Skip to main content

Articles

Page 4 of 4

  1. 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...

    Authors: Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston and Ilya G Goldberg
    Citation: Source Code for Biology and Medicine 2008 3:13
  2. 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 ...

    Authors: Alexei A Podtelezhnikov and David L Wild
    Citation: Source Code for Biology and Medicine 2008 3:12
  3. 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 ...

    Authors: Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant and Christopher Jones
    Citation: Source Code for Biology and Medicine 2008 3:11
  4. 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 off...

    Authors: Jacob Frelinger, Thomas B Kepler and Cliburn Chan
    Citation: Source Code for Biology and Medicine 2008 3:10
  5. 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-s...

    Authors: Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew and Klara Kedem
    Citation: Source Code for Biology and Medicine 2008 3:9
  6. Here 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.

    Authors: Pirkko Muhonen, Ranga N Parthasarathy, Anthony J Janckila, Kalman G Büki and H Kalervo Väänänen
    Citation: Source Code for Biology and Medicine 2008 3:8
  7. 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 devel...

    Authors: Ravi Teja Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis and Peter S Greene
    Citation: Source Code for Biology and Medicine 2008 3:7
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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