Coding Projects
Most of my reasearch is at the interface of computation, mathematics and statistics and involves coding algorithms, proving theorems and making decisions with real-world data. |
I write GNU General Public Licensed free software in C/C++ and the accompanying GNU Free Documentation Licensed documents with collaborators on my research projects.
The rationale behind using C++, a low-level object-oriented language that supports generic programming, for research, as opposed to ready-made programming environments, such as, MATLAB, MAPLE or R, is due to the elegance, ease and power provided by the language to implement "pretty much whatever" operations you can conjure up over sets of entities you can dream of without "reinventing the wheel".
The two major coding projects that parallel my current research interests, namely, (1) Mathematical and Statistical Genetics and (2) Set-valued Statistical Algorithms, are at the top of the following list, respectively.
- lce -- a c++ class library for lumped coalescent experiments [under construction]
- mrs -- a c++ class library for statistical set processing [beta version released]
- multiply -- a program to test the Schonhage-Strassen Algorithm using complex interval arithmetic.
- Quin/Septcunx Visual Cognitive Tool GUI
- codemlZ -- Detecting Physicochemical Selection
Resources to satisfy requirements on joint coding projects
- A free book about Version Control with Subversion (SVN), a new version control system designed to supplant CVS. All my coding projects use secure SVN repositories. Get a Wiki overview of SVN.
- All basic coding is done in C and C++. The standard template library as well as other template libraries are used.
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The following C and C++ libraries are used for mathematical, scientific and statistical computing.
- The GNU Scientific Library (GSL)
- C eXtended for Scientific Computing (C-XSC)
- libsequence, a C++ class library for population genetics.
- Doxygen is a source code documentation generator tool. It is used in all of my projects. See www.doxygen.org/.
Other coding resources worth exploring
- Google Directory: Math Software
- SAGE is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface. SAGE Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.
Last modified on Saturday, 24-Sep-2011 09:22:54 NZST and served on Friday, 10-Feb-2012 08:37:19 NZDT.