An assertion language for constraint logic programs

In an advanced program development environment, such as that discussed in the introduction of this book, several tools may coexist which handle both the program and information on the program in different ways. Also, these tools may interact among themselves and with the user. Thus, the different tools and the user need some way to communicate. It is our design principie that such communication be performed in terms of assertions. Assertions are syntactic objects which allow expressing properties of programs. Several assertion languages have been used in the past in different contexts, mainly related to program debugging. In this chapter we propose a general language of assertions which is used in different tools for validation and debugging of constraint logic programs in the context of the DiSCiPl project. The assertion language proposed is parametric w.r.t. the particular constraint domain and properties of interest being used in each different tool. The language proposed is quite general in that it poses few restrictions on the kind of properties which may be expressed. We believe the assertion language we propose is of practical relevance and appropriate for the different uses required in the tools considered.

Validation tool for smart screening of language disorders in pediatrics care

Primary-care pediatricians could play a key role in early detection of development disorders as quick as they might have enough time and knowledge for suitable screenings at clinical routine. This research paper focuses on the development and validation of a knowledge-based web tool whose aim is to support a smart detection of developmental disorders in early childhood. Thus, the use of the system can trigger the necessary preventive and therapeutic actions from birth until the age of six. The platform was designed on the basis of an analysis of significant 21 cases of children with language disorders that supported the creation of a specific knowledge base, its ontology and a set of description logic relations. The resulting system is being validated in a scalable approach with a team of seven experts from the fields of neonathology, pediatrics, neurology and language therapy.

A documentation generator for (C)LP systems

We describe lpdoc, a tool which generates documentation manuals automatically from one or more logic program source files, written in Ciao, ISO-Prolog, and other (C)LP languages. It is particularly useful for documenting library modules, for which it automatically generates a rich description of the module interface. However, it can also be used quite successfully to document full applications. A fundamental advantage of using lpdoc is that it helps maintaining a true correspondence between the program and its documentation, and also identifying precisely to what versión of the program a given printed manual corresponds. The quality of the documentation generated can be greatly enhanced by including within the program text assertions (declarations with types, modes, etc. ...) for the predicates in the program, and machine-readable comments. One of the main novelties of lpdoc is that these assertions and comments are written using the Ciao system asseriion language, which is also the language of communication between the compiler and the user and between the components of the compiler. This allows a significant synergy among specification, debugging, documentation, optimization, etc. A simple compatibility library allows conventional (C)LP systems to ignore these assertions and comments and treat normally programs documented in this way. The documentation can be generated interactively from emacs or from the command line, in many formats including texinfo, dvi, ps, pdf, info, ascii, html/css, Unix nroff/man, Windows help, etc., and can include bibliographic citations and images, lpdoc can also genérate "man" pages (Unix man page format), nicely formatted plain ASCII "readme" files, installation scripts useful when the manuals are included in software distributions, brief descriptions in html/css or info formats suitable for inclusión in on-line Índices of manuals, and even complete WWW and info sites containing on-line catalogs of documents and software distributions. The lpdoc manual, all other Ciao system manuals, and parts of this paper are generated by lpdoc.

Using global analysis, partial specifications, and an extensible assertion language for program validation and debugging

We discuss a framework for the application of abstract interpretation as an aid during program development, rather than in the more traditional application of program optimization. Program validation and detection of errors is first performed statically by comparing (partial) specifications written in terms of assertions against information obtained from (global) static analysis of the program. The results of this process are expressed in the user assertion language. Assertions (or parts of assertions) which cannot be checked statically are translated into run-time tests. The framework allows the use of assertions to be optional. It also allows using very general properties in assertions, beyond the predefined set understandable by the static analyzer and including properties defined by user programs. We also report briefly on an implementation of the framework. The resulting tool generates and checks assertions for Prolog, CLP(R), and CHIP/CLP(fd) programs, and integrates compile-time and run-time checking in a uniform way. The tool allows using properties such as types, modes, non-failure, determinacy, and computational cost, and can treat modules separately, performing incremental analysis.

Using global analysis, partial specifications, and an extensible assertion language for program validation and debugging

We present a framework for the application of abstract interpretation as an aid during program development, rather than in the more traditional application of program optimization. Program validation and detection of errors is first performed statically by comparing (partial) specifications written in terms of assertions against information obtained from static analysis of the program. The results of this process are expressed in the user assertion language. Assertions (or parts of assertions) which cannot be verified statically are translated into run-time tests. The framework allows the use of assertions to be optional. It also allows using very general properties in assertions, beyond the predefined set understandable by the static analyzer and including properties defined by means of user programs. We also report briefly on an implementation of the framework. The resulting tool generates and checks assertions for Prolog, CLP(R), and CHIP/CLP(fd) programs, and integrates compile-time and run-time checking in a uniform way. The tool allows using properties such as types, modes, non-failure, determinacy, and computational cost, and can treat modules separately, performing incremental analysis. In practice, this modularity allows detecting statically bugs in user programs even if they do not contain any assertions.

OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

Development of a Knowledge Base for smart screening of language disorders in primary care

Monitoring of neuro-evolutive development from birth until the age of six is a decisive factor in a child's quality of life. Early detection of development disorders in early childhood can facilitate necessary diagnosis and/or treatment. Primary-care pediatricians play a key role in early detection of development alterations as they can undertake the preventive and therapeutic actions necessary in the interest of a child's optimal development. The focus of this research paper is the construction of a Knowledge Base for smart screening aimed to assist pediatricians in processes of early referral in language disorders. The proposed model provides health professionals with a decision-making tool that supports referral processes. In this way, essential diagnostic and/or therapeutic actions are triggered for a comprehensive individual development. The resulting system was developed on the basis of an analysis and verification of 21 cases of children with language disorders.

Adding Usability Mechanisms into Agile Requirements: Tool Support with U-Kunagi

The growing interest for integrating agile methodologies and usability has brought various challenges to practitioners. This research focuses on a specific part of these challenges that is related to the integration of usability mechanisms (features such as cancel, undo, warning, etc.) into agile requirements, usually written in the form of user stories. For this aim, a framework has been developed, conformed first by a well-defined modeling language that aims to formalize previous empirical research in the field, models of the impact of usability mechanisms into user stories, and a tool to help practitioners applying them to user stories. Results show that the use of this framework helps agile developers to think about usability from the beginning of the development process, without needing to be an expert in the subject. Our proposal can therefore complement other usability practices to improve the quality of use of software developed using agile methodologies.

Deployment and validation of a smart system for screening of language disorders in primary care

Neuro-evolutive development from birth until the age of six years is a decisive factor in a child?s quality of life. Early detection of development disorders in early childhood can facilitate necessary diagnosis and/or treatment. Primary-care pediatricians play a key role in its detection as they can undertake the preventive and therapeutic actions requested to promote a child?s optimal development. However, the lack of time and little specific knowledge at primary-care avoid to applying continuous early-detection anomalies procedures. This research paper focuses on the deployment and evaluation of a smart system that enhances the screening of language disorders in primary care. Pediatricians get support to proceed with early referral of language disorders. The proposed model provides them with a decision-support tool for referral actions to trigger essential diagnostic and/or therapeutic actions for a comprehensive individual development. The research was conducted by starting from a sample of 60 cases of children with language disorders. Validation was carried out through two complementary steps: first, by including a team of seven experts from the fields of neonatology, pediatrics, neurology and language therapy, and, second, through the evaluation of 21 more previously diagnosed cases. The results obtained show that therapist positively accepted the system proposal in 18 cases (86%) and suggested system redesign for single referral to a speech therapist in three remaining cases.

A graphical tool for designing interactive video cognitive rehabilitation therapies

Acquired Brain Injury (ABI) has become one of the most common causes of neurological disability in developed countries. Cognitive disorders result in a loss of independence and therefore patients? quality of life. Cognitive rehabilitation aims to promote patients? skills to achieve their highest degree of personal autonomy. New technologies such as interactive video, whereby real situations of daily living are reproduced within a controlled virtual environment, enable the design of personalized therapies with a high level of generalization and a great ecological validity. This paper presents a graphical tool that allows neuropsychologists to design, modify, and configure interactive video therapeutic activities, through the combination of graphic and natural language. The tool has been validated creating several Activities of Daily Living and a preliminary usability evaluation has been performed showing a good clinical acceptance in the definition of complex interactive video therapies for cognitive rehabilitation.

MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

DCE@urLAB: a dynamic contrast-enhanced MRI pharmacokinetic analysis tool for preclinical data

Background DCE@urLAB is a software application for analysis of dynamic contrast-enhanced magnetic resonance imaging data (DCE-MRI). The tool incorporates a friendly graphical user interface (GUI) to interactively select and analyze a region of interest (ROI) within the image set, taking into account the tissue concentration of the contrast agent (CA) and its effect on pixel intensity. Results Pixel-wise model-based quantitative parameters are estimated by fitting DCE-MRI data to several pharmacokinetic models using the Levenberg-Marquardt algorithm (LMA). DCE@urLAB also includes the semi-quantitative parametric and heuristic analysis approaches commonly used in practice. This software application has been programmed in the Interactive Data Language (IDL) and tested both with publicly available simulated data and preclinical studies from tumor-bearing mouse brains. Conclusions A user-friendly solution for applying pharmacokinetic and non-quantitative analysis DCE-MRI in preclinical studies has been implemented and tested. The proposed tool has been specially designed for easy selection of multi-pixel ROIs. A public release of DCE@urLAB, together with the open source code and sample datasets, is available at http://www.die.upm.es/im/archives/DCEurLAB/ webcite.

The Role of Knowledge Modeling Techniques in Software Development: A General Approach Based on a Knowledge Management Tool

The aim of the paper is to discuss the use of knowledge models to formulate general applications. First, the paper presents the recent evolution of the software field where increasing attention is paid to conceptual modeling. Then, the current state of knowledge modeling techniques is described where increased reliability is available through the modern knowledge acquisition techniques and supporting tools. The KSM (Knowledge Structure Manager) tool is described next. First, the concept of knowledge area is introduced as a building block where methods to perform a collection of tasks are included together with the bodies of knowledge providing the basic methods to perform the basic tasks. Then, the CONCEL language to define vocabularies of domains and the LINK language for methods formulation are introduced. Finally, the object oriented implementation of a knowledge area is described and a general methodology for application design and maintenance supported by KSM is proposed. To illustrate the concepts and methods, an example of system for intelligent traffic management in a road network is described. This example is followed by a proposal of generalization for reuse of the resulting architecture. Finally, some concluding comments are proposed about the feasibility of using the knowledge modeling tools and methods for general application design.

Technology independent honeynet description language

Several languages have been proposed for the task of describing networks of systems, either to help on managing, simulate or deploy testbeds for testing purposes. However, there is no one specifically designed to describe the honeynets, covering the specific characteristics in terms of applications and tools included in the honeypot systems that make the honeynet. In this paper, the requirements of honeynet description are studied and a survey of existing description languages is presented, concluding that a CIM (Common Information Model) match the basic requirements. Thus, a CIM like technology independent honeynet description language (TIHDL) is proposed. The language is defined being independent of the platform where the honeynet will be deployed later, and it can be translated, either using model-driven techniques or other translation mechanisms, into the description languages of honeynet deployment platforms and tools. This approach gives flexibility to allow the use of a combination of heterogeneous deployment platforms. Besides, a flexible virtual honeynet generation tool (HoneyGen) based on the approach and description language proposed and capable of deploying honeynets over VNX (Virtual Networks over LinuX) and Honeyd platforms is presented for validation purposes.