup
• To start services (apache, tomcat, mysql)
• cbw.start
• mySQL
• Database location /u/USER/mysql/data
• phpMyAdmin - http//localhost8080/phpMyAdmin

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Administration

• CVS
• cvs -d pserveranonymous_at_cvs.iro.umontreal.ca/
  home/cvs/cvscbw/cvsroot login
• cvs -d pserveranonymous_at_cvs.iro.umontreal.ca/
  home/cvs/cvscbw/cvsroot checkout ltMODULEgt      
• Services
• apache     - http//localhost8080   (/u/USER/apa
  che/htdocs)
• tomcat     - http//localhost8081    (/u/USER/ja
  karta-tomcat/webapps)
• axis       - http//localhost8081/axis

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Sponsors
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BIOINFORMATICS INTRODUCTION
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What is Bioinformatics

• The application of computer technology to the
  management of biological information
• Software applications used to gather, store,
  analyze and integrate biological information
• Databases and algorithms designed for the purpose
  of enhancing the process of biological research

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What is Bioinformatics

• NCBI Research, development, or application of
  computational tools and approaches for expanding
  the use of biological, medical, behavioral or
  health data including those to acquire, store,
  archive, analyze, or visualize such data.
• Lincoln Stein Biologists using computers, or
  the other way around.

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Hot Bioinformatics Topics

• Gene Expression / Regulation
• Protein / RNA Structure
• Ontologies
• Genome Sequencing / Annotation
• Molecular Interactions

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Where is Bioinformatics Used

• Pharmaceuticals
• Universities
• Biotech Companies
• Public Good / Health Research Institutes
• Hardware Manufacturers
• Government Agencies
• THESE ARE OUR CLIENTS

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Why Do We Need Bioinformatics

• Accessibility of biological data
• Data integration at least within an organization
• Processing of data (data mining)
• Prediction and analysis
• Storage of mass amounts of data (high-throughput
  experiments)

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DATA INTRODUCTION
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How Much Data - GenBank
Source NCBI
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How Much Data - PDB
Source RSCB
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How Much Data - BIND
Source Blueprint North America
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How Much Data - PubMed
Source Israel Institute of Technology
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What Do We Do With All This Data?

• Design data structures to represent this
  information unambiguously
• Develop databases to house the data
• Develop accessible software to submit new data
• Develop fast applications to query the data
• Develop fast applications to analyze the data
  (data mining)

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APPLICATIONS INTRODUCTION
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Bioinformatics Application Trends

• Web based GUI tool accessibility
• Data marts
• Web services
• Integration Services
• Pre-analyzed Data Services

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Languages of Bioinformatics

• Perl
• Python
• Java
• C
• C
• And More

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Todays World of Bioinformatics
Note This is not intended to be an extensive
list of bioinformatics institutions
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All Sorts of Bioinformatics Tools
Note This is not intended to be an extensive
list of bioinformatics tools