Oscar Pastor López

Real-time deformable models for surgery simulation: a survey

Simulating the behaviour of elastic objects in real time is one of the current objectives of computer graphics. One of its fields of application lies in virtual reality, mainly in surgery simulation systems. In computer graphics, the models used for the construction of objects with deformable behaviour are known as deformable models. These have two conflicting characteristics: interactivity and motion realism. The different deformable models developed to date have promoted only one of these (usually interactivity) to the detriment of the other (biomechanical realism). In this paper, we present a classification of the different deformable models that have been developed. We present the advantages and disadvantages of each one. Finally, we make a comparison of deformable models and perform an evaluation of the state of the art and the future of deformable models.

Oasis: An object-oriented specification language

This paper introduces Oasis, a language for specifying object-oriented information systems using a deductive (temporal) approach ([3]). Oasis extends first versions of OBLOG ([17]) and MOL([12]), a trace based specification languages, with: 1. triggered relationships which enable specification of active objects 2. supporting rapid prototyping by generating the First Order Theory formally equivalent to a specification. 3. introducing class operators within an algebraic formal environment to deal with object reification.

Including Functional Usability Features in a Model-Driven Development Method

The Software Engineering (SE) community has historically focused on working with models to represent functionality and persistence, pushing interaction modelling into the background, which has been covered by the Human Computer Interaction (HCI) community. Recently, adequately modelling interaction, and specifically usability, is being considered as a key factor for success in user acceptance, making the integration of the SE and HCI communities more necessary. If we focus on the Model-Driven Development (MDD) paradigm, we notice that there is a lack of proposals to deal with usability features from the very first steps of software development process. In general, usability features are manually implemented once the code has been generated from models. This contradicts the MDD paradigm, which claims that all the analysts’ effort must be focused on building models, and the code generation is relegated to model to code transformations. Moreover, usability features related to functionality may involve important changes in the system architecture if they are not considered from the early steps. We state that these usability features related to functionality can be represented abstractly in a conceptual model, and their implementation can be carried out automatically.

Applying the Principles of an Ontology-Based Approach to a Conceptual Schema of Human Genome

Understanding the Human Genome is currently a significant challenge. Having a Conceptual Schema of Human Genome CSHG is in this context a first step to link a sound Information Systems Design approach with Bioinformatics. But this is not enough. The use of an adequate ontological commitment is essential to fix the real-world semantics of the analyzed domain. Starting from a concrete proposal for CSHG, the main goal of this paper is to apply the principles of a foundational ontology, as it is UFO, to make explicit the ontological commitments underlying the concepts represented in the Conceptual Schema. As demonstrated in the paper, this ontological analysis is also able to highlight some conceptual drawbacks present in the initial version of the CSHG.

Use of GeIS for Early Diagnosis of Alcohol Sensitivity

This study focuses on the importance of Genomic Information Systems (GeIS) today; the results of this research provide great benefits to the medical community through technological potential. The development of SILE (Search-Identification-Load-Exploitation) to GeIS improves the databases management with curated data. The studies are focused on improving the quality of data and time optimization. With SILE we perform a selective loading of genes and variations found for a specific disease from different data sources like: NCBI, dbSNP and others. When we worked with a selected group of genes/variations it is possible guaranteeing a more reliable diagnosis, thus sustaining the increase accuracy of the results with respect to data quality and improvements over time. Also, we integrate the association of genes/variations with population studies, for this way providing an early diagnosis for any disease of genetic origin.

Software Engineering and Genomics: The Two Sides of the Same Coin?

Programs are historically the basic notion in Software Engineering (SE) that represent the final artefact to be executed in a machine. These programs have been created by humans, using a silicon-based code, whose final components use a binary code represented by 0s and 1s. If we look at life as a program with a DNAbased genetic code and a final representation that uses four essential units (A, C, G and T), one challenging question emerges. Can we establish a correspondence between life -from a genomic perspectiveand programs -from a Software Engineering perspective-? This paper assumes a positive answer to this question and goes further into this mapping by proposing how conceptual models (CM) are not only required to understand life but to manage the huge amount of data generated in the genomic domain day after day. The main contributions focus on i) showing how to design such a Conceptual Model of the Human Genome (CMHG), analysing how it evolves as knowledge accumulates on the domain, and ii) how these ideas can be applied in an advanced, genome-based, precision medicine, under the assumption that this medicine will only reach our health systems if these sound SE practices are properly applied in the genomic domain.

GenDomus: Interactive and Collaboration Mechanisms for Diagnosing Genetic Diseases.

Considering the impact of Next Generation Sequence (NGS) technologies into the genetic field, the data analysis of huge amounts of sequenced DNA to transform it into knowledge has become a challenge. Within the diagnosis of genetic diseases, the data analysis is still a manual procedure where human cognitive endeavour and active collaboration of several stakeholders is required. Web technologies have been widely used to improve the collaboration between different devices. We present GenDomus, a web solution based on an underlying conceptual model that incorporates advanced interactions mechanisms and collaborative and cognitive aspects in order to support scientists in the diagnosis of genetic diseases. The relevant contribution is to describe the design guidelines and advances in the implementation of such a solution. The cognitive analysis perspective together with the collaborative environment in the complex context of the genome analysis domain conforms an attractive combination where web technologies can provide advanced efficient platforms to improve the genetic diagnosis.

An integration architecture framework for e-genomics services

Next Generation Sequencing (NGS) technologies are becoming a commodity and, thus, genomic services delivered on line (e-genomics) is a growing market. This has led to the development of a plethora of tools traditionally covering only a small set of features of the process, though its true than recently more complete tools have arisen. In such a scenario, integration between tools from different precedence becomes key to market evolution and consolidation. This paper proposes a service oriented framework factoring of the core services required to support NGS applications by identifying these services. This conforms a sound basis to provide a toolkit and a reference implementation, whose details are introduced in the work.

Diagen: A Model-Driven Framework for Integrating Bioinformatic Tools

Nowadays, the diagnosis of disease based on genomic information is feasible by searching genetic variations on DNA sequences. However, geneticists struggle with bioinformatic tools that are supposed to simplify DNA sequence analysis. As a universal tool to support every requirement is far from be implemented, geneticists themselves must solve the data exchange among several tools. Due to the fact that there are no standards to support this integration task, it must be managed in every analysis. This paper addresses this integration by means of a model-driven framework. The Diagen framework is a software implementation based on conceptual modeling principles that formalizes data exchange and simplifies bioinformatic tool integration. First, we analyze how conceptual modeling can be used to deal with data exchange among tools. Then, the presented framework is used to search for variations on the BRCA2 gene using real DNA samples and a set of specific bioinformatic tools.

GeRTiSS: a generic multi-model surgery simulator

The construction of surgery simulators will be a key tool in the development and diffusion of minimally invasive surgery. Nowadays, most simulators are oriented to training surgeons in only one surgery technique. Most of them only permit the modelling of tissues with only one kind of deformable model. In this paper, we present our generic surgery simulator for minimally invasive surgery. In this surgery simulator, surgeons can construct any surgery scenario that they want to practice. Our surgery simulator permits the surgeons to select the deformable model that best adjusts to the biomechanical properties of each organ. Once the surgeon has finished the training, our surgery simulator can generate a report that contains an assessment evaluation of that training.