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Recent Pathway Tools Performance Enhancements (Versions 13.0 to 14.5)

Recent Pathway Tools Performance Enhancements (Versions 13.0 to 14.5). Mario Latendresse. October 2010. Bioinformatics Research Group SRI International latendre@ai.sri.com. Web Server Improvements (version 13.0 through 14.5). Lossless Compression (version 13.0)

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Recent Pathway Tools Performance Enhancements (Versions 13.0 to 14.5)

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  1. Recent Pathway Tools Performance Enhancements(Versions 13.0 to 14.5) Mario Latendresse October 2010 Bioinformatics Research Group SRI International latendre@ai.sri.com

  2. Web Server Improvements (version 13.0 through 14.5) • Lossless Compression (version 13.0) • Compression of ‘.shtml’, ‘.html’, ‘.js’ files • “Minification” of JavaScript files (version 13.0) • JavaScript files (‘.js’) are statically minified • Keep-Alive (version 14.0) • An HTTP 1.1 mechanism to keep connected to the client to receive more than one HTTP requests. • File caching via the ‘expire’ HTTP parameter (version 14.5) • Web designers can specify their own expire duration (e.g., 2 days, 1 week, 3 months) when starting a Web server (parameter WWW-Browser-Static-Page-Expiry-Seconds in init-ptools.dat file) • Typically, Web requests are twice as fast when using all these improvements

  3. BioVelo Speed Improvements in Pathway Tools (version 14.5) • BioVelo is used in most searching commands on the Web • The searching interfaces for genes/proteins/RNAs, compounds, reactions, pathways (under the Search menu in the top menu bar) • The Advanced Searches (SAQP, FFAQP) • Not the quick search • Much faster in searching and generating large outputs • This improvement was achieved by removing a basic constraint in Ocelot when manipulating multiple databases • Version 14.5 is often 2 to 10 times faster compared to version 14.0 (speedup depends on the size of the generated output)

  4. Cellular Overview (14.5) • Much faster when visiting the different zoom levels (it takes about 4 seconds compared to 15 to 30 seconds in version 14.0) • Pre-generating the Cellular Overviews is key for good speedup (very soon an automatic way to do this for users) • Parsing the expression data is much faster (2 to 10 times faster) • More improvements are expected with new JavaScript engines for most popular browsers • Latest Chrome and Safari browsers are best now; Firefox is trailing behind; IE version 9 will be much better for JavaScript speed

  5. Comparative Analysis Improvements • Improvements for the Desktop as well as the Web versions • For the desktop version using the genome comparative tool, we measured a speedup of about 4 (based on a comparison between ecocyc trpA and 48 other databases) • Speed up came from improving the speed when switch between organisms

  6. Pathologic Speed Improvements • A new option “-fast” when starting Pathway Tools. • The creation of the PGDB is much faster due to several low-level Ocelot improvements • Quite noticeable on large genome or doing meta-genomics • It is about 5 times faster for large input files to Pathologic

  7. Pathologic Predictive Improvements • Taxonomic range can be used to better predict pathways • Some name matcher improvements (the full set of possible suffixes and prefixes is applied) • More key reactions specified in MetaCyc

  8. Recent Pathway Tools Performance Enhancements Questions?

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