Gregorio de Miguel Casado

Temporal logics for phylogenetic analysis via model checking

The need for general-purpose algorithms for the study of biological properties in phylogenetics motivates the research in formal verification frameworks so that researchers can focus their efforts exclusively on evolution modelling and property specification. To this end, model checking, a mature automated verification technique from computer science, is proposed for phylogenetic analysis. Three cornerstones found our approach: modelling evolution dynamics with transition systems; specifying phylogenetic properties using temporal logic formulae; and verifying the latter by means of automated computer tools. As prominent advantages stemming of studying phylogenetic properties with this approach, different models of evolution can be considered, complex properties can be specified as the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new ones can be undertaken by exploiting the verification results.

Management of social networks in the educational process

Social networks are complementary to educational websites to reach all aspects of learning.Disclosure through social networks is faster and wider than through educational websites.Community Manager in educational context is proved to be useful. The research developed in this work consists in proposing a set of techniques for management of social networks and their integration into the educational process. The proposals made are based on assumptions that have been proven with simple examples in a real scenario of university teaching.The results show that social networks have more capacity to spread information than educational web platforms. Moreover, educational social networks are developed in a context of freedom of expression intrinsically linked to Internet freedom. In that context, users can write opinions or comments which are not liked by the staff of schools. However, this feature can be exploited to enrich the educational process and improve the quality of their achievement.The network has covered needs and created new ones. So, the figure of the Community Manager is proposed as agent in educational context for monitoring network and aims to channel the opinions and to provide a rapid response to an academic problem.

Phylogenetic Analysis Using an SMV Tool

The need for general methods to verify biological properties in phylogenetics motivates research in formal frameworks so that biologists can focus their efforts exclusively in evolution modeling and property specification. Model checking is proposed to this end. Three pillars found this approach: modeling evolution dynamics as transition systems; specifying phylogenetic properties using temporal logic formulae; and verifying the former by means of automated computer tools. As prominent advantages for studying biological properties under our approach, different models of evolution can be considered, complex properties can be specified as the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new ones can be undertaken by exploiting the results of verification. Preliminary experimental results using the Cadence Symbolic Model Verifier support the feasibility of the methodology.

Temporal Logics for Phylogenetic Analysis via Model Checking

The need for general-purpose algorithms for studying biological properties in phylogenetics motivates research into formal verification frameworks. Researchers can focus their efforts exclusively on evolution trees and property specifications. To this end, model checking, a mature automated verification technique originating in computer science, is applied to phylogenetic analysis. Our approach is based on three cornerstones: a logical modeling of the evolution with transition systems; the specification of both phylogenetic properties and trees using flexible temporal logic formulas; and the verification of the latter by means of automated computer tools. The most conspicuous result is the inception of a formal framework which allows for a symbolic manipulation of biological data (based on the codification of the taxa). Additionally, different logical models of evolution can be considered, complex properties can be specified in terms of the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new properties can be undertaken by exploiting the verification results. Some experimental results using a symbolic model verifier support the feasibility of the approach.

Calculation scheme based on a weighted primitive: application to image processing transforms

This paper presents a method to improve the calculation of functions which specially demand a great amount of computing resources. The method is based on the choice of a weighted primitive which enables the calculation of function values under the scope of a recursive operation. When tackling the design level, the method shows suitable for developing a processor which achieves a satisfying trade-off between time delay, area costs, and stability. The method is particularly suitable for the mathematical transforms used in signal processing applications. A generic calculation scheme is developed for the discrete fast Fourier transform (DFT) and then applied to other integral transforms such as the discrete Hartley transform (DHT), the discrete cosine transform (DCT), and the discrete sine transform (DST). Some comparisons with other well-known proposals are also provided.This paper presents a method to improve the calculation of functions which specially demand a great amount of computing resources. The method is based on the choice of a weighted primitive which enables the calculation of function values under the scope of a recursive operation. When tackling the design level, the method shows suitable for developing a processor which achieves a satisfying trade-off between time delay, area costs, and stability. The method is particularly suitable for the mathematical transforms used in signal processing applications. A generic calculation scheme is developed for the discrete fast Fourier transform (DFT) and then applied to other integral transforms such as the discrete Hartley transform (DHT), the discrete cosine transform (DCT), and the discrete sine transform (DST). Some comparisons with other well-known proposals are also provided.

Sliced Model Checking for Phylogenetic Analysis

Model checking provides a powerful and flexible formal framework to state and verify biological properties on phylogenies. However, current model checking techniques fail to scale up the big amount of biological information relevant to each state of the system. This fact motivates the development of novel cooperative algorithms and slicing techniques that distribute not the graph structure of a phylogenetic system but the state information contained in its nodes.

PhyloFlow: A fully customizable and automatic workflow for phylogenetic reconstruction

Most phylogeny estimation systems such as SATe2 or DACTAL use fixed configurations and tools that make them suitable only for solving specific problems. Out of that scope, a hand-made combination of individual tools and methods has to be composed in order to get the desired phylogeny estimation. PhyloFlow is a new framework based on a workflow extendable to a wide range of tasks in phylogenetic analysis. This system is specially intended to build large phylogenies, where most of the methods do not provide a solution at all or the computing time required is not affordable. The workflow can scale to different phylogenetic estimation problems, the methods and stages already included can be fully customizable and once the user has set up the system, it will run automatically until the phylogenetic tree is completely estimated. With the current version we have recreated two different phy-logenetic systems: DACTAL and a study case for the human mitochondrial DNA. The first one displays the capabilities of our framework to reproduce the existing systems, in addition with the properties that a parallel system can provide. The second one shows the possibilities of building a real case workflow to estimate a phylogenetic tree for more than 23000 sequences of human mitochondrial DNA (16569 bp on average) applying biological knowledge to the process. Both workflows have been run sequentially and in parallel in a HTC cluster (HTCCondor and DAGMan). PhyloFlow source code, the datasets and the workflow configurations are available by request to the first author.

Algebraic Model of an Arithmetic Unit for TTE-Computable Normalized Rational Numbers

A formal specification of an arithmetic unit for computable normalized rational numbers is proposed. This specification, developed under the scope of the paradigm known as algebraic models of processors, exploits the connection between the signed digit representation for rational numbers in Type-2 Theory of Effectivity and online arithmetic in Computer Arithmetic. The proposal aims for specification formalization and calculation reliability together with implementation feasibility.

Parametric architecture for function calculation improvement

This paper presents a new approach to the problem caused by the exploding needs of computing resources in function calculation. The proposal argues for increasing the computing power at the primitive processing level in order to reduce the number of computing levels required to carry out the calculations. This trade-off is developed within the limits of function evaluation by substituting the usual primitives, namely sum and multiplication, by a unique weighted primitive that can be tuned for different values of the weighting parameters. All function points are carried out by successive iterations of the primitive. A parametric architecture implements the design. The case of combined trigonometric functions involved in the calculation of the Hough transform (HT) is analyzed under this scope. It provides memory and hard-ware resource saving as well as speed improvements, according to the experiments carried out with the HT.

The role of algebraic models and type-2 theory of effectivity in special purpose processor design

A theoretical approach to a novel design method for special purpose processors for computable integral transforms and related operations is presented. The method is based on algebraic processor models and Type-2 Theory of Effectivity and aims for specification formalization and calculation reliability together with implementation feasibility. The convolution operation is presented as a case of study.