César Domínguez

GelJ – a tool for analyzing DNA fingerprint gel images

BackgroundDNA fingerprinting is a technique for comparing DNA patterns that has applications in a wide variety of contexts. Several commercial and freely-available tools can be used to analyze DNA fingerprint gel images; however, commercial tools are expensive and usually difficult to use; and, free tools support the basic functionality for DNA fingerprint analysis, but lack some instrumental features to obtain accurate results.ResultsIn this paper, we present GelJ, a feather-weight, user-friendly, platform-independent, open-source and free tool for analyzing DNA fingerprint gel images. Some of the outstanding features of GelJ are mechanisms for accurate lane- and band-detection, several options for computing migration models, a number of band- and curve-based similarity methods, different techniques for generating dendrograms, comparison of banding patterns from different experiments, and database support.ConclusionsGelJ is an easy to use tool for analyzing DNA fingerprint gel images. It combines the best characteristics of both free and commercial tools: GelJ is light and simple to use (as free programs), but it also includes the necessary features to obtain precise results (as commercial programs). In addition, GelJ incorporates new functionality that is not supported by any other tool.

Database design learning: A project-based approach organized through a course management system

This paper describes an active method for database design learning through practical tasks development by student teams in a face-to-face course. This method integrates project-based learning, and project management techniques and tools. Some scaffolding is provided at the beginning that forms a skeleton that adapts to a great variety of student-proposed domain projects and emulates the real way of working in database design. We include a quasi-experimental study in which the results of five academic years are analyzed. The first three years a traditional strategy was followed and a course management system was used as material repository. The active method was introduced for the last two years and coexisted with the traditional one. The course management system greatly simplifies the management of the numerous documents produced, the description and scheduling of tasks, the identification of teams, as well as all communication needs. In this study we analyze aspects such as exam dropout rates, exam passing rates, exam marks, and class attendance. Students that followed this active learning approach obtained better results than those that followed a traditional strategy. Besides, the experience of the introduction of such a method in a student subgroup positively influenced the whole group.

Object oriented institutions to specify symbolic computation systems

The specification of the data structures used in EAT, a software system for symbolic computation in algebraic topology, is based on an operation that defines a link among different specification frameworks like hidden algebras and coalgebras. In this paper, this operation is extended using the notion of institution, giving rise to three institution encodings. These morphisms define a commutative diagram which shows three possible views of the same construction, placing it in an equational algebraic institution, in a hidden institution or in a coalgebraic institution. Moreover, these morphisms can be used to obtain a new description of the final objects of the categories of algebras in these frameworks, which are suitable abstract models for the EAT data structures. Thus, our main contribution is a formalization allowing us to encode a family of data structures by means of a single algebra (which can be described as a coproduct on the image of the institution morphisms). With this aim, new particular definitions of hidden and, coalgebraic institutions are presented.

Diagrammatic logic applied to a parameterisation process

This paper provides an abstract definition of a class of logics, called diagrammatic logics, together with a definition of morphisms and 2-morphisms between them. The definition of the 2-category of diagrammatic logics relies on category theory, mainly on adjunction, categories of fractions and limit sketches. This framework is applied to the formalisation of a parameterisation process. This process, which consists of adding a formal parameter to some operations in a given specification, is presented as a morphism of logics. Then the parameter passing process for recovering a model of the given specification from a model of the parameterised specification and an actual parameter is shown to be a 2-morphism of logics.

Effective homology of bicomplexes, formalized in Coq

In this paper, we present a complete formalization in the Coq theorem prover of an important algorithm in computational algebra, namely the calculation of the effective homology of a bicomplex. As a necessary tool, we encode a hierarchy of algebraic structures in constructive type theory, including graded and infinite data structures. The experience shows how some limitations of the Coq proof assistant to deal with this kind of algebraic data can be overcome by applying a separation of concerns principle; more concretely, we propose to distinguish in the representation of an algebraic structure (such as a group or a module) a behavioural part, containing operation signatures and axioms, and a structural part determining if the algebraic data is free, of finite type and so on.

Hidden Specification of a Functional System

This paper is devoted to the formal study of the data structures appearing in a symbolic computation system, namely the EAT system. One of the main features of the EAT system is that it intensively uses functional programming techniques. This implies that some formalisms for the algebraic specification of systems must be adapted to this functional setting. Specifically, this work deals with hidden and coalgebraic methodologies through an institutional framework. As a byproduct, the new concept of coalgebraic institution associated to an institution is introduced. Then, the problem of modeling functorial relationships between data structures is tackled, giving a hidden specification for this aspect of the EAT system and proving the existence of final objects in convenient categories, which accurately model the EAT way of working.

Modeling inheritance as coercion in a symbolic computation system

In this paper the analysis of the data structures used in a symbolic computation system, called Kenzo, is undertaken. We deal with the specification of the inheritance relationship since Kenzo is an object-oriented system, written in CLOS, the Common Lisp Object System. We focus on a particular case, namely the relationship between simplicial sets and chain complexes, showing how the order-sorted algebraic specifications formalisms can be adapted, through the “inheritance as coercion” metaphor, in order to model this Kenzo fragment.

Interuniversity telecollaboration to improve academic results and identify preferred communication tools

Telecollaboration is defined as a collaborative activity that involves people from distant geographic locations working together through Internet tools and other resources. This technique has not been frequently used in learning experiences and has produced diverse academic results, as well as degrees of satisfaction. This paper describes a telecollaboration experience among students at two universities. We analyzed data from 255 students divided into different groups in order to compare their academic results and satisfaction derived from the experience. We also studied the communication tools used by the telecollaborators and their effect on with student satisfaction. The telecollaborators obtained better academic results but lower levels of satisfaction than the face-to-face groups. Furthermore, the students preferred day-to-day tools, and the use of non-institutional email was the most popular option. Social networks and chat and voice tools also proved to be useful. And, those who employed synchronous tools were more satisfied with the experience.

Computing in coq with infinite algebraic data structures

Computational content encoded into constructive type theory proofs can be used to make computing experiments over concrete data structures. In this paper, we explore this possibility when working in Coq with chain complexes of infinite type (that is to say, generated by infinite sets) as a part of the formalization of a hierarchy of homological algebra structures.

Formalizing in Coq Hidden Algebras to Specify Symbolic Computation Systems

This work is an attempt to formalize, using the Coq proof assistant, the algebraic specification of the data structures appearing in two symbolic computation systems for algebraic topology called EAT and Kenzo. The specification of these structures have been obtained through an operation, called impoperation, between different specification frameworks as standard algebraic specifications and hidden specifications. Reusing previous Coq implementations of universal algebra and category theory we have proposed a Coq formalization of the impoperation, extending the representation to the particular hidden algebras which take part in this operation.