The Experts below are selected from a list of 2148 Experts worldwide ranked by ideXlab platform

Jorge H Ramirezprado - One of the best experts on this subject based on the ideXlab platform.

  • prfectblast a platform independent portable front end for the Command Terminal blast stand alone suite
    BioTechniques, 2012
    Co-Authors: Perfecto Santiagosotelo, Jorge H Ramirezprado
    Abstract:

    prfectBLAST is a multiplatform graphical user interface (GUI) for the stand-alone BLAST+ suite of applications. It allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases that are locally stored. It does not require any dependencies or installation and can be used from a portable flash drive. prfectBLAST is implemented in Java version 6 (SUN) and runs on all platforms that support Java and for which National Center for Biotechnology Information has made available stand-alone BLAST executables, including MS Windows, Mac OS X, and Linux. It is free and open source software, made available under the GNU General Public License version 3 (GPLv3) and can be downloaded at www.cicy.mx/sitios/jramirez or http://code.google.com/p/prfectblast/.

Perfecto Santiagosotelo - One of the best experts on this subject based on the ideXlab platform.

  • prfectblast a platform independent portable front end for the Command Terminal blast stand alone suite
    BioTechniques, 2012
    Co-Authors: Perfecto Santiagosotelo, Jorge H Ramirezprado
    Abstract:

    prfectBLAST is a multiplatform graphical user interface (GUI) for the stand-alone BLAST+ suite of applications. It allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases that are locally stored. It does not require any dependencies or installation and can be used from a portable flash drive. prfectBLAST is implemented in Java version 6 (SUN) and runs on all platforms that support Java and for which National Center for Biotechnology Information has made available stand-alone BLAST executables, including MS Windows, Mac OS X, and Linux. It is free and open source software, made available under the GNU General Public License version 3 (GPLv3) and can be downloaded at www.cicy.mx/sitios/jramirez or http://code.google.com/p/prfectblast/.

Tippey, Kathryn Genevieve - One of the best experts on this subject based on the ideXlab platform.

  • Supporting Multitasking: Evaluation of Novel Input and Output Characteristics to Support Primary and Secondary Task Performance Using Situation Awareness and Mental Workload
    2016
    Co-Authors: Tippey, Kathryn Genevieve
    Abstract:

    Driving and flying are examples of tasks in dynamic process control environments where performing secondary tasks poses risks to the user, potentially resulting in detrimental effects on situation awareness (SA) and mental workload (MWL). The predominant theories of multitasking emphasize the potential of using alternate information processing channels to better support multitasking, and hence prompt the exploration of novel interface characteristics that may reduce cognitive and structural interference. This dissertation uses measures of SA and MWL to evaluate the potential of input and output display characteristics found in novel technologies, such as Google Glass, Pebble Smartwatch, and Windows Surface, to support multitasking performance. Three experiments were performed to evaluate the following input and output characteristics: voice input (Experiments 1 and 3), head-up display (Experiment 1), size of display (Experiments 2 and 3), use of discrete tactile signals (Experiment 2), and use of continuously informing tactile signals (Experiment 3). Experiments 1 and 2 altered only interface characteristics associated with secondary task performance, while Experiment 1 also altered interface characteristics associated with primary task performance in the attempt to more effectively redistribute MWL. While Experiments 1 (Texting and Driving with Google Glass) and 2 (Weather Technology Characteristics in General Aviation Cockpits) indicate the potential SA and MWL benefits of using voice input and larger displays for secondary tasks in multitasking settings, Experiment 3 (Supporting Emergency Vehicle Mobile Command Terminal Use While Driving) sheds light on the limitations of these benefits with increasing task complexity. Experiment 1 showed that combining a head-up display with voice input provided additional marginal SA and MWL benefits. Experiment 2 also suggested SA and MWL benefits when using discrete tactile signals to aid in indicating the need for secondary task attentional shifts. Experiment 3 furthered this exploration of tactile signaling by presenting continuously informing vibrations relating to the primary task, exhibiting both the potential benefits of providing continuous information and the potential drawbacks of overreliance on such displays. These findings have the potential to fundamentally change the way users interact with technology by informing the development of and policies surrounding new products using these features

Eslabão, Marcus Redü - One of the best experts on this subject based on the ideXlab platform.

  • Square: a graphical and intuitive platform for annotation of bacterial genomes
    'Revista Brasileira de Hematologia e Hemoterapia (RBHH)', 2016
    Co-Authors: Eslabão, Marcus Redü
    Abstract:

    DNA sequencing is a technique that provides a vast source of information on various organisms. Currently, new sequencing methods known as Next-Generation Sequencing, are making this technique many times more rapid, accurate and affordable, making it popular and widespread in the scientific community. With the popularization of genome sequencing, laboratories that do not have an emphasis on DNA sequencing, are using this approach to complement their studies. However, the ease in obtaining a DNA sequence contrasts with the difficulty to process, analyze and annotate the genome, in order to obtain relevant biological information. To assist researchers who use this technique, several programs are available, however, they are generally not free, do not perform all the necessary analysis or are difficult to use, mainly because a considerable number of them make use of Command line to be executed, which is not intuitive. The objective of this study was to create a genome annotation software easy to use, with a user friendly interface, free and able to provide all the necessary information for the annotated genome to be submitted to GenBank. For software implementation named Square, Python and Object Pascal programming languages were used. The Prodigal algorithms, NCBI BLAST and tRNAscan-SE were also integrated in the software. At the end of the development stage, Square was tested with three genomes and compared to two popular annotators: RAST and BASYS. The result showed that the Square has higher accuracy than the other two annotator programs, as the results are similar to what is deposited in NCBI, and produce the result in a shorter time, as it runs locally. The Square proved to be a good alternative for users not familiar with the Linux Command Terminal and is available in http://sourceforge.net/projects/sqgenome/ address.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESO sequenciamento de DNA é uma técnica que fornece uma fonte vasta de informações sobre diversos organismos. Atualmente, novas metodologias de sequenciamento conhecidas como Next-Generation Sequencing, estão fazendo com que esta técnica fique inúmeras vezes mais rápida, precisa e economicamente acessível, tornando-se popular e disseminada no meio científico. Com a popularização do sequenciamento de genomas, laboratórios que não possuem ênfase em sequenciamento de DNA, utilizam desta abordagem para complementar seus estudos. Porém, a facilidade em obter a sequência do DNA contrasta com a dificuldade em processar, analisar e anotar o genoma, para que então seja possível obter informações biológicas relevantes sobre aquele organismo. Para auxiliar os pesquisadores que se utilizam desta técnica, alguns softwares estão disponíveis, porém, geralmente são pagos, não realizam toda a tarefa ou são de difícil utilização, neste último caso, por serem em sua grande maioria executados através de terminais de comando, que não contam com um ambiente gráfico para guiar os usuários. Com base nesta problemática, o presente trabalho teve por objetivo criar um software de anotação de genomas de fácil utilização e com interface gráfica amigável, gratuito e que anote com as informações necessárias para submissão ao GenBank. Para implementação do software, denominado Square, as linguagens de programação Python e Object Pascal foram utilizadas. Os algoritmos Prodigal, NCBI BLAST e tRNAscan-SE também foram integrados no software. Ao final da etapa de desenvolvimento, o Square foi testado com três genomas e comparado com dois anotadores populares: o RAST e o BASys. O resultado mostrou que o Square possui maior precisão que os dois outros anotadores, por se aproximar mais do resultado depositado no NCBI, e mais rápido, por ser executado localmente com rapidez. O Square demonstrou-se uma boa alternativa para usuários que não estão acostumados com o Terminal de comando Linux e está disponível no endereço http://sourceforge.net/projects/sqgenome/

Ian F Korf - One of the best experts on this subject based on the ideXlab platform.

  • laocoon a tool for high throughput automated cell counting
    bioRxiv, 2019
    Co-Authors: Kaitlin Lim, Mikaela Louie, Anne La Torre, Ian F Korf
    Abstract:

    STRUCTURED ABSTRACT Motivation There are current programs and plugins that automatically count the number of cells in a given image. However, many of these processes are not entirely automatic, as they require user input to specify a region of interest and are also frequently inaccurate. Results This project presents laocoon, a Python package specifically designed to automatically and efficiently count the number of fluorescently-labelled cells in images. This package not only allows for reliable cell counting, but returns the proportion of cells in each cell cycle relative to all the cells in the DAPI channel, which is currently used for research purposes, but could ultimately be utilized for clinical purposes. Availability and Implementation This package, its corresponding execution instructions, and further information about the underlying algorithms, are currently available in the GitHub repository https://github.com/edukait/laocoon under the MIT license and can be run on the Command Terminal of any operating system. Alternatively, laocoon is available in the Python Package Index (PyPi), so the user can use the pip Command to immediately download the package. Contact kaitlin.y.lim@gmail.com