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HAMSTER: visualizing microarray experiments as a set of minimum spanning treesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - November 20, 2009 Category: Information Technology Authors: Raymond WanLarisa KiselevaHajime HaradaHiroshi MamitsukaPaul Horton Source Type: journals

ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 20, 2009 Category: Information Technology Authors: Kazuharu MisawaNaoyuki Kamatani Source Type: journals

A web server for interactive and zoomable Chaos Game Representation imagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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/,...
Source: Source Code for Biology and Medicine - September 16, 2009 Category: Information Technology Authors: Kazuharu ArakawaKazuki OshitaMasaru Tomita Source Type: journals

Motmot, an open-source toolkit for realtime video acquisition and analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - July 21, 2009 Category: Information Technology Authors: Andrew StrawMichael Dickinson Source Type: journals

Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript formatEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - July 20, 2009 Category: Information Technology Authors: Justina KrawczykAlexander GoesmannRalf NolteMartin WerberBernd Weisshaar Source Type: journals

Permutation – based statistical tests for multiple hypothesesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 21, 2008 Category: Information Technology Authors: Anyela Camargo, Francisco Azuaje, Haiying Wang and Huiru Zheng Source Type: journals

Permutation - based statistical tests for multiple hypothesesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 21, 2008 Category: Information Technology Authors: Anyela Camargo, Francisco Azuaje, Haiying Wang and Huiru Zheng Source Type: journals

Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - September 23, 2008 Category: Information Technology Authors: Joy Scaria, Aswathy Sreedharan and Yung-Fu Chang Source Type: journals

Wndchrm – an open source utility for biological image analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - July 8, 2008 Category: Information Technology Authors: Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston and Ilya G Goldberg Source Type: journals

CRANKITE: A fast polypeptide backbone conformation samplerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 Co...
Source: Source Code for Biology and Medicine - June 24, 2008 Category: Information Technology Authors: Alexei A Podtelezhnikov and David L Wild Source Type: journals

OSPACS: Ultrasound image management systemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - June 20, 2008 Category: Information Technology Authors: Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant and Christopher Jones Source Type: journals

Flow: Statistics, visualization and informatics for flow cytometryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - June 17, 2008 Category: Information Technology Authors: Jacob Frelinger, Thomas B Kepler and Cliburn Chan Source Type: journals

FASH: A web application for nucleotides sequence searchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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.Availabili...
Source: Source Code for Biology and Medicine - May 27, 2008 Category: Information Technology Authors: Isana Veksler-Lublinsky, Danny Barash, Chai Avisar, Einav Troim, Paul Chew and Klara Kedem Source Type: journals

The Multiscale Systems Immunology project: software for cell-based immunological simulationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - April 28, 2008 Category: Information Technology Authors: Faheem Mitha, Timothy A. Lucas, Feng Feng, Thomas B. Kepler and Cliburn Chan Source Type: journals

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - April 18, 2008 Category: Information Technology Authors: Nicolas J Parker and Andrew G Parker Source Type: journals

A Perl toolkit for LIMS developmentEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - March 19, 2008 Category: Information Technology Authors: James A Morris, Simon A Gayther, Ian J Jacobs and Christopher Jones Source Type: journals

Epigrass: a tool to study disease spread in complex networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - February 26, 2008 Category: Information Technology Authors: Flavio C Coelho, Oswaldo G Cruz and Claudia T Codeco Source Type: journals

LSID Tester, a tool for testing Life Science Identifier resolution servicesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - February 18, 2008 Category: Information Technology Authors: Roderic DM Page Source Type: journals

Faunus: an objected oriented framework for molecular simulationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - February 1, 2008 Category: Information Technology Authors: Mikael Lund, Martin Trulsson and Bjorn Persson Source Type: journals

Bioinformatics process management: information flow via a computational journalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - December 3, 2007 Category: Information Technology Authors: Lance Feagan, Justin Rohrer, Alexander Garrett, Heather Amthauer, Ed Komp, David Johnson, Adam Hock, Terry Clark, Gerald Lushington, Gary Minden and Victor Frost Source Type: journals

NFU-Enabled FASTA: moving bioinformatics applications onto wide area networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No abstract available (Source: Source Code for Biology and Medicine)
Source: Source Code for Biology and Medicine - November 26, 2007 Category: Information Technology Authors: Erich J Baker, Guan N Lin, Huadong Liu and Ravi Kosuri Source Type: journals

TreeViewJ: an application for viewing and analyzing phylogenetic treesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 31, 2007 Category: Information Technology Authors: Matthew W Peterson and Marc E Colosimo Source Type: journals

Pspace: a program that assesses protein spaceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The possibility of extending this approach to the space of all proteins is discussed. (Source: Source Code for Biology and Medicine)
Source: Source Code for Biology and Medicine - October 23, 2007 Category: Information Technology Authors: Mihaly Mezei and Ming-Ming Zhou Source Type: journals

OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - September 18, 2007 Category: Information Technology Authors: Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I Grossman, Roberto Romero and Derek E Wildman Source Type: journals

PatentMatrix: an automated tool to survey patents related to large sets of genes or proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - September 6, 2007 Category: Information Technology Authors: Armin Lahm and Emanuele de Rinaldis Source Type: journals

HitKeeper, a generic software package for hit list managementEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - March 28, 2007 Category: Information Technology Authors: Jorg Hau, Michael Muller and Marco Pagni Source Type: journals

Genome display tool: visualizing features in complex data setsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - February 14, 2007 Category: Information Technology Authors: Lalitha Viswanath, Yue Lu and George E Fox Source Type: journals

Genome display tool: visualizing features in complex data setsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - February 14, 2007 Category: Information Technology Authors: Lalitha Viswanath, Yue Lu and George E Fox Source Type: journals

BISON: bio-interface for the semi-global analysis of network patternsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - November 29, 2006 Category: Information Technology Authors: Christopher Besemann, Anne Denton, Nathan J Carr and Birgit M Prüβ Source Type: journals

The Shivplot: a graphical display for trend elucidation and exploratory analysis of microarray dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - November 8, 2006 Category: Information Technology Authors: Owen Z Woody and Robert Nadon Source Type: journals

SLIMarray: Lightweight software for microarray facility managementEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 26, 2006 Category: Information Technology Authors: Bruz Marzolf and Pamela Troisch Source Type: journals

Gbrowse Moby: a Web-based browser for BioMoby ServicesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 24, 2006 Category: Information Technology Authors: Mark Wilkinson Source Type: journals

Welcome to Source Code for Biology and MedicineEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 12, 2006 Category: Information Technology Authors: Leif E Peterson and Emmanuel C Ifeachor Source Type: journals

EST-PAC a web package for EST annotation and protein sequence predictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 the...
Source: Source Code for Biology and Medicine - October 12, 2006 Category: Information Technology Authors: Yvan Strahm, David Powell and Christophe Lefèvre Source Type: journals

A traveling salesman approach for predicting protein functionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: Source Code for Biology and Medicine - October 12, 2006 Category: Information Technology Authors: Olin Johnson and Jing Liu Source Type: journals