Abstract
BackgroundMathematical modelling of biological processes often requires a large variety of different data sets for parameter estimation and validation. It is common practice that clinical data are not available in raw formats but are provided as graphical representations. Hence, in order to include these data into environments used for model simulations and statistical analyses, it is necessary to extract them from their presentations in the literature. For this purpose, we developed the freely available open source tool ycasd. After establishing a coordinate system by simple axes definitions, it supports convenient retrieval of data points from arbitrary figures.ResultsAfter describing the general functionality and providing an overview of the programme interface, we demonstrate on an example how to use ycasd. A major advantage of ycasd is that it does not require a certain input file format to open and process figures. All options of ycasd are accessible through a single window which eases handling and speeds up data extraction. For subsequent processing of extracted data points, results can be formatted as a Matlab or an R matrix. We extensively compare the functionality and other features of ycasd with other publically available tools. Finally, we provide a short summary of our experiences with ycasd in the context of modelling.ConclusionsWe conclude that our tool is suitable for convenient and accurate data retrievals from graphical representations such as papers. Comparison of tools reveals that ycasd is a good compromise between easy and quick capturing of scientific data from publications and complexity. Our tool is routinely applied in the context of biological modelling, where numerous time series data are required to develop models. The software can also be useful for other kinds of analyses for which published data are required but are not available in raw formats such as systematic reviews and meta-analyses.
Highlights
Mathematical modelling of biological processes often requires a large variety of different data sets for parameter estimation and validation
Time series data of numerous blood parameters are required for parameterisation and validation of our models of human thrombopoiesis [1], erythropoiesis [2], granulopoiesis under chemotherapy and growth-factor applications [3] and for other models currently under development
Since we believe that our tool is helpful especially for other research groups interested in dynamical modelling or meta-analyses, we aim at publishing it as an open source and freely available software
Summary
Mathematical modelling of biological processes often requires a large variety of different data sets for parameter estimation and validation. In order to include these data into environments used for model simulations and statistical analyses, it is necessary to extract them from their presentations in the literature For this purpose, we developed the freely available open source tool ycasd. Data of other groups are often not available in their raw formats but are presented in figures such as scatter plots, box plots, time series data or derived statistics such as Kaplan-Meier curves. Incorporating these data in research projects is often necessary to compare one’s own results with those of the literature. We describe the functionality and the interface of the programme, compare it with those of other publically available tools and provide a quick introduction to its use on the basis of example figures
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