Skip to main content


Open Research Computation

open research computation

Edited by: Cameron Neylon

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.

Last updated on 19 March 2013

  1. Software review

    Layout-aware text extraction from full-text PDF of scientific articles

    The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner present...

    Cartic Ramakrishnan, Abhishek Patnia, Eduard Hovy and Gully APC Burns

    Source Code for Biology and Medicine 2012 7:7

    Published on: 28 May 2012

  2. Software review

    Automatic Fortran to C++ conversion with FABLE

    In scientific computing, Fortran was the dominant implementation language throughout most of the second part of the 20th century. The many tools accumulated during this time have been difficult to integrate wi...

    Ralf W Grosse-Kunstleve, Thomas C Terwilliger, Nicholas K Sauter and Paul D Adams

    Source Code for Biology and Medicine 2012 7:5

    Published on: 28 May 2012

  3. Software review

    Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

    The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities...

    Ricardo H Ramirez-Gonzalez, Raoul Bonnal, Mario Caccamo and Daniel MacLean

    Source Code for Biology and Medicine 2012 7:6

    Published on: 28 May 2012

  4. Commentary

    How Not to Be a Bioinformatician

    Although published material exists about the skills required for a successful bioinformatics career, strangely enough no work to date has addressed the matter of how to excel at not being a bioinformatician. A se...

    Manuel Corpas, Segun Fatumo and Reinhard Schneider

    Source Code for Biology and Medicine 2012 7:3

    Published on: 28 May 2012

  5. Software review

    Scaffolder - software for manual genome scaffolding

    The assembly of next-generation short-read sequencing data can result in a fragmented non-contiguous set of genomic sequences. Therefore a common step in a genome project is to join neighbouring sequence regio...

    Michael D Barton and Hazel A Barton

    Source Code for Biology and Medicine 2012 7:4

    Published on: 28 May 2012

  6. Editorial

    Changing computational research. The challenges ahead

    Cameron Neylon, Jan Aerts, C Titus Brown, Simon J Coles, Les Hatton, Daniel Lemire, K Jarrod Millman, Peter Murray-Rust, Fernando Perez, Neil Saunders, Nigam Shah, Arfon Smith, Gaƫl Varoquaux and Egon Willighagen

    Source Code for Biology and Medicine 2012 7:2

    Published on: 28 May 2012