Evaluation of properties over phylogenetic trees using stochastic logics

Background: Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. Results: In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. Conclusions: We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our approach

Quantitative Analysis of Apache Storm Applications: The NewsAsset Case Study

The development of Information Systems today faces the era of Big Data. Large volumes of information need to be processed in real-time, for example, for Facebook or Twitter analysis. This paper addresses the redesign of NewsAsset, a commercial product that helps journalists by providing services, which analyzes millions of media items from the social network in real-time. Technologies like Apache Storm can help enormously in this context. We have quantitatively analyzed the new design of NewsAsset to assess whether the introduction of Apache Storm can meet the demanding performance requirements of this media product. Our assessment approach, guided by the Unified Modeling Language (UML), takes advantage, for performance analysis, of the software designs already used for development. In addition, we converted UML into a domain-specific modeling language (DSML) for Apache Storm, thus creating a profile for Storm. Later, we transformed said DSML into an appropriate language for performance evaluation, specifically, stochastic Petri nets. The assessment ended with a successful software design that certainly met the scalability requirements of NewsAsset

A UML Profile for the Design, Quality Assessment and Deployment of Data-intensive Applications

Big Data or Data-Intensive applications (DIAs) seek to mine, manipulate, extract or otherwise exploit the potential intelligence hidden behind Big Data. However, several practitioner surveys remark that DIAs potential is still untapped because of very difficult and costly design, quality assessment and continuous refinement. To address the above shortcoming, we propose the use of a UML domain-specific modeling language or profile specifically tailored to support the design, assessment and continuous deployment of DIAs. This article illustrates our DIA-specific profile and outlines its usage in the context of DIA performance engineering and deployment. For DIA performance engineering, we rely on the Apache Hadoop technology, while for DIA deployment, we leverage the TOSCA language. We conclude that the proposed profile offers a powerful language for data-intensive software and systems modeling, quality evaluation and automated deployment of DIAs on private or public clouds

Deficiencia de vitamina B12 en diabéticos tipo 2 tratados con metformina

Sr. Director: La metformina es uno de los tratamientos hipoglucemiantes más utilizados entre los diabéticos tipo 2. Son conocidos sus efectos secundarios gastrointestinales, causa no despreciable de abandono del tratamiento, pero es menos considerada su relación con la deficiencia de vitamina B12(vit. B12). La evaluación del fármaco (DrugDex) valora la incidencia de deficiencia de vit. B12 en el 7%. Parece que el riesgo de deficiencia aumenta en los pacientes que reciben dosis más altas de metformina y con tratamientos de mayor duración. Algo confirmado en un reciente ensayo clínico aleatorizado multicéntrico con diabéticos tipo 2 dependientes de insulina aleatorizados a recibir 850 mg de metformina o placebo tres veces al día durante 4,3 años..