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| Lecture | Speaker | Download |
| 1.0 Course Introduction | John J. Salama |
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| 1.1 Introduction to J2EE Development | John J. Salama |
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| 1.2 Eclipse, CVS, Tomcat, and Ant | Stephen Montgomery |
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| 1.3 Development Environment Basics | Dominik Gehl |
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| 2.0 Data Modeling I: XML & XSLT | Marc Dumontier |
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| 2.2 XML Schema & JAXB | Marc Dumontier |
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| 2.2 Microarray Data Modeling Lab | Sebastien Lemieux |
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| 2.3 Auto-generating Java classes using JAXB | Marc Dumontier |
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| 3.0 Biopackages I - sequence manipulation with BioJava | Sohrab Shah |
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| 3.1 MySQL and JDBC “Lets talk databases” | Sohrab Shah |
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| 3.2 MySQL Database Lab | Dominik Gehl |
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| 3.3 The NCBI C++ Toolkit | Doron Betel |
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| 4.0 Data Mining | Sebastien Lemieux |
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| 4.1 From Database to Data mining | Sohrab Shah |
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| 4.2 Algorithms | Sebastien Lemieux |
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| 5.0.1 Thread Safe Web Applications | John J. Salama |
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| 5.0 Java Servlets & Java Server Pages | François Major |
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| 5.1 Developing Servlets & JSPs | John J. Salama |
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| 5.2 Transforming Data: Using Apache Xalan to apply XSLT transformations | Marc Dumontier |
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| 6.0 Other Bioinformatics Tools | Howard Feldman |
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