A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

<p>Abstract</p> <p>Background</p> <p>Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes.</p> <p>Results</p> <p>This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra.</p> <p>Conclusions</p> <p>This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.</p

Automated Generation of Constraints from Use Case Specifications to Support System Testing

System testing plays a crucial role in safety-critical domains, e.g., automotive, where system test cases are used to demonstrate the compliance of software with its functional and safety requirements. Unfortunately, since requirements are typically written in natural language, significant engineering effort is required to derive test cases from requirements. In such a context, automated support for generating system test cases from requirements specifications written in natural language would be highly beneficial. Unfortunately, existing approaches have limited applicability. For example, some of them require that software engineers provide formal specifications that capture some of the software behavior described using natural language. The effort needed to define such specifications is usually a significant deterrent for software developers. This paper proposes an approach, OCLgen, which largely automates the generation of the additional formal specifications required by an existing test generation approach named UMTG. More specifically, OCLgen relies on semantic analysis techniques to automatically derive the pre- and post-conditions of the activities described in use case specifications. The generated conditions are used by UMTG to identify the test inputs that cover all the use case scenarios described in use case specifications. In practice, the proposed approach enables the automated generation of test cases from use case specifications while avoiding most of the additional modeling effort required by UMTG. Results from an industrial case study show that the approach can automatically and correctly generate more than 75% of the pre- and post-conditions characterizing the activities described in use case specifications

DECODER - DEveloper COmpanion for Documented and annotatEd code Reference

Software is everywhere and the productivity of Software Engineers has increased radically with the advent of new specifications, design and programming paradigms and languages. The main objective of the DECODER project is to introduce radical solutions to increase productivity by increasing the abstraction level, at specification stage, using requirements engineering techniques to integrate more complete specifications into the development process, and formal methods to reduce the time and efforts for integration testing. DECODER project will develop a methodology and tools to improve the productivity of the software development process for medium-criticality applications in the domains of IoT, Cloud Computing, and Operating Systems by combining Natural Language Processing techniques, modelling techniques and Formal Methods. A radical improvement is expected from the management and transformation of informal data into material (herein called knowledge ) that can be assimilated by any party involved in a development process. The project expects an average benefit of 20% in terms of efforts on several use cases belonging to the beforehand mentioned domains and will provide recommendations on how to generalize the approach to other medium-critical domains.This work has been developed with the financial support of the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 824231 and the Spanish State Research Agency under the project TIN2017-84094-R and co-financed with ERDF.Torres Bosch, MV.; Gil Pascual, M.; Pelechano Ferragud, V. (2019). DECODER - DEveloper COmpanion for Documented and annotatEd code Reference. Springer. 596-601. https://doi.org/10.1007/978-3-030-35333-9_44S59660

Using formal methods to support testing

Formal methods and testing are two important approaches that assist in the development of high quality software. While traditionally these approaches have been seen as rivals, in recent years a new consensus has developed in which they are seen as complementary. This article reviews the state of the art regarding ways in which the presence of a formal specification can be used to assist testing

Generating natural language descriptions of Z test cases

Critical software most often requires an independent validation and verification (IVV). IVV is usually performed by domain experts, who are not familiar with specific, many times formal, development technologies. In addition, model-based testing (MBT) is a promising testing technique for the verification of critical software. Test cases generated by MBT tools are logical descriptions. The problem is, then, to provide natural language (NL) descriptions of these test cases, making them accessible to domain experts. In this paper, we present ongoing research aimed at finding a suitable method for generating NL descriptions from test cases in a formal specification language. A first prototype has been developed and applied to a real-world project in the aerospace sector