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| CRT home > Guide to the JDO SigPath Benchmark |
The SigPath benchmark (version 1.0) is available from our web site at http://www.sigpath.org. The distribution contains the SigPath project frozen at the time we performed the benchmark described in this article, so that the results can be reproduced and the same code base can be used to benchmark new JDO implementations. This section of the appendix describes the steps that users need to follow to run the benchmark. SigPath can be built and compiled with the Java Development Kit 1.3+ and Jakarta Ant 1.5+. A detailed installation procedure is provided on our web site. The steps described below should be followed after the general installation procedure has been performed.
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Unpack the benchmark distribution (should contain the benchmark input data files, e.g., NCI open, SwissProt and TrEMBL databases formatted for import with SigPath).
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Define the IMPORT_DIR environment variable to the location of the input files. In the benchmark distribution, this location should point to the directory import_data under the main distribution directory.
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Create two new configuration targets in build/build_config.xml (follow similar instructions as described in the general instructions). Call the first target configure_fastobjects, and the second target configure_relational.
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Execute the new configuration target created in step 2: ant –f build\build_config.xml configure_fastobjects. This should configure the benchmark to run with FastObjects in your environment.
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Run ant –f build\build.xml test – This will compile, create an empty database, load the sample data and run the tests. If the tests succeed, proceed to the next step. Benchmark results for the tests are written to <test-results>
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Run ant –f build\benchmark.xml benchmark – This will run the pre-release steps of the SigPath benchmark. The results for this stage are written to <logs> and also to console output (stdout).
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Make a copy of the benchmark timing output files.
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Execute the configure_relational configuration target created in step 2: ant –f build\build_config.xml configure_relational – This should configure the benchmark to run with JDO relational mapping implementation in your own environment.
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Repeat steps 4 and 5 and collect the timing measurements for the JDO implementation under test.
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Jul 25th, 2005;
New SigPath beta release
[Release info]
Feb 9th, 2005;
New SigPath production release
[Release info]
Dec 9-11th, 2004;
The First SigPath workshop was held in New York City.
[Workshop info]
Nov 3rd, 2004;
New SigPath beta release
[Release info]
Oct 29th, 2004;
New SigPath production released [Release info]
Sep 22nd, 2004;
New beta release of SigPath available for preview and testing. [Release info]
Sep 3rd, 2004; A description of SigPath is now available in Science STKE. SigPath users may now cite
it as Quantitative information management for the biochemical computation of cellular networks. Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Science STKE 248:PL11. (2004). [SigPath]
Mar 2nd, 2004;
A new release of SigPath is now available. [SigPath]
Mar 1st, 2004; SigPath is now released under the GNU General Public
License [download source code]
[older news]
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Aug 25-29, 2008: Stanford University, CA - 7th Annual International Conference on Computational Systems Bioinformatics. Hosted by: Life Sciences Society [More]
Sep 22-26, 2008: Goettingen, Germany - Fall Course on Computational Neuroscience at the Max Planck Institute for Dynamics and Self-Organization. This annual course comprises tutorial lectures and seminar style coverage of selected current topics. Registration deadline: Aug 8, 2008. [More]
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