Software package DEBtum

DEBtum has been written by Fleur Kelping (coding), Ingeborg van Leeuwen (modelling) and Bas Kooijman (theoretical biology).
DEBtum is a user-friendly software package designed to analyze the results from long-term carcinogenicity studies.


What is DEBtum ?

The aim of the DEBtum software package is to provide a tool for the analysis of data from long-term carcinogenicity tests. The package can be used not only to study tumor incidence data but also, for instance, body growth data. Moreover, the package allows the user to analyze several kinds of data simultaneously. That is, for instance, tumor incidence data can be evaluated taking information on food consumption and body weight into account. Some important features of the package are:

Experimental Data

Input

The main purpose of the DEBtum package is to facilitate the analysis of results from long-term single-compound carcinogenicity studies. End points of interest in such carcinogenicity studies are primarily preneoplastic and neoplastic changes, but also include degree of malignancy, time to tumor appearance, multiplicity of (pre)neoplasia, and occurrence of metastasis. In addition to these endpoints, measurements of body weight and food consumption are usually recorded. Accurate interpretation of a dataset by the DEBtum package requires definition of the following details:

- Doses
- Food levels (relevant in caloric restriction studies)
- Initial number of animals in each group
- Species (e.g., B6C3F1 mice)
- Average age at study initiation (e.g., 4 weeks)
- Exposure route (inhalation, oral, ...)
- Time unit (days, weeks, months, ...)
- Additional info on columns in Excel file

Some of the entries above, as experimental species, are only required if the user wants to use the available sets of default parameter values.

Types of data that can be analyzed

Data concerning physiological aspects of the experimental animals:

Data concerning processes involved in chemical carcinogenesis: Data selection

The DEBtum package allows the user to select a subgroup from a dataset. A subgroup is defined as a set of restrains on dose-group, sex, age, food level (diet-group), etc. The package's applications can then be applied to the selected subgroup only.

Model Definition

As mentioned above, the DEBtum package includes two categories of mathematical models: In the context of the DEBtum package, a model is composed of one or more modules. The number of modules depends on the data to analyze. For instance, a model for body growth is constituted by a minimum of one module (a V-model) and a maximum of two modules (V-model and a F-model). Notice that the first model ignores the influence of food ingestion on body weight. For each possible dataset, the table below shows the module-composition of a model that can be fitted to the data. Italics means that the indicated category or module/process may be ignored. The user should be aware, however, that relevant processes may not be taken into account when a certain part/module is ignored.

Data to Analyze Modules
Body weights F-model + V-model
Food Intake/Body weight F-model + V-model
Respiration rates F-model + V-model
Mortality F-model + V-model + S-model
Internal concentration category A + K-model
Time to detectable tumor category A + K-model + I-model + T-model
Time to death with tumor category A + K-model + I-model + T-model + E-model



DEBtum Documentation


Other Relevant References



Disclaimer

The DEBtum-package was written as part of the research project DEBtum (VBI-4692), financially supported by the Netherlands Technology Foundation (STW) and DSM. Although the package has been written with care, authors, the Vrije Universiteit, nor the publisher will accept any responsibility for the results obtained with this package.

Go to the DEBtum-project Information, the Theoretical Biology Home page, the DEB information page or the DEB laboratory