ADVANCED COURSE: INTRODUCTION TO PROGRAMMING FOR BIOINFORMATICS USING JAVA

John Archer

This course will introduce students to the fundamentals of programming for bioinformatics using the Java programming language. Many of the concepts covered will be readily transferable to other languages. The course will largely focus on the Java language basics including, data types, program control structures and object-oriented programming features of the language, with an emphasis on usage within areas of bioinformatics, for example file manipulation, package use and calling external software. By the end of the course students will have had a primer on creating programmatic solutions to real world problems within the scope of their research.

PROGRAMME

Day 1:
What is Java and what does it have in common with other languages?
Installing Java
The Netbeans integrated development environment
A look at a simple Java program
Programming in Java 1
- Code style, simple data types and operators
- Arrays
- Program flow, code blocks, loops, conditions
- Implementing a simple calculator

Day 2:
Programming in Java 2
- Classes, objects and non-static methods: data encapsulation
- Constructor overriding
- Strings
- Static vs. non static methods
- Lists and Hash maps
- Implementing a simple sequence manipulator

Day 3:
- More work on the sequence editor
- Creating Alignments using external software
- Calculating pairwise distances
- Creating trees
- Using external packages
- More general file manipulation and altering data formats

Day 4:
- How to write code for a specific problem, i.e. psudo code to code
- Designing and implementing a more advanced algorithm – read mapping
- Basics on Program speed and memory usage

Day 5:
- Revision of previous topics
- Discussion about databases, graphics, recursion and other aspects of the language
- Code session

COURSE INSTRUCTORS
John Archer - CIBIO-InBIO | Bioinformatics

INTENDED AUDIENCE
The course will be open to a maximum number of 15 participants.

All the participants will be required to bring their laptops. Software we will be using from the start of the course will be the Java SDK latest (or recient 1.7 or higher) version and the Netbeans IDE. Having these pre-installed will be helpful.

75% of available student slots are reserved for BIODIV students. Priority will be given to:
• 1st year and other PhD students attending the BIODIV Doctoral Program;
• PhD students attending other courses;
• Other post-graduate students and researchers.

REGISTRATION

Participation is free of charge for BIODIV students | 95 € (students) / 200 € (other participants).CIBIO-InBIO members will have an additional discount of 20%. Does not include lunch nor coffee breaks.
To apply, please send an e-mail accompanied by your short CV (max. two A4 pages) to post.graduation@cibio.up.pt. Please refer your academic status (PhD student, MSc Student, Other) and the institution to which you are affiliated. BIODIV students should also mention which year of their PhD they are in. If you are interested in more than one course, you need to send a separate application for each of them.

Please note that new rules apply for all BIODIV students.