A short readable introduction to agent based models. Published by SAGE Publications. ISBN 978-4129-4964-4.
A very readable introduction to using CUDA to program GPUs. Published by Addison-Wesley. ISBN-13: 978-0-13-138-768-3. ISBN-10: 0-13-138-768-5.
There is a web page for the book. It has a link for downloading the source code files for the example code used in the book. Once downloaded, the main directory for the examples has a README.txt which has some useful information. Some of the examples (all but the simplest "Hello, World" type of examples) use the GLUT framework, which must be installed before those examples can be built and run.
The authoritative book on programming CUDA. Installed with the CUDA SDK (into /usr/local/cuda/doc). Here is a local copy. Also available from the CUDA SDK dowload page, from the documentation link for each operating system, which can be reached from this page. Used as a reference by other sources. Has more detail than CUDA by Example, Introduction to CUDA so it is a useful complement to those references.
Detailed information on safe programming and on optimizations for getting the most performance on a GPU. Installed with the CUDA SDK (into /usr/local/cuda/doc). Here is a local copy. Also available from the CUDA SDK dowload page, from the documentation link for each operating system, which can be reached from this page.
A reference manual to the CUDA API, the API referenced in CUDA by Example, CUDA C Best Practices Guide, and CUDA Toolkit Reference Manual. Installed with the CUDA SDK (into /usr/local/cuda/doc). Here is a local copy. Also available from the CUDA SDK dowload page, from the documentation link for each operating system, which can be reached from this page.
A text on data visualization techniques. It describes algorithms in general. It is not specific to any graphics library, programming language or operating system. Published by A. K. Peters, ISBN-13: 978-1-56881-306-6.
An open source book on GNU make. Available at GNU Make Manual. Here is a local copy.
A short readable introduction to the human immune system. Very useful for someone with little or no biology background. Published by Wiley-Blackwell. ISBN-10: 140516221X. ISBN-13: 978-1405162210
A series of online lectures from the VSCSE. This is the web page for the online lectures, but you have to be registered to access it (registration is free). The presenter is Joshua A. Anderson, who is a staff research scientist at the University of Michigan Dept. of Chemical Engineering.
Here are local copies of the lectures. The videos won't play in the Ubuntu default video player, Totem. There is probably a codec that can be installed so they will play in Totem. You can also install VLC which will play them.
The definitive guide to programming OpenGL. Often referred to as the OpenGL red book because of its red cover. Published by Addison-Wesley. ISBN-10: 0-321-48100-3. ISBN-13: 978-0-321-48100-9.
Published by Elsevier. ISBN: 978-0-12-381472-2.
A book on programming techniques for writing highly parallel programs. Geared toward programming GPUs using CUDA, but the techniques also apply to other parallel programming systems, such as openMP and MPI.
An introduction to using Subversion. Published by CreateSpace. ISBN-10: 1441437762. ISBN-13: 978-1441437761 There is also a free online version. This book describes using svn with the command line program, not a GUI version. Chapters 1 and 2 are especially useful for getting started using svn, even if you intend to use a GUI svn client, because it describes basic svn concepts, and also because the command line program is often useful and sometimes necessary.