The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets

A Comparative Look at Plea Bargaining in Australia, Canada, England, New Zealand, and the United States

In a world where the vast majority of criminal cases are resolved through some means other than the popularly depicted criminal trial, it is fundamental to a comprehensive understanding of comparative criminal procedure to study and appreciate the different mechanisms for criminal case resolution in different nations. This Article developed through a series of conversations (and ultimately a panel discussion) between six international criminal justice professionals - practicing attorneys, scholars, and judges - regarding the nature and effects of plea bargaining (and its comparative substitutes) in their respective countries. Providing a comparative look at different mechanisms for criminal case resolution, this Article examines the applicable practices and procedures in the common law nations of Australia, Canada, England, New Zealand, and the United States

A Comparative Examination of Police Interrogation of Criminal Suspects in Australia, Canada, England and Wales, New Zealand, and the United States

The interrogation process is central to the investigation and resolution of criminal matters throughout the world. It is fundamental to a comprehensive understanding of comparative criminal procedure to study and appreciate the different approaches to the interrogation process in different nations. This Article developed through a series of conversations between six international criminal justice professionals— practicing attorneys, scholars, and judges—regarding the interrogation practices and rules in their respective countries. Providing a comparative look at this important area, this Article examines the applicable practices and procedures in the common law nations of Australia, Canada, England and Wales, New Zealand, and the United States

Assistance tactile à la localisation de cibles périphériques pour des personnes à vision tubulaire

International audienceLa vision tubulaire est une déficience visuelle dans laquelle seul le champ central de la vision est préservé. Elle génère de grandes difficultés dans la vie quotidienne, notamment lorsqu’il s’agit de repérer un objet d’intérêt dans l’environnement. Des informations tactiles, considérées comme discrètes, personnelles et peu invasives, peuvent permettre d’améliorer le comportement de recherche visuelle. Dans cette étude, nous avons conçu quatre techniques tactiles permettant de localiser un point spécifique dans l’espace. Les stimulations tactiles étaient soit un seul stimulus soit un train de stimuli transmis dans un système de coordonnées cartésien ou polaire. Les quatre techniques ont été comparées dans une tâche d’orientation de la tête. La plus efficace des techniques a été évaluée avec une tâche de recherche visuelle dans un environnement virtuel complexe. L’évaluation impliquait dix sujets avec un champ visuel artificiellement restreint à 10°, et un sujet avec une vision tubulaire due à un glaucome. Notre dispositif d’assistance a significativement amélioré l’efficacité de la recherche visuelle d’un facteur trois. Le dispositif pourrait être facilement intégré dans des lunettes intelligentes et détecter des cibles d’intérêt, soit sur demande, soit de façon automatique (par ex. les obstacles potentiels), facilitant ainsi, la recherche visuelle et la perception spatiale de l’environnement

Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs

In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing (direct RNA seq.) experiment using critical oropharyngeal swab samples collected from Italian pa-tients infected with SARS-CoV-2 from the Palermo region in Sicily. Here, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retrotranscription. Using an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapsid (N) gene, which have been reported previously in studies conducted in other countries. In conclusion, to the best of our knowledge, the technique used in this study has not been used for SARS-CoV-2 detection previously owing to the difficulties in the extraction of RNA of sufficient quantity and quality from routine oropharyngeal swabs. Despite these limitations, this approach provides the advantages of true native RNA sequencing and does not include amplification steps that could introduce systematic errors. This study can provide novel information relevant to the current strategies adopted in SARS-CoV-2 next-generation sequencing

BITS2019: The sixteenth annual meeting of the Italian society of bioinformatics

The 16th Annual Meeting of the Bioinformatics Italian Society was held in Palermo, Italy, on June 26-28, 2019. More than 80 scientific contributions were presented, including 4 keynote lectures, 31 oral communications and 49 posters. Also, three workshops were organised before and during the meeting. Full papers from some of the works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting

A new SOM Initialization Algorithm for Nonvectorial Data

Self Organizing Maps (SOMs) are widely used mapping and clustering algorithms family. It is also well known that the performances of the maps in terms of quality of result and learning speed are strongly dependent from the neuron weights initialization. This drawback is common to all the SOM algorithms, and critical for a new SOM algorithm, the Median SOM (M-SOM), developed in order to map datasets characterized by a dissimilarity matrix. In this paper an initialization technique of M-SOM is proposed and compared to the initialization techniques proposed in the original paper. The results show that the proposed initialization technique assures faster learning and better performance in terms of quantization error

Knowledge organization for modelling workflows in Taverna environment

Today Workflow Management Systems (WFMS), like Taverna and Kepler, have a very important place in the everyday work of the scientist. These tools support the access to computational resources and act as interface for building complex data processing chains. The next step is to support decisions of the researcher on autonomously developing workflow parts guided by requirements of the scientist while she/he is working on the high-level goal of the experiment. To this aim, it is necessary an ontology to store the knowledge related to the experiments and tools used, and to make this knowledge available not only to the scientist, but also to a suitable artificial intelligent system. In this paper we present an ontological approach for knowledge organization in WFMS. The proposed approach is based on a previously developed ontology, called Data-Problem-Solution-to-Experiment (DPS2E); here we aim at matching the abstract workflow obtained by means of our ontology into a concrete set of processes in Taverna environment. As results, we instanced an ontology that uses Taverna components for making two different concrete workflows; then, we make them available in myExperiment repository