This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ http://www.scfbm.org The latest articles from Source Code for Biology and Medicine (ISSN 1751-0473) published by BioMed Central Background: Biological imaging is an emerging field, covering a wide range of applications in biological and clinical research. However, while machinery for automated experimenting and data acquisition has been developing rapidly in the past years, automated image analysis often introduces a bottleneck in high content screening. Methods: Wndchrm is an open source utility for biological image analysis. The software works by first extracting image content descriptors from the raw image, image transforms, and compound image transforms. Then, the most informative features are selected, and the feature vector of each image is used for classification and similarity measurement. Results: Wndchrm has been tested using several publicly available biological datasets, and provided results which are favorably comparable to the performance of task-specific algorithms developed for these datasets. The simple user interface allows researchers who are not knowledgeable in computer vision methods and have no background in computer programming to apply image analysis to their data. 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. http://www.scfbm.org/content/3/1/13 Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston and Ilya G Goldberg Source Code for Biology and Medicine 2008, 3:13 2008-07-08 doi:10.1186/1751-0473-3-13 Source Code for Biology and Medicine 1751-0473 3 13 2008-07-08 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. http://www.scfbm.org/content/3/1/12 Alexei A Podtelezhnikov and David L Wild Source Code for Biology and Medicine 2008, 3:12 2008-06-24 doi:10.1186/1751-0473-3-12 Source Code for Biology and Medicine 1751-0473 3 12 2008-06-24 Background: Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collections of anonymized ultrasound images gathered during a clinical screening trial. Results: We have developed a system enabling the accurate archiving and management of ultrasound images gathered during a clinical screening trial. It is based upon a Windows application utilizing an open-source DICOM image viewer and a relational database. The system automates the bulk import of DICOM files from removable media by cross-validating the patient information against an external database, anonymizing the data as well as the image, and then storing the contents of the file as a field in a database record. These image records may then be retrieved from the database and presented in a tree-view control so that the user can select particular images for display in a DICOM viewer or export them to external media. 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. http://www.scfbm.org/content/3/1/11 Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant and Christopher Jones Source Code for Biology and Medicine 2008, 3:11 2008-06-20 doi:10.1186/1751-0473-3-11 Source Code for Biology and Medicine 1751-0473 3 11 2008-06-20 Flow is an open source software application for clinical and experimental researchers to perform exploratory data analysis, clustering and annotation 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. http://www.scfbm.org/content/3/1/10 Jacob Frelinger, Thomas B Kepler and Cliburn Chan Source Code for Biology and Medicine 2008, 3:10 2008-06-17 doi:10.1186/1751-0473-3-10 Source Code for Biology and Medicine 1751-0473 3 10 2008-06-17 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 athttps://fash.bgu.ac.il:8443/fash/default.jsp (secured website) http://www.scfbm.org/content/3/1/9 Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew and Klara Kedem Source Code for Biology and Medicine 2008, 3:9 2008-05-27 doi:10.1186/1751-0473-3-9 Source Code for Biology and Medicine 1751-0473 3 9 2008-05-27 ObjectiveHere we report the improved results of a new siRNA design program and analysis tool called siRNA_profile that reveals an additional criterion for bioinformatic search of highly functional siRNA sequences. Methods: We retrospectively analysed over 2400 siRNA sequences from 34 genes and with known efficacies to categorize factors that differentiate highly, moderately and non-functional siRNA sequences in more detail. We tested the biological relevance of siRNA_profile in CHO cells stably expressing human TRACP. Results: The highly functional siRNA molecules exhibited lower overall stabilities than non-functional siRNAs after taking into consideration all the nucleotides from 5'-terminus to the 3'-terminus along the siRNA molecule, in addition to the 5'-section of the antisense strand and the region between 9–14 nucleotides as previously has been acknowledged. Comparison of the siRNA_profile program to five other programs resulted in a wide range of selected siRNA sequences with diverse gene silencing capacities, even when the target was only 197 nucleotides long. Six siRNA design programs selected 24 different siRNA sequences, and only 6 of them were selected by two or more programs. The other 18 sequences were individually selected by these six programs. Conclusion: Low general stability of dsRNA plays a significant role in the RNAi pathway and is a recommended criterion to consider, in addition to 5'-instability, internal instability, nucleotide preferences and target mRNA position, when designing highly efficient siRNAs. http://www.scfbm.org/content/3/1/8 Pirkko Muhonen, Ranga N Parthasarathy, Anthony J Janckila, Kalman G Büki and H Kalervo Väänänen Source Code for Biology and Medicine 2008, 3:8 2008-05-21 doi:10.1186/1751-0473-3-8 Source Code for Biology and Medicine 1751-0473 3 8 2008-05-21 Background: As the demands for competency-based education grow, the need for standards-based tools to allow for publishing and discovery of competency-based learning content is more pressing. This project focused on developing federated discovery services for competency-based medical e-learning content. Methods: We built a tool suite for authoring and discovery of medical e-learning metadata. The end-user usability of the tool suite was evaluated through a web-based survey. Results: The suite, implemented as an open-source system, was evaluated to identify areas for improvement. Conclusion: The MERG suite is a starting point for organizations implementing competency-based e-learning resources. http://www.scfbm.org/content/3/1/7 Ravi Teja Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis and Peter S Greene Source Code for Biology and Medicine 2008, 3:7 2008-05-14 doi:10.1186/1751-0473-3-7 Source Code for Biology and Medicine 1751-0473 3 7 2008-05-14 Background: Computer simulations are of increasing importance in modeling biological phenomena. Their purpose is to predict behavior and guide future experiments. The aim of this project is to model the early immune response to vaccination by an agent based immune response simulation that incorporates realistic biophysics and intracellular dynamics, and which is sufficiently flexible to accurately model the multi-scale nature and complexity of the immune system, while maintaining the high performance critical to scientific computing. Results: The Multiscale Systems Immunology (MSI) simulation framework is an object-oriented, modular simulation framework written in C++ and Python. The software implements a modular design that allows for flexible configuration of components and initialization of parameters, thus allowing simulations to be run that model processes occurring over different temporal and spatial scales. Conclusion: MSI addresses the need for a flexible and high-performing agent based model of the immune system. http://www.scfbm.org/content/3/1/6 Faheem Mitha, Timothy A Lucas, Feng Feng, Thomas B Kepler and Cliburn Chan Source Code for Biology and Medicine 2008, 3:6 2008-04-28 doi:10.1186/1751-0473-3-6 Source Code for Biology and Medicine 1751-0473 3 6 2008-04-28 Background: The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. Methods: A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Results: Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension. Conclusion: 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. http://www.scfbm.org/content/3/1/5 Nicolas J Parker and Andrew G Parker Source Code for Biology and Medicine 2008, 3:5 2008-04-18 doi:10.1186/1751-0473-3-5 Source Code for Biology and Medicine 1751-0473 3 5 2008-04-18 Background: High throughput laboratory techniques generate huge quantities of scientific data. Laboratory Information Management Systems (LIMS) are a necessary requirement, dealing with sample tracking, data storage and data reporting. Commercial LIMS solutions are available, but these can be both costly and overly complex for the task. The development of bespoke LIMS solutions offers a number of advantages, including the flexibility to fulfil all a laboratory's requirements at a fraction of the price of a commercial system. The programming language Perl is a perfect development solution for LIMS applications because of Perl's powerful but simple to use database and web interaction, it is also well known for enabling rapid application development and deployment, and boasts a very active and helpful developer community. The development of an in house LIMS from scratch however can take considerable time and resources, so programming tools that enable the rapid development of LIMS applications are essential but there are currently no LIMS development tools for Perl. Results: We have developed ArrayPipeline, a Perl toolkit providing object oriented methods that facilitate the rapid development of bespoke LIMS applications. The toolkit includes Perl objects that encapsulate key components of a LIMS, providing methods for creating interactive web pages, interacting with databases, error tracking and reporting, and user and session management. The MT_Plate object provides methods for manipulation and management of microtitre plates, while a given LIMS can be encapsulated by extension of the core modules, providing system specific methods for database interaction and web page management. Conclusion: 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. http://www.scfbm.org/content/3/1/4 James A Morris, Simon A Gayther, Ian J Jacobs and Christopher Jones Source Code for Biology and Medicine 2008, 3:4 2008-03-19 doi:10.1186/1751-0473-3-4 Source Code for Biology and Medicine 1751-0473 3 4 2008-03-19