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  1. Content type: Software review

    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 respo...

    Authors: Faheem Mitha, Timothy A Lucas, Feng Feng, Thomas B Kepler and Cliburn Chan

    Citation: Source Code for Biology and Medicine 2008 3:6

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  2. Content type: Software review

    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 d...

    Authors: James A Morris, Simon A Gayther, Ian J Jacobs and Christopher Jones

    Citation: Source Code for Biology and Medicine 2008 3:4

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  3. Content type: Research

    The construction of complex spatial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequen...

    Authors: Flávio C Coelho, Oswaldo G Cruz and Cláudia T Codeço

    Citation: Source Code for Biology and Medicine 2008 3:3

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  4. Content type: Software review

    We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additi...

    Authors: Mikael Lund, Martin Trulsson and Björn Persson

    Citation: Source Code for Biology and Medicine 2008 3:1

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  5. Content type: Research

    This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involv...

    Authors: Lance Feagan, Justin Rohrer, Alexander Garrett, Heather Amthauer, Ed Komp, David Johnson, Adam Hock, Terry Clark, Gerald Lushington, Gary Minden and Victor Frost

    Citation: Source Code for Biology and Medicine 2007 2:9

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  6. Content type: Research

    We describe a computer program named Pspace designed to a) obtain a reliable basis for the description of three-dimensional structures of a given protein family using homology modeling through selection of an ...

    Authors: Mihaly Mezei and Ming-Ming Zhou

    Citation: Source Code for Biology and Medicine 2007 2:6

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  7. Content type: Brief reports

    Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural select...

    Authors: Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I Grossman, Roberto Romero and Derek E Wildman

    Citation: Source Code for Biology and Medicine 2007 2:5

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  8. Content type: Software review

    Carbohydrates play a critical role in human diseases and their potential utility as biomarkers for pathological conditions is a major driver for characterization of the glycome. However, the additional complex...

    Authors: Alessio Ceroni, Anne Dell and Stuart M Haslam

    Citation: Source Code for Biology and Medicine 2007 2:3

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  9. Content type: Software review

    The automated annotation of biological sequences (protein, DNA) relies on the computation of hits (predicted features) on the sequences using various algorithms. Public databases of biological sequences provid...

    Authors: Jörg Hau, Michael Muller and Marco Pagni

    Citation: Source Code for Biology and Medicine 2007 2:2

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  10. Content type: Research

    The enormity of the information contained in large data sets makes it difficult to develop intuitive understanding. It would be useful to have software that allows visualization of possible correlations betwee...

    Authors: Lalitha Viswanath, Yue Lu and George E Fox

    Citation: Source Code for Biology and Medicine 2007 2:1

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  11. Content type: Research

    The large amount of genomics data that have accumulated over the past decade require extensive data mining. However, the global nature of data mining, which includes pattern mining, poses difficulties for user...

    Authors: Christopher Besemann, Anne Denton, Nathan J Carr and Birgit M Prüβ

    Citation: Source Code for Biology and Medicine 2006 1:8

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  12. Content type: Methodology

    Randomized, prospective trials involving multi-institutional collaboration have become a central part of clinical and translational research. However, data management and coordination of multi-center studies i...

    Authors: Lam Nguyen, Anand Shah, Matthew Harker, Henrique Martins, Mariana McCready, Andreia Menezes, Danny O Jacobs and Ricardo Pietrobon

    Citation: Source Code for Biology and Medicine 2006 1:7

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  13. Content type: Software review

    Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be ...

    Authors: Bruz Marzolf and Pamela Troisch

    Citation: Source Code for Biology and Medicine 2006 1:5

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  14. Content type: Software review

    The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 ...

    Authors: Mark Wilkinson

    Citation: Source Code for Biology and Medicine 2006 1:4

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  15. Content type: Editorial

    This editorial introduces Source Code for Biology and Medicine, a new journal for publication of programming source code used in biology and medicine. Source Code for Biology and Medicine is an open access indepe...

    Authors: Leif E Peterson and Emmanuel C Ifeachor

    Citation: Source Code for Biology and Medicine 2006 1:1

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