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. Sat, 10 Dec 2011 07:39:37 +0100 http://www.medworm.com/index.php?rid=5316546&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F15 Conclusions: Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5316546 Thu, 13 Oct 2011 04:00:00 +0100 5316546 http://www.medworm.com/index.php?rid=5210326&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F14 With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels). Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5210326 Thu, 08 Sep 2011 04:00:00 +0100 5210326 http://www.medworm.com/index.php?rid=5145167&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F13 Conclusions: We conclude that using Nephele can substantially decrease the processing time required for generating genotype trees of tens to hundreds of organisms at genome scale sequence coverage. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5145167 Wed, 17 Aug 2011 23:00:00 +0100 5145167 http://www.medworm.com/index.php?rid=4962192&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F12 Conclusions: The DBRF-MEGN method provides all of the exact solutions of the most parsimonious SDGs consistent with expression profiles of gene deletion mutants. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4962192 Thu, 23 Jun 2011 23:00:00 +0100 4962192 http://www.medworm.com/index.php?rid=4955320&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F11 Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping.Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlin... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4955320 Mon, 20 Jun 2011 23:00:00 +0100 4955320 http://www.medworm.com/index.php?rid=4855084&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F10 Conclusions: ParaHaplo 3.0 is an invaluable tool for conducting haplotype-based GWASs. The need for faster genotype imputation and haplotype reconstruction using parallel computing will become increasingly important as the data sizes of such projects continue to increase. ParaHaplo executable binaries and program sources are available at http://en.sourceforge.jp/projects/parallelgwas/releases/. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4855084 Mon, 23 May 2011 23:00:00 +0100 4855084 http://www.medworm.com/index.php?rid=4822886&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F9 Conclusions: By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the immediate benefits of improved data visibility, audit and overall data quality. The open-source availability of this software allows others to rapidly implement a LIMS which in itself might sufficiently address user requirements. In situations where this software does not meet require... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4822886 Thu, 12 May 2011 23:00:00 +0100 4822886 http://www.medworm.com/index.php?rid=4764299&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F8 The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Services (KBWS), adds functionalities of local and multiple alignment ... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4764299 Thu, 28 Apr 2011 23:00:00 +0100 4764299 http://www.medworm.com/index.php?rid=4687426&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F7 Conclusions: WordCloud provides a concise visual summary of annotations which is helpful for network analysis and interpretation. WordCloud is freely available at http://baderlab.org/Software/WordCloudPlugin (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4687426 Wed, 06 Apr 2011 23:00:00 +0100 4687426 http://www.medworm.com/index.php?rid=4665782&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F6 Conclusions: Rwui enables statisticians to create web applications for R scripts without the need to learn web programming. Creating a web application provides users access to an R based analysis without the need to learn R. Recent updates to Rwui have increased its applicability in the field of spatial epidemiological analysis. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4665782 Thu, 31 Mar 2011 23:00:00 +0100 4665782 http://www.medworm.com/index.php?rid=4617419&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F5 Conclusions: The command line tool Sig2BioPAX is a resource that enables experimental and computational systems biologists to contribute their identified networks and pathways of molecular interactions for integration and reuse with the rest of the research community. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4617419 Mon, 21 Mar 2011 00:00:00 +0100 4617419 http://www.medworm.com/index.php?rid=4611765&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F4 Conclusions: We have used MOSIX to run a wide variety of software programs in parallel with good results. The limitations and benefits of using MOSIX are discussed and compared to other platforms. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4611765 Fri, 18 Mar 2011 00:00:00 +0100 4611765 http://www.medworm.com/index.php?rid=4356970&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F3 Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-service, and an open source general purpose clustering web-server infrastructure designed to facilitate easy deployment of integrated cluster analysis servers based on clustering and functional annotation algorithms implemented in R. Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results. The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical re... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4356970 Mon, 17 Jan 2011 00:00:00 +0100 4356970 http://www.medworm.com/index.php?rid=4346196&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F2 Conclusions: With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4346196 Thu, 13 Jan 2011 00:00:00 +0100 4346196 http://www.medworm.com/index.php?rid=4310757&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F6%2F1%2F1 Conclusions: A web server with user interface and source codes are available at the website http://www.csbio.unc.edu/epistasis/. The source codes are also available at SourceForge http://sourceforge.net/projects/epistasis/. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4310757 Tue, 04 Jan 2011 00:00:00 +0100 4310757 http://www.medworm.com/index.php?rid=4268186&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F10 Research laboratories studying the genetics of companion animals have no database tools specifically designed to aid in the management of the many kinds of data that are generated, stored and analyzed. We have developed a relational database, "DOG-SPOT," to provide such a tool. Implemented in MS-Access, the database is easy to extend or customize to suit a lab's particular needs. With DOG-SPOT a lab can manage data relating to dogs, breeds, samples, biomaterials, phenotypes, owners, communications, amplicons, sequences, markers, genotypes and personnel. Such an integrated data structure helps ensure high quality data entry and makes it easy to track physical stocks of biomaterials and oligonucleotides. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4268186 Wed, 15 Dec 2010 00:00:00 +0100 4268186 http://www.medworm.com/index.php?rid=3989847&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F9 Conclusions: EHR is being deployed in several countries. The EHR infrastructure will be continuously evolving to embrace advances in the information technology domain. Our software is built on a web framework to allow for an easy evolution with web technology. The testing software is publicly available; it can be used by system implementers to test their implementations. It can also be used by site integrators to verify and test the interoperability of systems, or by developers to understand specifications ambiguities and resolve implementations difficulties. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3989847 Mon, 20 Sep 2010 23:00:00 +0100 3989847 http://www.medworm.com/index.php?rid=3818737&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F8 Background: Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Information about interactions can hint at molecular causes of diseases, and can provide clues for new therapeutic approaches. Several (usually expensive and time consuming) experimental methods can probe protein - protein interactions. Data sets, derived from such experiments make the development of prediction methods feasible, and make the creation of protein-protein interaction network predicting tools possible. Methods: Here we report the development of a simple open source program module (OpenPPI_predictor) that can generate a putative protein- protein interaction network for ... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3818737 Tue, 03 Aug 2010 23:00:00 +0100 3818737 http://www.medworm.com/index.php?rid=3748160&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F7 Gaggle Tool Creator (GTC) is a web application which provides access to public annotation, interaction, orthology, and genomic data for hundreds of organisms, and enables instant analysis of the data using many popular web-based and desktop applications. (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3748160 Mon, 12 Jul 2010 23:00:00 +0100 3748160 http://www.medworm.com/index.php?rid=3681577&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F6 We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/ (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3681577 Sun, 20 Jun 2010 23:00:00 +0100 3681577 http://www.medworm.com/index.php?rid=3627332&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F5 Conclusion: ParaHaplo is a useful tool for haplotype-based GWAS. The executable binaries and program sources of ParaHaplo are available at http://en.sourceforge.jp/projects/parallelgwas/releases/ (Source: Source Code for Biology and Medicine) Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3627332 Thu, 03 Jun 2010 23:00:00 +0100 3627332 http://www.medworm.com/index.php?rid=3405875&cid=s_34095_21_f&fid=34095&url=http%3A%2F%2Fwww.scfbm.org%2Fcontent%2F5%2F1%2F4 Michigan's Department of Community Health (MDCH) is responsible for managing hospitals through the utilization of a Certificate of Need (CON) Commission. Regulation is achieved by limiting the number of beds a hospital can use for inpatient services. MDCH assigns hospitals to service areas and sub areas by use patterns. Hospital beds are then assigned within these Hospital Service Areas and Facility Sub Areas. The determination of the number of hospital beds a facility subarea is authorized to hold, called bed need, is defined in the Michigan Hospital Standards and published by the CON Commission and MDCH. These standards vaguely define a methodology for calculating hospital bed need for a projection year, five years ahead of the base year (defined as the most recent year for which patient... Source Code for Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3405875 Thu, 25 Mar 2010 00:00:00 +0100 3405875 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