Andris Zarins

The possibility of automatic construction of a complete set of program tests is considered. A test set system is said to be complete if every feasible program branch (segment) is executed by it. The complete test set construction algorithm for commercially oriented data processing programs is outlined, and the results of its functioning on real programs are analyzed.

UNLABELLED: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. AVAILABILITY: The source code, documentation and initialization scripts are available at http://simbioms.org.

BACKGROUND: One of the crucial aspects of day-to-day laboratory information management is collection, storage and retrieval of information about research subjects and biomedical samples. An efficient link between sample data and experiment results is absolutely imperative for a successful outcome of a biomedical study. Currently available software solutions are largely limited to large-scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but often implies sufficient investment of time, effort and funds, which are not always available. There is a clear need for lightweight open source systems for patient and sample information management. RESULTS: We present a web-based tool for submission, management and retrieval of sample and research subject data. The system secures confidentiality by separating anonymized sample information from individuals' records. It is simple and generic, and can be customised for various biomedical studies. Information can be both entered and accessed using the same web interface. User groups and their privileges can be defined. The system is open-source and is supplied with an on-line tutorial and necessary documentation. It has proven to be successful in a large international collaborative project. CONCLUSION: The presented system closes the gap between the need and the availability of lightweight software solutions for managing information in biomedical studies involving human research subjects.

In this paper we introduce a novel wide-profile graphical tool-building platform GrTP which is based on the principle of separating semantic domain model processing and user interface components. This principle is enabled in GrTP by a meta-model for visual information presentation (“interface meta-model”). A novel feature of GrTP is that it consistently bases all work of connecting the domain and interface models on model transformations. These transformations can be produced for different domain models, thus obtaining concrete tools tailored to specific domains within GrTP. The visualization component of GrTP is based on an original high-performance graphical diagram presentation engine which embodies advanced graph drawing algorithms. The paper explains the GrTP platform along with the first practical experience of its usage.