OBI-Warp

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.

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.

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.

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.

Building

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.

Prerequisites

ruby and rake. rake comes standard with the newer ruby (1.9.X), but it can also be installed using rubygems (for ruby versions below 1.9):

gem install rake

Optional: valgrind can be used for memory testing and matrix2png can be used to create images of the various matrices.

Compiling

rake
# creates bin/obiwarp   (notice it is in the *bin* directory)

This will compile all the code and link it into the obiwarp executable. NOTE: All executables will be created in the bin directory (testing executables stay in the lib dir).

If you want to explore other options:

rake -T

From within the lib directory, the generation of any file, intermediate, or test can be invoked by name. For example:

# build the lmat2lmata binary:
rake lmat2lmata    # note, it will be in created in the bin directory
# this also works
rake ../bin/lmat2lmata

From the top directory, all the tasks (not necessarily filetasks) are available:

# from the top level directory
rake memtest
# from the lib directory
rake memtest

Installation

Binaries are compiled and depositied in the bin folder. System installation is left to the user, but it can be as simple as:

rake      # make sure it is compiled and linked
sudo cp bin/obiwarp /usr/local/bin/

Testing

# 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>'

tasks found in the lib Rakefile are also available from the top level Rakefile using the 'lib:' prefix: