Search results for "computer interface"
showing 10 items of 189 documents
X!TandemPipeline: a tool to manage sequence redundancy for protein inference and phosphosite identification
2017
X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!Tandem…
OMICfpp: a fuzzy approach for paired RNA-Seq counts
2019
© The Author(s) 2019.
Teaching clinical reasoning and decision-making skills to nursing students: Design, development, and usability evaluation of a serious game
2016
Background\ud \ud Serious games (SGs) are a type of simulation technology that may provide nursing students with the opportunity to practice their clinical reasoning and decision-making skills in a safe and authentic environment. Despite the growing number of SGs developed for healthcare professionals, few SGs are video based or address the domain of home health care.\ud \ud Aims\ud \ud This paper aims to describe the design, development, and usability evaluation of a video based SG for teaching clinical reasoning and decision-making skills to nursing students who care for patients with chronic obstructive pulmonary disease (COPD) in home healthcare settings.\ud \ud Methods\ud \ud A prototy…
Haptic and Visual Feedback Assistance for Dual-Arm Robot Teleoperation in Surface Conditioning Tasks
2020
Contact driven tasks, such as surface conditioning operations (wiping, polishing, sanding, etc.), are difficult to program in advance to be performed autonomously by a robotic system, specially when the objects involved are moving. In many applications, human-robot physical interaction can be used for the teaching, specially in learning from demonstrations frameworks, but this solution is not always available. Robot teleoperation is very useful when user and robot cannot share the same workspace due to hazardous environments, inaccessible locations, or because of ergonomic issues. In this sense, this article introduces a novel dual-arm teleoperation architecture with haptic and visual feedb…
Machine Learning Approaches for Activity Recognition and/or Activity Prediction in Locomotion Assistive Devices—A Systematic Review
2020
Locomotion assistive devices equipped with a microprocessor can potentially automatically adapt their behavior when the user is transitioning from one locomotion mode to another. Many developments in the field have come from machine learning driven controllers on locomotion assistive devices that recognize/predict the current locomotion mode or the upcoming one. This review synthesizes the machine learning algorithms designed to recognize or to predict a locomotion mode in order to automatically adapt the behavior of a locomotion assistive device. A systematic review was conducted on the Web of Science and MEDLINE databases (as well as in the retrieved papers) to identify articles published…
On Detection of Network-Based Co-residence Verification Attacks in SDN-Driven Clouds
2017
Modern cloud environments allow users to consume computational and storage resources in the form of virtual machines. Even though machines running on the same cloud server are logically isolated from each other, a malicious customer can create various side channels to obtain sensitive information from co-located machines. In this study, we concentrate on timely detection of intentional co-residence attempts in cloud environments that utilize software-defined networking. SDN enables global visibility of the network state which allows the cloud provider to monitor and extract necessary information from each flow in every virtual network in online mode. We analyze the extracted statistics on d…
Reactome graph database: Efficient access to complex pathway data
2018
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…
A framework for data-driven adaptive GUI generation based on DICOM
2018
Computer applications for diagnostic medical imaging provide generally a wide range of tools to support physicians in their daily diagnosis activities. Unfortunately, some functionalities are specialized for specific diseases or imaging modalities, while other ones are useless for the images under investigation. Nevertheless, the corresponding Graphical User Interface (GUI) widgets are still present on the screen reducing the image visualization area. As a consequence, the physician may be affected by cognitive overload and visual stress causing a degradation of performances, mainly due to unuseful widgets. In clinical environments, a GUI must represent a sequence of steps for image investi…
Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations.
2017
We present a new approach that incorporates flexibility based on extensive MD simulations of protein-ligand complexes into structure-based pharmacophore modeling and virtual screening. The approach uses the multiple coordinate sets saved during the MD simulations and generates for each frame a pharmacophore model. Pharmacophore models with the same pharmacophore features are pooled. In this way the high number of pharmacophore models that results from the MD simulation is reduced to only a few hundred representative pharmacophore models. Virtual screening runs are performed with every representative pharmacophore model; the screening results are combined and rescored to generate a single hi…
CLOVE: classification of genomic fusions into structural variation events
2017
Background A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than …