Book title: Springer, Berlin, Heidelberg, 2012.
Abstract A “knowledge turn” is a cycle of a process by a professional, including the learning generated by the experience, deriving more good and leading to advance. The majority of scientific advances in the public domain result from collective efforts that depend on rapid exchange and effective reuse of results. We have powerful computational instruments, […]
Methods Enzymol, Issue 500, pages 629-55, 2011. 10.1016/B978-0-12-385118-5.00029-3.
Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be heterogeneous and often involves high-throughput “omics” analyses. Models are developed iteratively from data generated in the projects and from the literature. Consequently, there is a growing requirement […]
Bioinformatics, Issue 27:14, pages 2021 - 2022, 2011. 10.1093/bioinformatics/btr312.
Motivation: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. Results: RightField is an open source application that […]
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
BMC Systems Biology, Issue 5:1, pages 198, 2011. 10.1186/1752-0509-5-198.
Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software […]
BMC Bioinformatics, Issue 1, pages 1--19, 2011. 10.1186/1471-2105-12-468.
Background: Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis […]