Eloy Mata

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.

Generative Communication with Semantic Matching in Distributed Heterogeneous Environments

Different standard middleware proposals have emerged to provide computing models and communication among components in open distributed systems. Nowadays, Internet is becoming an increasingly relevant alternative to middleware platforms, due to the success of Web services in solving problems of application-to-application integration in distributed and highly heterogeneous environments. However, a coordination model is necessary to build open and flexible systems from active and independent distributed components. In this paper, we present a Web-enabled Coordination Service to orchestrate heterogeneous applications based on the Generative Communication model with semantic matching. Our aim is to use Internet as a real distributed computing platform, considering heterogeneous semantic interoperability.

Towards an Efficient Rule-Based Coordination of Web Services

Web services coordination has become a central topic for further development of Internet-based distributed computing. One approach to this coordination task is supported by generative communication, and more specifically by some implementations of the Linda model as JavaSpaces. However, when applying these coordination strategies to real projects, some drawbacks appear. One of the main limitations is the lack of transactional queries. In this paper we deal with this problem extending the matching mechanism of the Linda model. Then, a variant of the well-known RETE algorithm can be devised in order to implement our extended Linda model efficiently. This also opens new research lines in which Artificial Intelligence techniques (as advanced blackboard architectures) could be applied to the field of web services coordination.

Formal modelling of a coordination system: from practice to theory, and back again

In this work, we report an experience that illustrates the interplay between formal methods and real software development. Starting from aWeb-enable Coordination Service (WCS) based on JavaSpaces technology which had been successfully used in an industrial project, we built a formal model for the system in order to study its properties; specifically, our aim was to prove that Linda semantics was preserved in several layers of complex mappings from XML documents to Java objects. Once this objective was achieved (at least in a simplified, idealistic version), we observed several possibilities of extending the coordination system at the model level. In particular, we identified that it was possible to enhance the formal model with transactional capabilities, taking advantage of the similarity of our model to rule-based systems. At present, we are working on the translation of this theoretical result to practice, in order to improve our Web Coordination Service.

Antibiogramj: A tool for analysing images from disk diffusion tests

BACKGROUND AND OBJECTIVES Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow. METHODS Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation. RESULTS We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result. CONCLUSIONS AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory.

DecoFungi: a web application for automatic characterisation of dye decolorisation in fungal strains

BackgroundFungi have diverse biotechnological applications in, among others, agriculture, bioenergy generation, or remediation of polluted soil and water. In this context, culture media based on color change in response to degradation of dyes are particularly relevant; but measuring dye decolorisation of fungal strains mainly relies on a visual and semiquantitative classification of color intensity changes. Such a classification is a subjective, time-consuming and difficult to reproduce process.ResultsDecoFungi is the first, at least up to the best of our knowledge, application to automatically characterise dye decolorisation level of fungal strains from images of inoculated plates. In order to deal with this task, DecoFungi employs a deep-learning model, accessible through a user-friendly web interface, with an accuracy of 96.5%.ConclusionsDecoFungi is an easy to use system for characterising dye decolorisation level of fungal strains from images of inoculated plates.

DetectionEvaluationJ: A Tool to Evaluate Object Detection Algorithms

Object detection is an area of computer vision with applications in several contexts such as biomedicine and security; and it is currently growing thanks to the availability of datasets of images, and the use of deep learning techniques. In order to apply object detection algorithms is instrumental to know the quality of the regions detected by them; however, such an evaluation is usually performed using ad-hoc tools for each concrete problem; and, up to the best of our knowledge, it does not exist a simple and generic tool to conduct this task. In this paper, we present DetectionEvaluationJ an open-source tool that has been designed to evaluate the goodness of object detection algorithms in any context and using several metrics. This tool is independent from the programming language employed to implement the detection algorithms and also from the concrete problem where such algorithms are applied.

Extending GelJ for interoperability

BACKGROUND AND OBJECTIVE The manual transformation of DNA fingerprints of dominant markers into the input of tools for population genetics analysis is a time-consuming and error-prone task; especially when the researcher deals with a large number of samples. In addition, when the researcher needs to use several tools for population genetics analysis, the situation worsens due to the incompatibility of data-formats across tools. The goal of this work consists in automating, from banding patterns of gel images, the input-generation for the great diversity of tools devoted to population genetics analysis. METHODS After a thorough analysis of tools for population genetics analysis with dominant markers, and tools for working with phylogenetic trees; we have detected the input requirements of those systems. In the case of programs devoted to phylogenetic trees, the Newick and Nexus formats are widely employed; whereas, each population genetics analysis tool uses its own specific format. In order to handle such a diversity of formats in the latter case, we have developed a new XML format, called PopXML, that takes into account the variety of information required by each population genetics analysis tool. Moreover, the acquired knowledge has been incorporated into the pipeline of the GelJ system - a tool for analysing DNA fingerprint gel images - to reach our automatisation goal. RESULTS We have implemented, in the GelJ system, a pipeline that automatically generates, from gel banding patterns, the input of tools for population genetics analysis and phylogenetic trees. Such a pipeline has been employed to successfully generate, from thousands of banding patterns, the input of 29 population genetics analysis tools and 32 tools for managing phylogenetic trees. CONCLUSIONS GelJ has become the first tool that fills the gap between gel image processing software and population genetics analysis with dominant markers, phylogenetic reconstruction, and tree editing software. This has been achieved by automating the process of generating the input for the latter software from gel banding patterns processed by GelJ.

WekaBioSimilarity—Extending Weka with Resemblance Measures

The classification of organisms is a daily-basis task in biology as well as other contexts. This process is usually carried out by comparing a set of descriptors associated with each object. However, general-purpose statistical packages offer a limited number of methods to perform such a comparison, and specific tools are required for each concrete problem. Weka is a freely-available framework that supports both supervised and unsupervised machine-learning algorithms. Here, we present WekaBioSimilarity, an extension of Weka implementing several resemblance measures to compare different kinds of descriptors. Namely, WekaBioSimilarity works with binary, multi-value, string, numerical, and heterogeneous data. WekaBioSimilarity, together with Weka, offers the functionality to classify objects using different resemblance measures, and clustering and classification algorithms. The combination of these two systems can be used as a standalone application or can be incorporated in the workflow of other software systems that require a classification process. WekaBioSimilarity is available at http://wekabiosimilarity.sourceforge.net.

Formal reasoning on a web coordination system

In this paper, a first step toward the use of Artificial Intelligence tools (namely proof assistants) in the formal analysis of programs for Web services coordination is presented. This first attempt consists in the formal modeling of a system with transactional capabilities. The model is devised on a variant of the well-known Linda model for generative communication. We explore then the role of the Rete algorithm to implement efficiently a transactional read operation, opening the way for a further formal analysis of it, by means of automated testing against a certified program (i.e. a program verified with the help of a proof assistant).