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

2. Lecture 1.02 Today’s Talk Course Introduction Bioinformatics Introduction Data Introduction Applications Introduction

3. Lecture 1.03 COURSE INTRODUCTION

4. Lecture 1.04 Introductions What is your work experience? How will bioinformatics help you in your work? What do you hope to learn from this course?

5. Lecture 1.05 Canadian Bioinformatics Workshops Bioinformatics Genomics Proteomics Developing the Tools www.bioinformatics.ca

6. Lecture 1.06 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

7. Lecture 1.07 Detailed Schedule Day 1 (May 3 rd ) Day 2 (May 4 th ) Day 3 (May 5 th ) Day 4 (May 6 th ) Day 5 (May 7 th ) Day 6 (May 8 th ) 08:30Registration & Breakfast Breakfast 09:001.0 Welcome and Course Introduction John Salama 2.0 Data Modeling I XML & XSLT Marc Dumontier 3.0 Bio Packages I Doron Betel 4.0 Data Mining Sebastien Lemieux 5.0 Java Servlets & Java Server Pages Francois Major 6.0 Existing Tools in Bioinformatics Howard Feldman 10.30Break 11:001.1 Introduction to J2EE Development (MVC) John Salama 2.1 Data Modeling II XML Schema & JAXB Marc Dumontier 3.1 Bio Packages II Sohrab Shah 4.1 Data Mining Lab Sohrab Shah 5.1 Development Servlets and JSPs Lab John Salama Open Lab 12:30Lunch on your own 13:451.2 Preparing your Development Environment Lab Dominik Gehl 2.2 Microarray Data Modeling Lab Sebastien Lemieux 3.2 MySQL/JDBC Sohrab Shah 4.2 Algorithms Sebastien Lemieux/ Francois Major 5.2 Transforming Data: Using Apache Xalan to apply an XSLT in Java Marc Dumontier Open Lab 15:15Break Evaluation survey and roundtable discussion 15:451.3 Eclipse, Tomcat, and ANT (CVS) Steve Montgomery 2.3 Auto-generating Java classes using JAXB Marc Dumontier 3.3 Creating a mySQL Database Lab Dominik Gehl 4.3 Algorithms Lab Sebastien Lemieux/ Francois Major Open Lab 17:15Dinner on your own No-host social 19:00 – 21:00 1.4 Microarray Guest Lecture Rob Kearney (Mc Gill Univeristy) Open Lab

8. Lecture 1.08 Assignments & Marking Scheme DayBrief DescriptionNumber % of Final 2 Modelling microarray data and auto-generating Java 1a25 4Data Mining225 4Algorithms325 5 Selecting from a database and displaying XML in a browser 1b25

9. Lecture 1.09 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://localhost:8080/phpMyAdmin

10. Lecture 1.010 Administration CVS –$ cvs -d :pserver:anonymous@cvs.iro.umontreal.ca:/home/cvs/cvscbw/cvsroot login –$ cvs -d :pserver:anonymous@cvs.iro.umontreal.ca:/home/cvs/cvscbw/cvsroot checkout Services –apache - http://localhost:8080 (/u/$USER/apache/htdocs) –tomcat - http://localhost:8081 (/u/$USER/jakarta-tomcat/webapps) –axis - http://localhost:8081/axis

11. Lecture 1.011 Sponsors UOttawa

12. Lecture 1.012 BIOINFORMATICS INTRODUCTION

13. Lecture 1.013 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

14. Lecture 1.014 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.”

15. Lecture 1.015 “Hot” Bioinformatics Topics Gene Expression / Regulation Protein / RNA Structure Ontologies Genome Sequencing / Annotation Molecular Interactions

16. Lecture 1.016 Where is Bioinformatics Used Pharmaceuticals Universities Biotech Companies Public Good / Health Research Institutes Hardware Manufacturers Government Agencies THESE ARE OUR CLIENTS

17. Lecture 1.017 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)

18. Lecture 1.018 DATA INTRODUCTION

19. Lecture 1.019 How Much Data - GenBank Source: NCBI

20. Lecture 1.020 How Much Data - PDB Source: RSCB

21. Lecture 1.021 How Much Data - BIND Source: Blueprint North America

22. Lecture 1.022 How Much Data - PubMed Source: Israel Institute of Technology

23. Lecture 1.023 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)

24. Lecture 1.024 APPLICATIONS INTRODUCTION

25. Lecture 1.025 Bioinformatics Application Trends Web based GUI tool accessibility Data marts Web services Integration Services Pre-analyzed Data Services

26. Lecture 1.026 Languages of Bioinformatics Perl Python Java C++ C And More…

27. Lecture 1.027 Today’s World of Bioinformatics Note: This is not intended to be an extensive list of bioinformatics institutions

28. Lecture 1.028 All Sorts of Bioinformatics Tools Note: This is not intended to be an extensive list of bioinformatics tools