title: On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data.
abstract: The move towards in silico experimentation has resulted in the use of computational models, in addition to traditional experimental models, to generate the raw data that is analysed and published as research findings. This change requires new methods to be introduced to facilitate independent validation of the underlying models and the reported results. The promotion of co-operative research has the potential to help to both validate results and explore wider problem areas. In this paper we leverage and extend two existing software frameworks to develop an infrastructure that has the potential to both promote the sharing of data between researchers pre-publication and enable access to the data for interested parties post-publication. The pre-publication sharing of data would enable larger problem spaces to be explored by distributed research groups; enabling access to the data post-publication would allow reviewers and the wider community to independently verify the published results which would, in the longer term, help to increase confidence in published results. The framework is used to perform reproducible and numerically validated individual-based computational experiments into the onset of colorectal cancer. Existing results are verified and new insights into the top-down versus bottom-up hypothesis of colorectal crypt invasion are given.
authors.affiliation: Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD UK.
authors.forename: Mark
authors.initials: M
authors.lastname: Slaymaker
authors.forename: James
authors.initials: J
authors.lastname: Osborne
authors.forename: Andrew
authors.initials: A
authors.lastname: Simpson
authors.forename: David
authors.initials: D
authors.lastname: Gavaghan
keywords: Colorectal cancer; Data management; Systems biology