http://www.almob.org/comments The latest comments on all articles published by Algorithms for Molecular Biology 2013-03-14T16:57:25Z http://www.almob.org/content/6/1/25/comments#1429696 <p>By author's mistake the affiliation of Mikhail A.Roytberg was not shown properly. The correct affiliation is as follows: <br/>Mikhail A. Roytberg 2,3 <br/>2) Institute of Mathematical Problems in Biology, RAS, Pushchino, 142290, Russia <br/>3) National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia</p> Mikhail Roytberg 2013-03-14T16:57:25Z http://www.almob.org/content/6/1/25 Polyanovsky et al. Algorithms for Molecular Biology 6 25 Thu Oct 27 00:00:00 BST 2011 http://www.almob.org/content/5/1/9/comments#393655 <p>The linear search implementation uses several layers of overhead on top of the CDK Tanimoto calculation code, which in turn creates an intermediate bitset object. I expect that quite a bit of the compute time is spent just in function call and object management overhead. <br/> <br/>The linear search data structure uses a lot of memory. Based on figure 9, the implementation uses about 330 bytes for a 1024-bit fingerprint, which only needs 128 bytes. Adding perhaps 10 bytes for the identifier and a few bytes for overhead leads to a memory requirement of about 150 bytes, which is less than half used by the implementation. <br/> <br/>I have implemented the linear search code using Python for file I/O and memory management and C for search speed. By using a single byte array, with the fingerprints stored as byte-based bitstrings identified by offset into the array, the memory requirements are little higher than the raw data. My hardware is about the same as used in the paper, and my performance was about 8x to 10x faster. <br/> <br/>A similar implementation is possible in Java. I don't know if Java can come close to C performance, but I would expect it to be within a factor of 2, which is still 4x to 5x faster than the authors reported. <br/> <br/>The same optimization apply to the Baldi implementation, so in figure 7 the performance line for Baldi line should be about the same slope as the multibit tree. <br/> <br/>The multibit code may have its own set of speedups, but I have not analyzed that. I write to point out that the graph for the linear searches reflect a rather high implementation overhead. <br/></p> Andrew Dalke 2010-05-25T11:01:02Z http://www.almob.org/content/5/1/9 Kristensen et al. Algorithms for Molecular Biology 5 9 Mon Jan 04 13:51:34 GMT 2010 http://www.almob.org/content/4/1/2/comments#410675 <p>CHSMiner has been added to Softpedia's database of software programs for Mac OS on May, 2010. It is featured with a description text, screenshots, download links and technical details on this page: <br/>http://mac.softpedia.com/get/Math-Scientific/CHSMiner.shtml <br/> <br/>CHSMiner has been tested in the Softpedia labs using several industry-leading security solutions and found to be completely clean of adware/spyware components. More information about the product's certification is available on this page: <br/>http://mac.softpedia.com/progClean/CHSMiner-Clean-77916.html <br/></p> Zhen Wang 2010-05-25T11:00:02Z http://www.almob.org/content/4/1/2 Wang et al. Algorithms for Molecular Biology 4 2 Thu Jan 15 12:55:58 GMT 2009 http://www.almob.org/content/2/1/1/comments#335609 <p>Carmack <i>et al.</i> (<i>Algorithms for Molecular Biology</i> 2007, doi:10.1186/1748-7188-2-1) includes a web link to the <a href='http://bayesweb.wadsworth.org/cgi-bin/phylo_web.pl'>Phyloscan Version 1</a> web server, which analyzes genomic sequence data from <i>E. coli</i> and related proteobacteria. There is now a <a href='http://bayesweb.wadsworth.org/cgi-bin/phyloscanV2.pl'>Phyloscan Version 2</a> web server that permits analysis of user-supplied sequence data. The new web server can be found at <a href='http://bayesweb.wadsworth.org/cgi-bin/phyloscanV2.pl'>http://bayesweb.wadsworth.org/cgi-bin/phyloscanV2.pl</a>.</p> Lee Newberg 2009-03-24T17:48:32Z http://www.almob.org/content/2/1/1 Carmack et al. Algorithms for Molecular Biology 2 1 Tue Jan 23 14:49:07 GMT 2007 http://www.almob.org/content/2/1/12/comments#310620 <p>The datasets used for benchmarking in this paper are now available for download at:</p><p>http://www.cbs.dtu.dk/services/InterMap3D/Coevolution_Benchmarking_datasets.zip</p><p>We hope they can be of use to other researchers.</p> Rodrigo Gouveia-Oliveira 2009-02-10T01:12:38Z http://www.almob.org/content/2/1/12 Gouveia-Oliveira et al. Algorithms for Molecular Biology 2 12 Wed Oct 03 14:15:15 BST 2007 http://www.almob.org/content/1/1/1/comments#237521 <p>I was interested to read about the new journal, Algorithms for Molecular Biology. I was curious to know whether the journal would accept algorithms related to systems biology?</p> Herbert Sauro 2006-07-05T17:00:08Z http://www.almob.org/content/1/1/1 Morgenstern et al. Algorithms for Molecular Biology 1 1 Tue Feb 28 00:00:00 GMT 2006