Abstract
As a member of the PLOS family, PLOS Computational Biology promotes open and unrestricted access to scientific publications and the research products that support them. For PLOS Computational Biology, this specifically includes computational methods and the software that implements them. To foster a culture of open exchange and reuse of software, we created a new category of manuscripts called Software Articles. We have been accepting submissions in this category for over a year now, and all articles published in this category are now also available as an online collection (http://www.ploscollections.org/software). This is a collection of articles spanning a wide range of different topics in computational biology, starting from video image analysis in “Automated Tracking of Whiskers in Videos of Head Fixed Rodents” [1], over to simulation and analysis of biological system models in “Hybrid Models and Biological Model Reduction with PyDSTool” [2]. We have published articles describing genomic tools, such as “Podbat: Genomic Tool for Epigenetic Meta-Analysis” [3] and “Exploring Massive, Genome Scale Datasets with the GenometriCorr Package” [4], computational chemistry, in “AutoClickChem: Click Chemistry in Silico” [5], and protein science, in “ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin” [6] and “CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures” [7]. As new Software Articles get published in this journal, they will be added to this collection.
Highlights
This is a collection of articles spanning a wide range of different topics in computational biology, starting from video image analysis in ‘‘Automated Tracking of Whiskers in Videos of Head Fixed Rodents’’ [1], over to simulation and analysis of biological system models in ‘‘Hybrid Models and Biological Model Reduction with PyDSTool’’ [2]
– Increased quality is a natural consequence of more eyes looking at the source code, and more developers trying to reuse the code in their own applications
As anyone who has ever tried to obtain software for an algorithm published some time ago will know, scientific software often becomes unavailable only a few years after its publication, unless the authors had the foresight to use an open-source repository for their development. This is one of the reasons why PLOS Computational Biology requires source code to be uploaded during submission of a manuscript, so that a copy of record can be preserved
Summary
As a member of the PLOS family, PLOS Computational Biology promotes open and unrestricted access to scientific publications and the research products that support them. We have been accepting submissions in this category for over a year and all articles published in this category are available as an online collection (http://www.ploscollections.org/ software). This is a collection of articles spanning a wide range of different topics in computational biology, starting from video image analysis in ‘‘Automated Tracking of Whiskers in Videos of Head Fixed Rodents’’ [1], over to simulation and analysis of biological system models in ‘‘Hybrid Models and Biological Model Reduction with PyDSTool’’ [2]. As new Software Articles get published in this journal, they will be added to this collection
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