Dóra Hidy

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology

BackgroundMaking forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as “Web services”) and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust “in silico” science. However, use of this approach in biodiversity science and ecology has thus far been quite limited.ResultsBioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on-line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible ‘virtual laboratory’, free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity.ConclusionsOur work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.

Modelling of carbon isotope discrimination by vegetation

The paper presents a simple box model simulating the temporal variation of atmospheric 13CO2 concentration, atmospheric CO2 mixing ratio and 13C content of plant material. The model is driven by observed meteorological and measured biosphere-atmosphere CO2 exchange data. The model was calibrated and validated using measurements from a Hungarian atmospheric monitoring station. The simulated atmospheric stable carbon isotope ratio data agreed well with the measured ratios considering both the magnitude and the seasonal dynamics. Observed deviations between the measured and simulated δ13Cair values were systematically negative in winters, while deviations were random in sign and smaller by an order of magnitude during periods when the vegetation was photosynthetically active. This difference, supported by a significant correlation between the deviation and modeled fossil fuel contributions to CO2 concentration, suggests the increased contribution of 13C-depleted fossil fuel CO2 from heating and the lower boundary layer heights during winter.