Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years.

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Features of software development tools /

Item 247.

On the Models of Development and Distribution of Software

The notion model of development and distribution of software (MDDS) is introduced and its role for the efficiency of the software products is stressed. Two classical MDDS are presented and some attempts to adapt them to the contemporary trends in web-based software design are described. Advantages and shortcomings of the obtained models are outlined. In conclusion the desired features of a better MDDS for web-based solutions are given.

A Practical Case of Software Localization after System Development

Internationalization of software as a previous step for localization is usually taken into account during early phases of the life-cycle of software development. However, the need to adapt software applications into different languages and cultural settings can appear once the application is finished and even in the market. In these cases, software localization implies a high cost of time and resources. This paper shows a real case of a existent software application, designed and developed without taking into account future necessities of localization, whose architecture and source code were modified to include the possibility of straightforward adaptation into new languages. The use of standard languages and advanced programming languages has permitted the authors to adapt the software in a simple and straightforward mode.

Traceability Management Architectures Supporting Total Traceability in the Context of Software Engineering

In the area of Software Engineering, traceability is defined as the capability to track requirements, their evolution and transformation in different components related to engineering process, as well as the management of the relationships between those components. However the current state of the art in traceability does not keep in mind many of the elements that compose a product, specially those created before requirements arise, nor the appropriated use of traceability to manage the knowledge underlying in order to be handled by other organizational or engineering processes. In this work we describe the architecture of a reference model that establishes a set of definitions, processes and models which allow a proper management of traceability and further uses of it, in a wider context than the one related to software development.

An Analysis and Forecast of Software and Services Research in Bulgaria

In the last 40 years much has been achieved in Software Engineering research and still more is to be done. Although significant progress is being made on several fronts in Service-Oriented Architecture (SOA), there is still no set of clear, central themes to focus research activity on. A task within the EU FP7 Sister project aimed at defining research priorities for the Faculty of Mathematics and Informatics (Sofia University) in the area of Software and Services. A dedicated methodology was proposed and developed, based on various sources of information. The information accumulated was systematised and processed according to this methodology. The final results obtained are described and discussed here.

Model Mining and Efficient Verification of Software Product Lines

Software product line modeling aims at capturing a set of software products in an economic yet meaningful way. We introduce a class of variability models that capture the sharing between the software artifacts forming the products of a software product line (SPL) in a hierarchical fashion, in terms of commonalities and orthogonalities. Such models are useful when analyzing and verifying all products of an SPL, since they provide a scheme for divide-and-conquer-style decomposition of the analysis or verification problem at hand. We define an abstract class of SPLs for which variability models can be constructed that are optimal w.r.t. the chosen representation of sharing. We show how the constructed models can be fed into a previously developed algorithmic technique for compositional verification of control-flow temporal safety properties, so that the properties to be verified are iteratively decomposed into simpler ones over orthogonal parts of the SPL, and are not re-verified over the shared parts. We provide tool support for our technique, and evaluate our tool on a small but realistic SPL of cash desks.

Smart Alerts: Development of Software to Optimize Data Monitoring

Dherte PM, Negrao MPG, Mori Neto S, Holzhacker R, Shimada V, Taberner P, Carmona MJC - Smart Alerts: Development of a Software to Optimize Data Monitoring. Background and objectives: Monitoring is useful for vital follow-ups and prevention, diagnosis, and treatment of several events in anesthesia. Although alarms can be useful in monitoring they can cause dangerous user`s desensitization. The objective of this study was to describe the development of specific software to integrate intraoperative monitoring parameters generating ""smart alerts"" that can help decision making, besides indicating possible diagnosis and treatment. Methods: A system that allowed flexibility in the definition of alerts, combining individual alarms of the parameters monitored to generate a more elaborated alert system was designed. After investigating a set of smart alerts, considered relevant in the surgical environment, a prototype was designed and evaluated, and additional suggestions were implemented in the final product. To verify the occurrence of smart alerts, the system underwent testing with data previously obtained during intraoperative monitoring of 64 patients. The system allows continuous analysis of monitored parameters, verifying the occurrence of smart alerts defined in the user interface. Results: With this system a potential 92% reduction in alarms was observed. We observed that in most situations that did not generate alerts individual alarms did not represent risk to the patient. Conclusions: Implementation of software can allow integration of the data monitored and generate information, such as possible diagnosis or interventions. An expressive potential reduction in the amount of alarms during surgery was observed. Information displayed by the system can be oftentimes more useful than analysis of isolated parameters.