OBI-Warp Code
Status: Alpha
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| File | Date | Author | Commit |
|---|---|---|---|
| lib | 2010-12-15 |
John Prince
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[43f49b] silenced warnings with -O3 optimization |
| sdk | 2009-11-14 |
John Prince
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[679617] init commit |
| .gitignore | 2010-12-14 |
John Prince
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[f46055] progress |
| History | 2010-12-15 |
John Prince
|
[43f49b] silenced warnings with -O3 optimization |
| LICENSE | 2009-11-14 |
John Prince
|
[679617] init commit |
| README.html | 2010-12-14 |
John Prince
|
[f46055] progress |
| README.md | 2010-12-14 |
John Prince
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[f46055] progress |
| Rakefile | 2010-12-15 |
John Prince
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[43f49b] silenced warnings with -O3 optimization |
| VERSION | 2010-12-13 |
John Prince
|
[92727a] progress |
Read Me
<html> <head><title>README.md</title></head> <body> <h1>OBI-Warp</h1> <p>Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets.</p> <p>OBI-Warp was developed specifically for the chromatographic alignment of complex mass spectrometry (MS) proteomics data. Using high confidence MS/MS identifications as time standards, OBI-Warp default parameters have been optimized to give accurate alignments under a variety of real-world conditions including datasets with little overlapping signal. Command-line options to override defaults are available (e.g., gap penalty, local weights and number of bijective anchors). Though developed for MS proteomics data, OBI-Warp is suited to a wide variety of alignment problems.</p> <p>Pearson's correlation coefficient, covariance, dot product, and Euclidean distance have been implemented as the available vector similarity functions. Redundant calculations for correlation coefficient and covariance are cached in the n x m comparisons to give the algorithmic equivalent of calculating the dot product.</p> <p>The dynamic programming algorithm is written to allow any arbitrary gap penalty function, or users may use a linear initiation and elongation penalty. Local weighting schemes may also be controlled.</p> <h3>Links</h3> <ul> <li><a href="://sourceforge.net/projects/obi-warp/">Project Summary Page</a></li> <li><a href="://sourceforge.net/project/showfiles.php?group_id=161548">Download OBI-Warp</a></li> <li><a href="://dx.doi.org/10.1021/ac0605344">Analytical Chemistry Publication</a></li> <li><a href="://bioinformatics.icmb.utexas.edu/obi-warp/">Supplementary Material for Publication</a> (<em>this server is currently down</em>)</li> </ul> <h2>Building</h2> <p>Building is tested rigorously on Ubuntu and should work fine on any POSIX system. Windows compilation under VC++ should be possible and compilation with cygwin, or msys/mingw should work without any problems.</p> <h3>Prerequisites</h3> <p><a href="http://www.ruby-lang.org">ruby</a> and <em>rake</em>. <em>rake</em> comes standard with the newer ruby (1.9.X), but it can also be installed using <a href="http://rubygems.org/pages/download">rubygems</a> (for ruby versions below 1.9):</p> <pre><code>gem install rake </code></pre> <p>Optional: <em>valgrind</em> can be used for memory testing and <a href="http://www.bioinformatics.ubc.ca/matrix2png/download.html">matrix2png</a> can be used to create images of the various matrices.</p> <h3>Compiling</h3> <pre><code>rake # creates bin/obiwarp (notice it is in the *bin* directory) </code></pre> <p>This will compile all the code and link it into the obiwarp executable. <strong>NOTE</strong>: All executables will be created in the <strong>bin</strong> directory (testing executables stay in the lib dir).</p> <p>If you want to explore other options:</p> <pre><code>rake -T </code></pre> <p>From within the <em>lib</em> directory, the generation of any file, intermediate, or test can be invoked by name. For example:</p> <pre><code># build the lmat2lmata binary: rake lmat2lmata # note, it will be in created in the bin directory # this also works rake ../bin/lmat2lmata </code></pre> <p>From the top directory, all the tasks (not necessarily filetasks) are available:</p> <pre><code># from the top level directory rake memtest # from the lib directory rake memtest </code></pre> <h3>Installation</h3> <p>Binaries are compiled and depositied in the <strong>bin</strong> folder. System installation is left to the user, but it can be as simple as:</p> <pre><code>rake # make sure it is compiled and linked sudo cp bin/obiwarp /usr/local/bin/ </code></pre> <h3>Testing</h3> <pre><code># run all tests rake test # if you have valgrind installed: rake memtest rake test_cmdparser.rb # for tests written in ruby rake run_test_dynprog # for tests written in cxxtest 'run_test_<whatever>' </code></pre> <p>tasks found in the lib Rakefile are also available from the top level Rakefile using the 'lib:' prefix:</p> <pre><code>rake clean # from inside the lib directory rake lib:clean # from the top dir </code></pre> </body> </html>
