What are the core issues of Java

Java for the life sciences

Learn basic Java techniques that are required for evaluating biodata

  • An introduction to Java for life scientists with programming experience
  • Provides background biological information that is useful in understanding the problem
  • With numerous exercises and code examples

This introduction to applied bioinformatics with Java teaches you the basic Java techniques needed for analyzing data in the life sciences. The book is aimed at students, scientists and practitioners with a basic knowledge of a high-level programming language. It offers you a well-founded introduction to the core topics of programming in the life sciences.

Meaningful examples from bioinformatics illustrate all the necessary steps so that you can achieve results with Java in a short time. Biological relationships are always described if they are helpful for understanding the problem. With the help of numerous practical projects and exercises, you will learn to write your own, well-thought-out software solutions.

Topics of the book:

  • The Java working environment: installation and setup of JDK, Eclipse, Git and Maven
  • Java to refresh: programming concepts such as variables, arrays and loops as well as object-oriented programming
  • Data engineering: workflows for the data lifecycle, working with XML, JSON, SQL, API interfaces and BASH
  • Data mining: methods of classification and clustering such as binning, hashing, statistical models and k-means
  • Network analysis: Introduction to the JGraphT library, graphs as a method for representing biological processes
  • Image processing: working with ImageJ for particle analysis, object classification and color analysis
  • Sequence analysis: the BioJava library, Sequence Alignment, BLAST and Next-Generation Sequencing

Jens Dörpinghaus / Sebastian Schaaf / Vera Weil

Jens Dörpinghaus studied mathematics and computer science. After a few years at the German Center for
neurodegenerative diseases, he has been working as a postdoc at the Fraunhofer Institute for Algorithms and Scientific Computing SCAI (Sankt Augustin) in the bioinformatics department. He teaches Life Science Informatics at the University of Bonn.
Sebastian Schaaf studied biology and bioinformatics and then did his doctorate in bioinformatics. After a few years at the LMU Munich and the local location of the German Cancer Research Center, he is also working as a postdoc at the Fraunhofer Institute for Algorithms and Scientific Computing SCAI in the Bioinformatics department, increasingly in medical informatics projects. He also teaches the Life Science Informatics course at the University of Bonn.
Vera Weil studied mathematics and computer science and then did her doctorate in computer science. She worked for two years as a postdoc at RWTH Aachen University at the Institute for Management Science. For some time she has been teaching computer science at the University of Cologne, where she mainly teaches programming with Java.

  • Students of biology, life sciences, bioinformatics, computer science, natural sciences
  • Practitioners who evaluate biodata
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