Coalescent: an open-source and scalable framework for exact calculations in coalescent theory

Tewari, Susanta; Spouge, John L.
March 2012
BMC Bioinformatics;2012, Vol. 13 Issue 1, p1
Academic Journal
Background: Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but also make them truly accessible. Results: As a first attempt, we built a framework and user application for the domain of exact calculations in coalescent analysis. The framework provides an API with the concepts of model, data, statistic, phylogeny, gene tree and recursion. Infinite-alleles and infinite-sites models are considered. It defines pluggable computations such as counting and listing all the ancestral configurations and genealogies and computing the exact probability of data. It can visualize a gene tree, trace and visualize the internals of the recursion algorithm for further improvement and attach dynamically a number of output processors. The user application defines jobs in a plug-in like manner so that they can be activated, deactivated, installed or uninstalled on demand. Multiple jobs can be run and their inputs edited. Job inputs are persisted across restarts and running jobs can be cancelled where applicable. Conclusions: Coalescent theory plays an increasingly important role in analysing molecular population genetic data. Models involved are mathematically difficult and computationally challenging. An open-source, scalable framework that lets users immediately take advantage of the progress made by others will enable exploration of yet more difficult and realistic models. As models become more complex and mathematically less tractable, the need for an integrated computational approach is obvious. Object oriented designs, though has upfront costs, are practical now and can provide such an integrated approach.


Related Articles


    Neuroph is an open source Java neural network framework, developed at the Faculty of Organisational Sciences, University of Belgrade. It provides a set of Java classes and a GUI tool for working with neural networks. It has a clear structure and,is easy to learn and modify, which makes Neuroph...

  • Supporting Java Components in the SID Simulation System. Ma'ruf, Hasrul; Febiansyah, Hidayat; Kwon, Jin Baek // Journal of Information Processing Systems;Mar2012, Vol. 8 Issue 1, p101 

    Embedded products are becoming richer in features. Simulation tools facilitate low-costs and the efficient development of embedded systems. SID is an open source simulation software that includes a library of components for modeling hardware and software components. SID components were...

  • FullSync gets grip on archiving tasks. Garcia, Andrew // eWeek;3/28/2005, Vol. 22 Issue 13, p55 

    This article reports that FullSync, a free open-source Java-based application can archive or synchronize data to external hard drives, networked Windows shares or even FTP repositories. FullSync works well for archiving data to an external drive or network share, but it is not so good for...

  • WEKA--Experiences with a Java Open-Source Project. Bouckaert, Remco R.; Frank, Eibe; Hall, Mark A.; Holmes, Geoffrey; Pfahringer, Bernhard; Reutemann, Peter; H.Witten, Ian // Journal of Machine Learning Research;9/1/2010, Vol. 11 Issue 9, p2533 

    No abstract available.

  • Bits and snippets. Pavlicek, Russell // InfoWorld;12/2/2002, Vol. 24 Issue 48, p22 

    Discusses several topics related to open-source computing as of December 2002. Use of the Java programming language to write platform-dependent code; Examples of distributions that allow users to try Linux without actually installing the operating system on a personal computer; Web page...

  • JAMSIM: a Microsimulation Modelling Policy Tool. Mannion, Oliver; Lay-Yee, Roy; Wrapson, Wendy; Davis, Peter; Pearson, Janet // Journal of Artificial Societies & Social Simulation;Jan2012, Vol. 15 Issue 1, p16 

    JAMSIM (JAva MicroSIMulation) is an innovative synthesis of open source packages that provides an environment and set of features for the creation of dynamic discrete-time microsimulation models that are to be executed, manipulated and interrogated by non-technical, policy-oriented users....

  • Trapped in a dream. Lewis, Bob // InfoWorld;8/27-9/3/2001, Vol. 23 Issue 35/36, p46 

    Reports the innovation of the open-source license model of Linux desktop. Installation of a Windows program; Use of Netware servers; Application of MS Office XP.

  • Group saves Java for Domino. Fontana, John // Network World;3/4/2002, Vol. 19 Issue 9, p8 

    Reports the creation of open source replacement for computer software Java Server Pages (JSP) by the group of developers in the U.S. Enhancement of the way to plug any JSP engine into Domino; Management of the link between Domino and any JSP engine; Benefits of Java 2 Platform Extended Edition...

  • Strategies for De facto Compatibility: Standardization, Proprietary and Open Source Approaches to Java. Egyedi, Tineke // Knowledge, Technology & Policy;Summer2001, Vol. 14 Issue 2, p113 

    Standardization is a means to achieve software compatibility, and not an end in itself. De facto, compatibility can also be achieved by market dominance—irrespective of the software development process, which may range from a proprietary to an open source approach. This article explores...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics