Although more elaborated methods for calculation of coordinate pairs x 3, y 3 are conceivable to account for non-linearly distorted figures (by scanning), our approach allows for rotation and linear skewness and is straightforward to implement into a C programme. The assumption that k α a → and k β b → are always parallel to the y and x axis is simple. Y err is only valid for non-logarithmically scaled y axes. In the present paper, 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. 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. Time series data of numerous blood parameters are required for parameterisation and validation of our models of human thrombopoiesis, erythropoiesis, granulopoiesis under chemotherapy and growth-factor applications and for other models currently under development. The development of ycasd was motivated by our own work in the field of modelling blood formation. For a typical example see Additional file 1. The problem of skewed diagrams obtained from scanning papers is also addressed. To support this task, we developed the tool ycasd ( y casd captures and scales data) which can capture data from many kinds of graphical representations. In order to include these data into environments used for model simulations, it is necessary to extract them from the presentations chosen in the literature. This especially applies for systems-biological modelling for which time series data under different clinical conditions are required to calibrate the models and to validate their predictions. However, incorporating these data in research projects is often necessary to compare one’s own results with those of the literature. In medical literature, 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. 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. Our tool is routinely applied in the context of biological modelling, where numerous time series data are required to develop models. Comparison of tools reveals that ycasd is a good compromise between easy and quick capturing of scientific data from publications and complexity. We conclude that our tool is suitable for convenient and accurate data retrievals from graphical representations such as papers. Finally, we provide a short summary of our experiences with ycasd in the context of modelling. We extensively compare the functionality and other features of ycasd with other publically available tools. For subsequent processing of extracted data points, results can be formatted as a Matlab or an R matrix. All options of ycasd are accessible through a single window which eases handling and speeds up data extraction. A major advantage of ycasd is that it does not require a certain input file format to open and process figures. ResultsĪfter describing the general functionality and providing an overview of the programme interface, we demonstrate on an example how to use ycasd. After establishing a coordinate system by simple axes definitions, it supports convenient retrieval of data points from arbitrary figures. For this purpose, we developed the freely available open source tool ycasd. 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. It is common practice that clinical data are not available in raw formats but are provided as graphical representations. Engauge Digitizer is used by individuals such as grad students and researchers as well as engineers and employees in large government and commercial organizations for processing single files but also managing databases of thousands of image files.Mathematical modelling of biological processes often requires a large variety of different data sets for parameter estimation and validation. It provides assistance in enhancing the image quality and matching the data points. Conceptually, it is thus the opposite of a graphing tool that converts data points to graphs. The Engauge Digitizer tool assists in interactively extracting numbers from images of graphs.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |