Karlis Podnieks

A System for Information Management in BioMedical Studies –SIMBioMS

Summary: 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. Contact: support@simbioms.org; mariak@ebi.ac.uk

PASSIM – an open source software system for managing information in biomedical studies

BackgroundOne 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.ResultsWe 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.ConclusionThe 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.

Inductive Inference of Recursive Functions: Complexity Bounds

This survey includes principal results on complexity of inductive inference for recursively enumerable classes of total recursive functions. Inductive inference is a process to find an algorithm from sample computations. In the case when the given class of functions is recursively enumerable it is easy to define a natural complexity measure for the inductive inference, namely, the worst-case mindchange number for the first n functions in the given class. Surely, the complexity depends not only on the class, but also on the numbering, i.e. which function is the first, which one is the second, etc. It turns out that, if the result of inference is Goedel number, then complexity of inference may vary between log2n+o(log2n) and an arbitrarily slow recursive function. If the result of the inference is an index in the numbering of the recursively enumerable class, then the complexity may go up to const·n. Additionally, effects previously found in the Kolmogorov complexity theory are discovered in the complexity of inductive inference as well.

Editor Definition Language and Its Implementation

Universal graphical editor definition language based on logical metamodel extended by presentation classes is proposed. Implementation principles of this language, based on Graphical Diagramming Engine are described.

Towards Integrated Computer Aided Systems and Software Engineering Tool for Information Systems Design

The paper starts with a brief overview of the current situation in the world of CASE tools for information systems. Then there follows the outline of the basic ideas and principles of integrated CASE tool GRADE. The most outstanding characteristics of GRADE are that the tool is based on a unified specification language GRAPES and that it supports all information system development phases including analysis, requirements specification, design and implementation.