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	1. 1801 Accesses	Brief reports Git can facilitate greater reproducibility and increased transparency in science Karthik Ram Source Code for Biology and Medicine 2013, 8:7 (28 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	2. 831 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 \| Cited on BioMed Central
	3. 672 Accesses	Commentary How Not to Be a Bioinformatician Manuel Corpas, Segun Fatumo, Reinhard Schneider Source Code for Biology and Medicine 2012, 7:3 (28 May 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment
	4. 614 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
	5. 400 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
	6. 405 Accesses	Methodology The non-negative matrix factorization toolbox for biological data mining Yifeng Li, Alioune Ngom Source Code for Biology and Medicine 2013, 8:10 (16 April 2013) Abstract \| Provisional PDF \| PubMed
	7. 386 Accesses	Research BioPatRec: A modular research platform for the control of artificial limbs based on pattern recognition algorithms Max Ortiz-Catalan, Rickard Brånemark, Bo Håkansson Source Code for Biology and Medicine 2013, 8:11 (18 April 2013) Abstract \| Provisional PDF \| PubMed
	8. 355 Accesses	Software review Automatic Fortran to C++ conversion with FABLE Ralf W Grosse-Kunstleve, Thomas C Terwilliger, Nicholas K Sauter, Paul D Adams Source Code for Biology and Medicine 2012, 7:5 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
	9. 311 Accesses	Software review SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies Mehdi Pirooznia, Fayaz Seifuddin, Fernando S Goes, Jeffrey T Leek, Peter P Zandi Source Code for Biology and Medicine 2013, 8:8 (11 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	10. 292 Accesses	Software review Layout-aware text extraction from full-text PDF of scientific articles Cartic Ramakrishnan, Abhishek Patnia, Eduard Hovy, Gully APC Burns Source Code for Biology and Medicine 2012, 7:7 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
	11. 270 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
	12. 271 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
	13. 208 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
	14. 195 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 \| Full text \| PDF \| PubMed \| 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.
	15. 185 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 \| Cited on BioMed Central
	16. 177 Accesses	Editorial Changing computational research. The challenges ahead Cameron Neylon, Jan Aerts, C Brown, Simon J Coles, Les Hatton, Daniel Lemire, K Millman, Peter Murray-Rust, Fernando Perez, Neil Saunders, Nigam Shah, Arfon Smith, Gaël Varoquaux, Egon Willighagen Source Code for Biology and Medicine 2012, 7:2 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
	17. 184 Accesses	Brief reports RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics Akiko Izawa, Jun Sese Source Code for Biology and Medicine 2013, 8:6 (26 February 2013) Abstract \| Full text \| PDF \| PubMed
	18. 169 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
	19. 163 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 \| Cited on BioMed Central
	20. 156 Accesses	Software review Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes Andrew J Perry, Bosco K Ho Source Code for Biology and Medicine 2013, 8:9 (19 March 2013) Abstract \| Provisional PDF \| PubMed
	21. 149 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
	22. 154 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
	23. 149 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
	24. 135 Accesses	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) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25. 138 Accesses	Software review Scaffolder - software for manual genome scaffolding Michael D Barton, Hazel A Barton Source Code for Biology and Medicine 2012, 7:4 (28 May 2012) Abstract \| Full text \| PDF \| PubMed
	26. 139 Accesses	Research PathNet: a tool for pathway analysis using topological information Bhaskar Dutta, Anders Wallqvist, Jaques Reifman Source Code for Biology and Medicine 2012, 7:10 (24 September 2012) Abstract \| Full text \| PDF \| PubMed
	27. 142 Accesses	Software review FCC – An automated rule-based processing tool for life science data Simon Barkow-Oesterreicher, Can Türker, Christian Panse Source Code for Biology and Medicine 2013, 8:3 (11 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	28. 133 Accesses	Methodology Knowledge Driven Variable Selection (KDVS) – a new approach to enrichment analysis of gene signatures obtained from high–throughput data Grzegorz Zycinski, Annalisa Barla, Margherita Squillario, Tiziana Sanavia, Barbara Di Camillo, Alessandro Verri Source Code for Biology and Medicine 2013, 8:2 (9 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	29. 138 Accesses	Methodology CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals Annick Nembot-Simo, Jinko Graham, Brad McNeney Source Code for Biology and Medicine 2013, 8:5 (6 February 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	30. 136 Accesses	Software review IHE cross-enterprise document sharing for imaging: interoperability testing software Rita Noumeir, Bérubé Renaud Source Code for Biology and Medicine 2010, 5:9 (21 September 2010) Abstract \| Full text \| PDF \| PubMed
	31. 132 Accesses	Software review MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads Alexander V Tyakht, Anna S Popenko, Maxim S Belenikin, Ilya A Altukhov, Alexander V Pavlenko, Elena S Kostryukova, Oksana V Selezneva, Andrei K Larin, Irina Y Karpova, Dmitry G Alexeev Source Code for Biology and Medicine 2012, 7:13 (7 December 2012) Abstract \| Full text \| PDF \| PubMed
	32. 86 Accesses	Methodology EEGgui: a program used to detect electroencephalogram anomalies after traumatic brain injury Justin Sick, Eric Bray, Amade Bregy, W Dalton Dietrich, Helen M Bramlett, Thomas Sick Source Code for Biology and Medicine 2013, 8:12 (21 May 2013) Abstract \| Provisional PDF \| PubMed
	33. 125 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
	34. 128 Accesses	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
	35. 119 Accesses	Methodology MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data Guy N Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia Webb, Robert M Greene, M Michele Pisano Source Code for Biology and Medicine 2013, 8:1 (8 January 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	36. 115 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 \| Cited on BioMed Central
	37. 119 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
	38. 117 Accesses	Brief reports CADLIVE optimizer: web-based parameter estimation for dynamic models Kentaro Inoue, Kazuhiro Maeda, Yuki Kato, Shinpei Tonami, Shogo Takagi, Hiroyuki Kurata Source Code for Biology and Medicine 2012, 7:9 (28 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	39. 112 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
	40. 114 Accesses	Software review ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing Kazuharu Misawa, Naoyuki Kamatani Source Code for Biology and Medicine 2010, 5:5 (4 June 2010) Abstract \| Full text \| PDF \| PubMed
	41. 118 Accesses	Software review Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo, Daniel MacLean Source Code for Biology and Medicine 2012, 7:6 (28 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	42. 113 Accesses	Software review Tools for efficient epistasis detection in genome-wide association study Xiang Zhang, Shunping Huang, Fei Zou, Wei Wang Source Code for Biology and Medicine 2011, 6:1 (4 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	43. 112 Accesses	Brief reports BlaSTorage: a fast package to parse, manage and store BLAST results Massimiliano Orsini, Simone Carcangiu Source Code for Biology and Medicine 2013, 8:4 (30 January 2013) Abstract \| Full text \| PDF \| PubMed
	44. 107 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
	45. 114 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
	46. 104 Accesses	Research A CellML simulation compiler and code generator using ODE solving schemes Florencio Rusty Punzalan, Yoshiharu Yamashita, Naoki Soejima, Masanari Kawabata, Takao Shimayoshi, Hiroaki Kuwabara, Yoshitoshi Kunieda, Akira Amano Source Code for Biology and Medicine 2012, 7:11 (19 October 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed
	47. 103 Accesses	Software review 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 \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	48. 104 Accesses	Software review JobCenter: an open source, cross-platform, and distributed job queue management system optimized for scalability and versatility Daniel Jaschob, Michael Riffle Source Code for Biology and Medicine 2012, 7:8 (30 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Laboratories can efficiently distribute computational work among all available resources by using 'JobCenter'; an open source client-server application for job management and distributed job execution.
	49. 106 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
	50. 105 Accesses	Brief reports WordCloud: a Cytoscape plugin to create a visual semantic summary of networks Layla Oesper, Daniele Merico, Ruth Isserlin, Gary D Bader Source Code for Biology and Medicine 2011, 6:7 (7 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central