GigaScience launches: overseeing the transition from papers to “executable research objects” 2012-07-20


“Research papers have been the predominant form of scholarly communication for the past few centuries, and despite moves towards online publication and open access, the process and structure of publication has not fundamentally changed in that time. With biological and biomedical research becoming increasingly data-driven, and the amount of information, computational tools, and code supporting a publication in areas such as genomics and imaging growing at exponential rates, the lack of access to the resources that the paper is built upon is leading to a growing ‘reproducibility gap’. Recent scandals relating to falsified data that went long undetected ... further highlight the need to make data easily accessible for purposes of validation and to maintain public trust in science. As research has shifted to work within, and handle, this data-rich environment and to utilize advances such as cloud computing and automated workflow systems, publishing needs to be able to follow in a similar direction. For a number of years much talk has been made about the potential for executable papers: aiding review and re-use of data by having all of the tools and data associated with a publication accessible in a reproducible and standardized environment. An important first step in the path has been reached today with the first articles published in GigaScience. Aiming to become a home to research from the growing number of biological and biomedical fields handling ‘big-data’, GigaScience is a new type of open access, open data journal that provides standard scientific publishing linked directly to a database that hosts its relevant data. Our associated GigaDB database, launched last year, provides a home to all of the supporting data and tools associated with research, thus overcoming one of the biggest challenges holding back reproducible research. Through GigaDB, we assign DataCite DOIs to these accompanying datasets to provide additional credit to the authors who make their data publicly available and to boost data discoverability and tracking of data... Using the data hosting capabilities and expertise in data handling and cloud computing of our partner, BGI, we are able to host a much larger and broader range of datasets than journal supplementary files are usually able to handle, outside the capacities of most other journals and repositories. We have been testing and building up our new informatics platform by releasing a number of datasets from BGI to demonstrate new mechanisms of pre-publication data-release. For example, the deadly 2011 outbreak E. coli dataset was the first we released, and this led to the crowdsourcing of its analysis, which was cited in the recent Royal Society ‘Science as an Open Enterprise’ report as an example of ‘The power of intelligently open data’...The GigaDB website is continuing to evolve and the next version will be released in a few months with a more extensive search interface. As the final step in attaining fully executable and reproducible papers, we will be working with authors to make the computational tools and data processing pipelines described in their papers available and, where possible, executable on an informatics platform ... We hope that by making both the data and processes involved in their analysis freely accessible, this novel form of publication will help articles published in our journal to have a much higher impact in the scientific literature and to maximize their reuse within the community...”



08/16/2012, 06:08

From feeds:

Open Access Tracking Project (OATP) »


oa.medicine oa.licensing oa.comment oa.open_science oa.crowd oa.interoperability oa.impact oa.standards oa.pd oa.reports oa.floss oa.neuro oa.bmc oa.citations oa.biomedicine oa.gigascience oa.dois oa.datacite oa.gigadb oa.bgi oa.imaging oa.royal_society oa.libre oa.journals oa.copyright



Date tagged:

07/20/2012, 16:24

Date published:

07/19/2012, 16:06