MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Source Code for Biology and Medicine' source. Sun, 21 Mar 2010 15:18:54 +0100 http://www.medworm.com/index.php?rid=3317250&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F3 Conclusions: The use of MADAM enables a user to focus on one package, in turn enabling them to work with the same data types across a set of methods. By making use of the snow package, MADAM can be made compatible with an existing parallel computing infrastructure. MADAM is open source and freely available within CRAN (http://cran.r-project.org). (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3317250 Mon, 01 Mar 2010 00:00:00 +0100 3317250 http://www.medworm.com/index.php?rid=3173741&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F2 Conclusions: Analysis of virtual screening was facilitated and enhanced by Dockres in both the authors' laboratories as well as laboratories elsewhere. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3173741 Thu, 14 Jan 2010 00:00:00 +0100 3173741 http://www.medworm.com/index.php?rid=3169223&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F1 Conclusions: Our software provides an inexpensive, flexible, and productivity-enhancing alternative to manual hand tally counters. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3169223 Wed, 13 Jan 2010 00:00:00 +0100 3169223 http://www.medworm.com/index.php?rid=3010253&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F4%2F1%2F8 Conclusions: Researchers may find it helpful to include HAMSTER in their microarray analysis workflow as it can offer insights that differ from hierarchical clustering. We believe that HAMSTER would be useful for certain types of gradient data sets (e.g time-series data) and data that indicate relationships between cells/tissues. Both the source and the web server variant of HAMSTER are available from http://hamster.cbrc.jp/. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3010253 Fri, 20 Nov 2009 00:00:00 +0100 3010253 http://www.medworm.com/index.php?rid=2914090&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F4%2F1%2F7 Conclusion: ParaHaplo is a useful tool for haplotype-based GWAS. The executable binaries and program sources of ParaHaplo are available at http://sourceforge.jp/projects/parallelgwas/?_sl=1. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2914090 Tue, 20 Oct 2009 23:00:00 +0100 2914090 http://www.medworm.com/index.php?rid=2802252&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F4%2F1%2F6 Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study of characteristic sequence motifs. However, in order to fully utilize the scale-independent properties of CGR, it should be accessible through scale-independent user interface instead of static images. Here we describe a web server and Perl library for generating zoomable CGR images utilizing Google Maps API, which is also easily searchable for specific motifs. The web server is freely accessible at http://www.g-language.org/wiki/cgr/, and the Perl library as well as the source code is distributed with the G-language Genome Analysis Environment under GNU General Public License. (Source: Source Code for... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2802252 Wed, 16 Sep 2009 23:00:00 +0100 2802252 http://www.medworm.com/index.php?rid=2628282&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F4%2F1%2F5 Conclusions: Motmot enables realtime image processing and display using the Python computer language. In addition to the provided complete applications, the architecture allows the user to write relatively simple plugins, which can accomplish a variety of computer vision tasks and be integrated within larger software systems. The software is available at http://code.astraw.com/projects/motmot (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2628282 Tue, 21 Jul 2009 23:00:00 +0100 2628282 http://www.medworm.com/index.php?rid=2623550&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F4%2F1%2F4 Conclusions: The software toolkits provide useful applications to convert sequencing and fragment analysis files from a proprietary into a more common, human-readable format. Trace2PS and FSA2PS are useful and capable in data management workflow systems like SAMS, or laboratory information systems that are used for displaying trace and fragment analysis results via web-based tools over an intranet or internet connection to users that can view their results directly on the screen. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2623550 Mon, 20 Jul 2009 23:00:00 +0100 2623550 http://www.medworm.com/index.php?rid=2073363&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F15 Conclusion: The analytical options offered by the software can be applied to support a significant spectrum of hypothesis testing tasks in functional genomics, using both numerical and categorical data. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2073363 Tue, 21 Oct 2008 04:00:00 +0100 2073363 http://www.medworm.com/index.php?rid=1900871&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F15 Conclusions: The analytical options offered by the software can be applied to support a significant spectrum of hypothesis testing tasks in functional genomics, using both numerical and categorical data. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1900871 Tue, 21 Oct 2008 04:00:00 +0100 1900871 http://www.medworm.com/index.php?rid=1824427&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F14 Conclusions: MDAW is a new resource that is customised for the data analysis requirements for microbial diagnostic array. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1824427 Tue, 23 Sep 2008 04:00:00 +0100 1824427 http://www.medworm.com/index.php?rid=1645469&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F13 Conclusion: We suggest that wndchrm can be effectively used for a wide range of biological image analysis tasks. Using wndchrm can allow scientists to perform automated biological image analysis while avoiding the costly challenge of implementing computer vision and pattern recognition algorithms. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1645469 Tue, 08 Jul 2008 04:00:00 +0100 1645469 http://www.medworm.com/index.php?rid=1542123&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F12 Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1542123 Tue, 24 Jun 2008 04:00:00 +0100 1542123 http://www.medworm.com/index.php?rid=1530627&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F11 Conclusion: This system provides error-free automation of ultrasound image archiving and management, suitable for use in a clinical trial. An open-source project has been established to promote continued development of the system. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1530627 Fri, 20 Jun 2008 04:00:00 +0100 1530627 http://www.medworm.com/index.php?rid=1525530&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F10 Flow is an open source software application for clinical and experimental researchers to perform exploratory data analysis, clustering and classification of flow cytometric data. Flow is an extensible system that offers the ease of use commonly found in commercial flow cytometry software packages and the statistical power of academic packages like the R BioConductor project. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1525530 Tue, 17 Jun 2008 04:00:00 +0100 1525530 http://www.medworm.com/index.php?rid=1472143&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F9 FASH (Fourier Alignment Sequence Heuristics) is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a query sequence and a long text-sequence (e.g, the human genome), FASH detects subsequences within the text that are remotely-similar to the query. FASH offers an alternative approach to Blast/Fasta for querying long RNA/DNA sequences. FASH differs from these other approaches in that it does not depend on the existence of contiguous seed-sequences in its initial detection phase. The FASH web server is user friendly and very easy to operate.AvailabilityFASH can be accessed at https://fash.bgu.ac.il:8443/fash/default.jsp (secured website) (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1472143 Tue, 27 May 2008 04:00:00 +0100 1472143 http://www.medworm.com/index.php?rid=1403954&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F6 Conclusion: MSI addresses the need for a flexible and high-performing agent based model of the immune system. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1403954 Mon, 28 Apr 2008 04:00:00 +0100 1403954 http://www.medworm.com/index.php?rid=1382205&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F5 Conclusions: The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1382205 Fri, 18 Apr 2008 04:00:00 +0100 1382205 http://www.medworm.com/index.php?rid=1313947&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F4 Conclusions: This important addition to the Perl developer's library will make the development of in house LIMS applications quicker and easier encouraging laboratories to create bespoke LIMS applications to meet their specific data management requirements. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1313947 Wed, 19 Mar 2008 04:00:00 +0100 1313947 http://www.medworm.com/index.php?rid=1257831&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F3 Conclusions: Epigrass is shown to facilitate greatly the construction, simulation and analysis of complex network models. The output of model results in standard GIS file formats facilitate the post-processing and analysis of results by means of sophisticated GIS software. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1257831 Tue, 26 Feb 2008 05:00:00 +0100 1257831 http://www.medworm.com/index.php?rid=1239152&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F2 Conclusions: The software provides a tool for testing a LSID resolution service. Source code is available from http://code.google.com/p/lsid-php/, and an instance of the application can be viewed at http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1239152 Mon, 18 Feb 2008 05:00:00 +0100 1239152 http://www.medworm.com/index.php?rid=1194662&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F3%2F1%2F1 Conclusions: C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modelling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1194662 Fri, 01 Feb 2008 05:00:00 +0100 1194662 http://www.medworm.com/index.php?rid=1067049&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F9 This report discusses the features determined critical by our system and other projects along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1067049 Mon, 03 Dec 2007 05:00:00 +0100 1067049 http://www.medworm.com/index.php?rid=1051092&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F8 No abstract available (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=1051092 Mon, 26 Nov 2007 05:00:00 +0100 1051092 http://www.medworm.com/index.php?rid=994707&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F7 Conclusions: TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=994707 Wed, 31 Oct 2007 04:00:00 +0100 994707 http://www.medworm.com/index.php?rid=972328&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F6 Conclusions: The possibility of extending this approach to the space of all proteins is discussed. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=972328 Tue, 23 Oct 2007 04:00:00 +0100 972328 http://www.medworm.com/index.php?rid=882188&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F5 Conclusions: The OCPAT program facilitates large-scale evolutionary and phylogenetic analyses of entire biological processes, pathways, and diseases. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=882188 Tue, 18 Sep 2007 04:00:00 +0100 882188 http://www.medworm.com/index.php?rid=847116&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F4 Conclusions: PatentMatrix allows a rapid survey of patents associated with genes or proteins in a particular area of interest as defined by keywords. It can be efficiently used to evaluate the IP-related novelty of scientific findings and to rank genes or proteins according to their IP position. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=847116 Thu, 06 Sep 2007 04:00:00 +0100 847116 http://www.medworm.com/index.php?rid=506463&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F2 Conclusions: The software provides a generic and modular framework to handle the redundancy and incremental updates of biological databases, and an original query language. It is published under the terms and conditions of version 2 of the GNU Public License and available at http://hitkeeper.sourceforge.net. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=506463 Wed, 28 Mar 2007 04:00:00 +0100 506463 http://www.medworm.com/index.php?rid=415084&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F1 Conclusions: The GDT software provides the user with a powerful tool that allows development of an intuitive understanding of the relative distribution of features in a large data set. As additional features are added to the data set, the number of possible correlations that can be visualized grows rapidly. Although described here for use in bacterial genomics, the principle is general and similar software might be useful in other contexts such as patient studies. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=415084 Wed, 14 Feb 2007 07:00:00 +0100 415084 http://www.medworm.com/index.php?rid=440767&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F2%2F1%2F1 Conclusion: The GDT software provides the user with a powerful tool that allows development of an intuitive understanding of the relative distribution of features in a large data set. As additional features are added to the data set, the number of possible correlations that can be visualized grows rapidly. Although described here for use in bacterial genomics, the principle is general and similar software might be useful in other contexts such as patient studies. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=440767 Wed, 14 Feb 2007 05:00:00 +0100 440767 http://www.medworm.com/index.php?rid=362882&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F8 Conclusion: In summary, we have a tool that can be used for a wide variety of applications in biology, medicine, or agriculture. The pattern mining engine is global in the way that patterns are determined across the entire network. The tool still permits a localized analysis for users who want to analyze a subportion of the total network. We have named the tool BISON (Bio-Interface for the Semi-global analysis Of Network patterns). (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362882 Wed, 29 Nov 2006 07:00:00 +0100 362882 http://www.medworm.com/index.php?rid=362883&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F6 Conclusion: The utility of the new display is illustrated with microarray data sets. The proposed graph, retaining all the information of its precursors, conserves space and minimizes redundancy, but also highlights features of the data that would be difficult to appreciate from the individual display components. We recommend the use of the shivplot both for exploratory data analysis and for the communication of experimental data in publications. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362883 Wed, 08 Nov 2006 07:00:00 +0100 362883 http://www.medworm.com/index.php?rid=362884&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F5 Conclusion: SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362884 Thu, 26 Oct 2006 06:00:00 +0100 362884 http://www.medworm.com/index.php?rid=362885&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F4 Conclusion: Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362885 Tue, 24 Oct 2006 06:00:00 +0100 362885 http://www.medworm.com/index.php?rid=362888&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F1 We describe the journal aims, scope, benefits of open access, article processing charges, competing interests, content and article format, peer review policy and publication, and introduce the Editorial Board. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362888 Thu, 12 Oct 2006 06:00:00 +0100 362888 http://www.medworm.com/index.php?rid=362887&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F2 With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST) from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet.In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST) annotation. EST-PAC provides a solution for the administrat... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362887 Thu, 12 Oct 2006 06:00:00 +0100 362887 http://www.medworm.com/index.php?rid=362886&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F1%2F1%2F3 Conclusion: Our method is a promising one to be used as a general tool to predict functions of uncharacterized proteins and a successful sample of using computer science knowledge and algorithms to study biological problems. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=362886 Thu, 12 Oct 2006 06:00:00 +0100 362886