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Wndchrm  an open source utility for biological image analysis
Lior Shamir, Nikita Orlov, D Mark Eckley, Tomasz Macura, Josiah Johnston, Ilya G Goldberg
Source Code for Biology and Medicine 2008, 3:13 (8 July 2008)
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Methodology
CRANKITE: A fast polypeptide backbone conformation sampler
Alexei A Podtelezhnikov, David L Wild
Source Code for Biology and Medicine 2008, 3:12 (24 June 2008)
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Software review
OSPACS: Ultrasound image management system
Will Stott, Andy Ryan, Ian J Jacobs, Usha Menon, Conrad Bessant, Christopher Jones
Source Code for Biology and Medicine 2008, 3:11 (20 June 2008)
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Software review
Flow: Statistics, visualization and informatics for flow cytometry
Jacob Frelinger, Thomas B Kepler, Cliburn Chan
Source Code for Biology and Medicine 2008, 3:10 (17 June 2008)
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Brief reports
FASH: A web application for nucleotides sequence search
Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew, Klara Kedem
Source Code for Biology and Medicine 2008, 3:9 (27 May 2008)
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Brief reports
Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules
Pirkko Muhonen, Ranga N Parthasarathy, Anthony J Janckila, Kalman G Büki, H Kalervo Väänänen
Source Code for Biology and Medicine 2008, 3:8 (21 May 2008)
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Research
The MERG Suite: Tools for discovering competencies and associated learning resources
Ravi Teja Bhupatiraju, William R Hersh, Valerie Smothers, Michael Fordis, Peter S Greene
Source Code for Biology and Medicine 2008, 3:7 (14 May 2008)
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Software review
The Multiscale Systems Immunology project: software for cell-based immunological simulation
Faheem Mitha, Timothy A Lucas, Feng Feng, Thomas B Kepler, Cliburn Chan
Source Code for Biology and Medicine 2008, 3:6 (28 April 2008)
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Methodology
Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data
Nicolas J Parker, Andrew G Parker
Source Code for Biology and Medicine 2008, 3:5 (18 April 2008)
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Software review
A Perl toolkit for LIMS development
James A Morris, Simon A Gayther, Ian J Jacobs, Christopher Jones
Source Code for Biology and Medicine 2008, 3:4 (19 March 2008)
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Research
Epigrass: a tool to study disease spread in complex networks
Flávio C Coelho, Oswaldo G Cruz, Cláudia T Codeço
Source Code for Biology and Medicine 2008, 3:3 (26 February 2008)
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Software review
LSID Tester, a tool for testing Life Science Identifier resolution services
Roderic DM Page
Source Code for Biology and Medicine 2008, 3:2 (18 February 2008)
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Software review
Faunus: An object oriented framework for molecular simulation
Mikael Lund, Martin Trulsson, Björn Persson
Source Code for Biology and Medicine 2008, 3:1 (1 February 2008)
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Research
Bioinformatics process management: information flow via a computational journal
Lance Feagan, Justin Rohrer, Alexander Garrett, Heather Amthauer, Ed Komp, David Johnson, Adam Hock, Terry Clark, Gerald Lushington, Gary Minden, Victor Frost
Source Code for Biology and Medicine 2007, 2:9 (3 December 2007)
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Methodology
NFU-Enabled FASTA: moving bioinformatics applications onto wide area networks
Erich J Baker, Guan N Lin, Huadong Liu, Ravi Kosuri
Source Code for Biology and Medicine 2007, 2:8 (26 November 2007)
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Software review
TreeViewJ: An application for viewing and analyzing phylogenetic trees
Matthew W Peterson, Marc E Colosimo
Source Code for Biology and Medicine 2007, 2:7 (31 October 2007)
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Research
Pspace: a program that assesses protein space
Mihaly Mezei, Ming-Ming Zhou
Source Code for Biology and Medicine 2007, 2:6 (23 October 2007)
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Brief reports
OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences
Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I Grossman, Roberto Romero, Derek E Wildman
Source Code for Biology and Medicine 2007, 2:5 (18 September 2007)
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Methodology
PatentMatrix: an automated tool to survey patents related to large sets of genes or proteins
Armin Lahm, Emanuele de Rinaldis
Source Code for Biology and Medicine 2007, 2:4 (6 September 2007)
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Software review
The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures
Alessio Ceroni, Anne Dell, Stuart M Haslam
Source Code for Biology and Medicine 2007, 2:3 (7 August 2007)
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