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MADAM - An open source meta-analysis toolbox for R and
Bioconductor
Karl G Kugler, Laurin AJ Mueller, Armin Graber
Source Code for Biology and Medicine 2010, 5:3 (1 March 2010)
[Abstract] [Provisional PDF] [PubMed] [Related articles]
Software review
Dockres: a computer program that analyzes the output of virtual screening of small molecules
Mihaly Mezei, Ming-Ming Zhou
Source Code for Biology and Medicine 2010, 5:2 (14 January 2010)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Software review
VersaCount: customizable manual tally software for cell counting
Charles C Kim, Joseph L DeRisi
Source Code for Biology and Medicine 2010, 5:1 (13 January 2010)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Methodology
HAMSTER: visualizing microarray experiments as a set of minimum spanning trees
Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka, Paul Horton
Source Code for Biology and Medicine 2009, 4:8 (20 November 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Software review
ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing
Kazuharu Misawa, Naoyuki Kamatani
Source Code for Biology and Medicine 2009, 4:7 (21 October 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Brief reports
A web server for interactive and zoomable Chaos Game Representation images
Kazuharu Arakawa, Kazuki Oshita, Masaru Tomita
Source Code for Biology and Medicine 2009, 4:6 (17 September 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Research
Motmot, an open-source toolkit for realtime video acquisition and analysis
Andrew D Straw, Michael H Dickinson
Source Code for Biology and Medicine 2009, 4:5 (22 July 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Software review
Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format
Justina Krawczyk, Alexander Goesmann, Ralf Nolte, Martin Werber, Bernd Weisshaar
Source Code for Biology and Medicine 2009, 4:4 (21 July 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Methodology
KinImmerse: Macromolecular VR for NMR ensembles
Jeremy N Block, David J Zielinski, Vincent B Chen, Ian W Davis, E Claire Vinson, Rachael Brady, Jane S Richardson, David C Richardson
Source Code for Biology and Medicine 2009, 4:3 (17 February 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Methodology
GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction
Fiona Browne, Haiying Wang, Huiru Zheng, Francisco Azuaje
Source Code for Biology and Medicine 2009, 4:2 (26 January 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles] [Cited on BioMed Central]
Software review
A software pipeline for processing and identification of fungal ITS sequences
R Henrik Nilsson, Gunilla Bok, Martin Ryberg, Erik Kristiansson, Nils Hallenberg
Source Code for Biology and Medicine 2009, 4:1 (15 January 2009)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Research
Purposeful selection of variables in logistic regression
Zoran Bursac, C Heath Gauss, David Keith Williams, David W Hosmer
Source Code for Biology and Medicine 2008, 3:17 (16 December 2008)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Methodology
Boolean network simulations for life scientists
István Albert, Juilee Thakar, Song Li, Ranran Zhang, Réka Albert
Source Code for Biology and Medicine 2008, 3:16 (14 November 2008)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Software review
Permutation  based statistical tests for multiple hypotheses
Anyela Camargo, Francisco Azuaje, Haiying Wang, Huiru Zheng
Source Code for Biology and Medicine 2008, 3:15 (21 October 2008)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Software review
Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis
Joy Scaria, Aswathy Sreedharan, Yung-Fu Chang
Source Code for Biology and Medicine 2008, 3:14 (23 September 2008)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
Research
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)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
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)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
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)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
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)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
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)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]
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