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		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		Brief reports RMol: a toolset for transforming SD/Molfile structure information into R objects Martin Grabner, Kurt Varmuza, Matthias Dehmer Source Code for Biology and Medicine 2012, 7:12 (14 November 2012) Abstract \| Full text \| PDF \| PubMed
		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
		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
		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
		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.
		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
		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
		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
		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
		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
		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
		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.

	All
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		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
		Brief reports RMol: a toolset for transforming SD/Molfile structure information into R objects Martin Grabner, Kurt Varmuza, Matthias Dehmer Source Code for Biology and Medicine 2012, 7:12 (14 November 2012) Abstract \| Full text \| PDF \| PubMed
		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
		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
		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
		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.
		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
		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
		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
		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
		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
		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
		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.