BACKGROUND: The Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom. RESULTS: We present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly. CONCLUSIONS: With the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aimed to simplify and make more reproducible ONT DNA sequence analysis. The NanoDJ package code, documentation and installation instructions are freely available at https://github.com/genomicsITER/NanoDJ .

UNLABELLED: We introduce IonGAP, a publicly available Web platform designed for the analysis of whole bacterial genomes using Ion Torrent sequence data. Besides assembly, it integrates a variety of comparative genomics, annotation and bacterial classification routines, based on the widely used FASTQ, BAM and SRA file formats. Benchmarking with different datasets evidenced that IonGAP is a fast, powerful and simple-to-use bioinformatics tool. By releasing this platform, we aim to translate low-cost bacterial genome analysis for microbiological prevention and control in healthcare, agroalimentary and pharmaceutical industry applications. AVAILABILITY AND IMPLEMENTATION: IonGAP is hosted by the ITER's Teide-HPC supercomputer and is freely available on the Web for non-commercial use at http://iongap.hpc.iter.es. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The study that we are presenting in this paper has been conducted with Computer Science Engineering students. We have selected a group of volunteers to use an educational software platform called Vocabulary Notebook to acquire specific vocabulary/concepts that are taught in the subjects “Technical English” and “IT Project Management”. In this study we are assessing both the usability of the tool (observing students while using it and extracting conclusions and metrics) and also observing and analyzing the methodology that students apply when it comes to organizing the concepts, by using their own categories, definitions, applying filters and doing self-assessment tests. By the end of the study we will collect this data into a survey and a questionnaire, where we will ask students for feedback about the process and tool. In addition to analyzing the results, by the end of the semester we will also compare the marks obtained by our subject students with the marks of the rest of the class.

Dynamic programming is an important paradigm that has been widely used to solve problems in various areas such as control theory, operation research, biology and computer science. We generalize the finite automaton formal model for dynamic programming deriving pipeline parallel algorithms. The optimality of these algorithms is established for the new class of non-decreasing finite automata. As an intermediate step for the construction of a skeleton for the automatic parallelization of dynamic programming, we have developed a tool for the implementation of pipeline algorithms. The tool maps the processes in the pipeline in the target architecture following a mix of block and cyclic policies adapted to the grain of the machine. Based on the former tool, the automatic parallelization of dynamic programming is straightforward. The use of the model and its associated tools is illustrated with the Single Resource Allocation Problem. The performance and portability of these tools is compared with specific ‘hand made’ code written by experienced programmers. The experimental results on distributed memory and shared distributed memory architectures prove the scalability of the proposed paradigm and its associated tools. Copyright © 2000 John Wiley & Sons, Ltd.

Recent publications prove that runtime systems oriented to the Bulk Synchronous Parallel Model usually achieve remarkable accuracy in their predictions. That accuracy can be seen in the capacity of the software for packing the messages generated during the superstep and their capability to find a rearrangement of the messages sent at the end of the superstep. Unfortunately, barrier synchronisation imposes some limits both in the range of available algorithms and in their performance. The asynchronous nature of many MPI/PVM programs makes their expression difficult or infeasible using a BSP oriented library. Through the generalisation of the concept of superstep we propose two extensions of the BSP model: the BSP Without Barriers (BSPWB) and the Message Passing Machine (MPM) models. These new models are oriented to MPI/PVM parallel programming. The parameters of the models and their quality are evaluated on four standard parallel platforms. The use of these BSP extensions is illustrated using the Fast Fourier Transform and the Parallel Sorting by Regular Sampling algorithms. Copyright © 1999 John Wiley & Sons, Ltd.

A sequential algorithm with complexity O(M2+n) for the integer knapsack problem is presented. M is the capacity of the knapsack, and n the number of objects. The algorithm admits an efficient parallelization on a p-processor ring machine. The corresponding parallel algorithm is O(M2/p+n). The parallel algorithm is compared with a version of the well-known Lee algorithm adapted to the integer knapsack problem. Computational results on both a local area network and a transputer are reported.

Article Integral knapsack problems: parallel algorithms and their implementations on distributed systems Share on Authors: D. Morales Dpto. Estadística,Investigación Operativa y Computación, Universidad de La Laguna Dpto. Estadística,Investigación Operativa y Computación, Universidad de La LagunaView Profile , J. Roda Dpto. Estadística,Investigación Operativa y Computación, Universidad de La Laguna Dpto. Estadística,Investigación Operativa y Computación, Universidad de La LagunaView Profile , F. Almeida Dpto. Estadística,Investigación Operativa y Computación, Universidad de La Laguna Dpto. Estadística,Investigación Operativa y Computación, Universidad de La LagunaView Profile , C. Rodríguez Dpto. Estadística,Investigación Operativa y Computación, Universidad de La Laguna Dpto. Estadística,Investigación Operativa y Computación, Universidad de La LagunaView Profile , F. García Dpto. Estadística,Investigación Operativa y Computación, Universidad de La Laguna Dpto. Estadística,Investigación Operativa y Computación, Universidad de La LagunaView Profile Authors Info & Claims ICS '95: Proceedings of the 9th international conference on SupercomputingJuly 1995 Pages 218–226https://doi.org/10.1145/224538.224564Online:03 July 1995Publication History 10citation522DownloadsMetricsTotal Citations10Total Downloads522Last 12 Months8Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access