Vico Pascual

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.

An Object-oriented Interpretation of the EAT System

Abstract.In a previous paper we characterized, in the Category Theory setting, a class of implementations of Abstract Data Types, which has been suggested by the way of programming in the EAT system. (EAT, Effective Algebraic Topology, is one of Sergeraert’s systems for effective homology and homotopy computation.) This characterization was established using classical tools, in an unrelated way to the current mainstream topics in the field of Algebraic Specifications. Looking for a connection with these topics, we have found, rather unexpectedly, that our approach is related to some object-oriented formalisms, namely hidden specifications and the coalgebraic view. In this paper, we explore these relations making explicit the implicit object-oriented features of the EAT system and generalizing the data structure analysis we had previously done.

fKenzo: A user interface for computations in Algebraic Topology

a b s t r a c t fKenzo (= f riendly Kenzo) is a graphical user interface providing a user-friendly front-end for the Kenzo system, a Common Lisp pro- gram devoted to Algebraic Topology. The fKenzo system provides the user interface itself, an XML intermediary generator-translator and, finally the Kenzo kernel. We describe in this paper the main points of fKenzo, and we explain also the advantages and limita- tions of fKenzo with respect to Kenzo itself. The text is separated into two parts, trying to cover both the user and the developer perspectives.

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.

Proving with ACL2 the correctness of simplicial sets in the kenzo system

Kenzo is a Common Lisp system devoted to Algebraic Topology. Although Kenzo uses higher-order functional programming intensively, we show in this paper how the theorem prover ACL2 can be used to prove the correctness of first order fragments of Kenzo. More concretely, we report on the verification in ACL2 of the implementation of simplicial sets. By means of a generic instantiation mechanism, we achieve the reduction of the proving effort for each family of simplicial sets, letting ACL2 automate the routine parts of the proofs.

Mediated Access to Symbolic Computation Systems

Kenzo is a symbolic computation system devoted to Algebraic Topology. It has been developed by F. Sergeraert mainly as a research tool. The challenge is now to increase the number of users and to improve its usability. Instead of designing simply a friendly front-end, we have undertaken the task of devising a mediatedaccess to the system, constraining its functionality, but providing guidance to the user in his navigation on the system. This objective is reached by constructing an intermediary layer, allowing us an intelligentaccess to some features of the system. This intermediary layer is supported by XML technology and interplays between a graphical user interface and the pureCommon Lisp Kenzo system.

Using Open Mathematical Documents to Interface Computer Algebra and Proof Assistant Systems

Mathematical Knowledge can be encoded by means of Open Mathematical Documents (OMDoc) to interface both Computer Algebra and Proof Assistant systems. In this paper, we show how a unique OMDoc structure can be used to dynamically generate, both a Graphical User Interface for a Computer Algebra system and a script for a Proof Assistant. So, the OMDoc format can be used for representing different aspects. This generic approach has been made concrete through a first prototype interfacing the Kenzo Computer Algebra system and the ACL2 Theorem Prover, both based on the Common Lisp programming language. An OMDoc repository has been developed allowing the user to customize the application in an easy way.

A certified module to study digital images with the kenzo system

Kenzo is a Computer Algebra system devoted to Algebraic Topology, written in the Common Lisp programming language. In this paper, programs which allow us to analyze monochromatic digital images with the Kenzo system are presented. Besides a complete automated proof of the correctness of our programs is provided. The proof is carried out using ACL2, a system for proving properties of programs written in (a subset of) Common Lisp.

Integrating multiple sources to answer questions in algebraic topology

We present in this paper an evolution of a tool from a user interface for a concrete Computer Algebra system for Algebraic Topology (the Kenzo system), to a front-end allowing the interoperability among different sources for computation and deduction. The architecture allows the system not only to interface several systems, but also to make them cooperate in shared calculations.

Remote access to a symbolic computation system for algebraic topology: a client-server approach

Kenzo is a Symbolic Computation system created by Sergeraert for computing in Algebraic Topology. It is programmed in Common Lisp and this programming language also acts as user interface. In this paper, a prototype to provide remote access for Kenzo is presented. This has been accomplished by using Corba technology: clients have been developed both in Java and Common Lisp (the server is always in Common Lisp, being a wrapper of the original Kenzo program). Instead of using one CORBA IDL to encode each data structure, our approach incorporates a generic way of transfering every data structure through XML strings; specifically, by means of an XML extension of MathML. This research should be understood as a first step towards building a distributed computation system for Algebraic Topology.