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	1. 881 Accesses	Research Yabi: An online research environment for Grid, High Performance and Cloud computing Adam A Hunter, Andrew B Macgregor, Tamas O Szabo, Crispin A Wellington, Matthew I Bellgard Source Code for Biology and Medicine 2012, 7:1 (15 February 2012) Abstract \| Provisional PDF \| Editor’s summary Yabi, a new online research environment, provides transparent access to existing High Performance Computing (HPC) resources and complements current workflow environments by providing a rich and intuitive webbased user interface.
	2. 416 Accesses	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
	3. 326 Accesses	Software review SNIT: SNP identification for strain typing Ravi Vijaya Satya, Nela Zavaljevski, Jaques Reifman Source Code for Biology and Medicine 2011, 6:14 (8 September 2011) Abstract \| Full text \| PDF \| PubMed
	4. 324 Accesses	Software review LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine Timothy G Bath, Selcuk Bozdag, Vackar Afzal, Daniel Crowther Source Code for Biology and Medicine 2011, 6:9 (13 May 2011) Abstract \| Full text \| PDF \| PubMed
	5. 291 Accesses	Software review Genes2WordCloud: a quick way to identify biological themes from gene lists and free text Caroline Baroukh, Sherry L Jenkins, Ruth Dannenfelser, Avi Ma'ayan Source Code for Biology and Medicine 2011, 6:15 (13 October 2011) Abstract \| Full text \| PDF \| PubMed
	6. 282 Accesses	Software review SAMMate: a GUI tool for processing short read alignments in SAM/BAM format Guorong Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik Flemington, Dongxiao Zhu Source Code for Biology and Medicine 2011, 6:2 (13 January 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment
	7. 262 Accesses	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) Abstract \| Full text \| PDF \| PubMed
	8. 256 Accesses	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
	9. 253 Accesses	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
	10. 188 Accesses	Software review A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks Koji Kyoda, Kotaro Baba, Hiroaki Kitano, Shuichi Onami Source Code for Biology and Medicine 2011, 6:12 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
	11. 187 Accesses	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) Abstract \| Full text \| PDF \| PubMed
	12. 183 Accesses	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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	13. 177 Accesses	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
	14. 169 Accesses	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
	15. 154 Accesses	Methodology A methodology for projecting hospital bed need: a Michigan case study Shaun A Langley, Steven P Fuller, Joseph P Messina, Ashton M Shortridge, Sue C Grady Source Code for Biology and Medicine 2010, 5:4 (25 March 2010) Abstract \| Full text \| PDF \| PubMed
	16. 150 Accesses	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
	17. 147 Accesses	Software review Nephele: genotyping via complete composition vectors and MapReduce Marc E Colosimo, Matthew W Peterson, Scott Mardis, Lynette Hirschman Source Code for Biology and Medicine 2011, 6:13 (18 August 2011) Abstract \| Full text \| PDF \| PubMed
	18. 141 Accesses	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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19. 141 Accesses	Software review Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information Chandra Sekhar Pedamallu, Janos Posfai Source Code for Biology and Medicine 2010, 5:8 (4 August 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	20. 136 Accesses	Brief reports EntrezAJAX: direct web browser access to the Entrez Programming Utilities Nicholas J Loman, Mark J Pallen Source Code for Biology and Medicine 2010, 5:6 (21 June 2010) Abstract \| Full text \| PDF \| PubMed
	21. 134 Accesses	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
	22. 128 Accesses	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) Abstract \| Full text \| PDF \| PubMed
	23. 122 Accesses	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
	24. 116 Accesses	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
	25. 113 Accesses	Software review CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo, Alessio Mengoni Source Code for Biology and Medicine 2011, 6:11 (21 June 2011) Abstract \| Full text \| PDF \| PubMed