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RBIF 123

Java Programming for Bioinformatics

This course provides a foundation in bioinformatics and scientific computing using the Java programming language. Following a brief introduction to Java and integrated development environments, the course focuses on developing basic bioinformatics tools, including the use of the BioJava API to retrieve and manipulate sequences, advanced I/O and indexing techniques to handle and search large sequence databases, JDBC methods to query complex genomic databases, and the application of code optimization techniques and numerical recipes to CPU intensive bioinformatics algorithms.

At the end of the course, students will be able to:

Develop various tools within the BioJava framework.

Use JDBC to retrieve genomic data from SQL databases.

Write Java code to efficiently search large biological sequence databases.

Implement CPU intensive bioinformatics algorithms.

Implement numerical recipes in Java.

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