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Open Research Computation

Edited by: Dr Cameron Neylon

Collection published: 28 May 2012

Last updated: 19 March 2013

The Open Research Computation thematic series publishes peer reviewed articles that describe the development, capacities, and uses of software designed for use by researchers. Submissions relating to software for use in any area of research are welcome as are articles dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries. The Open Research Computation thematic series requires for software source code to be made available under an Open Source Initiative compliant license, and assesses the quality of documentation and testing of the software. In addition to articles describing software the thematic series also welcomes submissions that review or describe developments relating to software based tools for research. These include, but are not limited to, reviews or proposals for standards, discussion of best practice in research software development, educational and support resources and tools for researchers that develop or use software based tools.

		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 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

		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 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