PubMed Journals Articles About "OpenEye Scientific Software, Inc." RSS

00:35 EST 21st November 2018 | BioPortfolio

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Showing "OpenEye Scientific Software" PubMed Articles 1–25 of 4,700+

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these application...

Implementation and applications of EMOD, an individual-based multi-disease modeling platform.

Individual-based models provide modularity and structural flexibility necessary for modeling of infectious diseases at the within-host and population levels, but are challenging to implement. Levels of complexity can exceed the capacity and timescales for students and trainees in most academic institutions. Here we describe the process and advantages of a multi-disease framework approach developed with formal software support. The epidemiological modeling software, EMOD, has undergone a decade of software d...

An unexploited dimension: new software for mixture analysis by 3D diffusion-ordered NMR spectroscopy.

3D DOSY experiments have the potential to provide unique and valuable information but are underused, in part due to the lack of efficient processing software. Here we illustrate the power of 3D DOSY and present MAGNATE (Multidimensional Analysis for the GNAT Environment), an open-source and free software package for the analysis of pulsed field gradient (PFG) 3D NMR diffusion data, distributed under the GNU General Public Licence. The new software makes it possible for the first time to efficiently analyse ...

Prediction of Biochemical Endpoints by the CORAL Software: Prejudices, Paradoxes, and Results.

Quantitative structure-activity relationships (QSARs) for prediction of toxicological endpoints built up with the CORAL software are discussed. Prejudices related to these QSAR models are listed. Possible ways to improve the software are discussed.

Verification of modified receiver-operating characteristic software using simulated rating data.

ROCKIT, which is a receiver-operating characteristic (ROC) curve-fitting software package, was developed by Metz et al. In the early 1990s, it is a very frequently used ROC software throughout the world. In addition to ROCKIT, DBM-MRMC software was developed for multi-reader multi-case analysis of the difference in average area under ROC curves (AUCs). Because this old software cannot run on a PC with Windows 7 or a more recent operating system, we developed new software that employs the same basic algorith...

GHEP-ISFG collaborative exercise on mixture profiles (GHEP-MIX06). Reporting conclusions: Results and evaluation.

One of the main goals of the Spanish and Portuguese-Speaking Group of the International Society for Forensic Genetics (GHEP-ISFG) is to promote and contribute to the development and dissemination of scientific knowledge in the field of forensic genetics. Due to this fact, GHEP-ISFG holds different working commissions that are set up to develop activities in scientific aspects of general interest. One of them, the Mixture Commission of GHEP-ISFG, has organized annually, since 2009, a collaborative exercise o...

SBOL on the Web: Bringing the Synthetic Biology Open Language to the Web browser.

The Synthetic Biology Open Language (SBOL) is a data standard for the in silico representation of biological designs, such as engineered genetic circuits and their constituent DNA and protein components. The SBOL specification is implemented in the form of software libraries, which can then be used to add SBOL support to both new and existing software tools. Examples of existing SBOL libraries include libSBOLj for Java, libSBOL for C, and pySBOL for Python. These libraries can be used to develop software th...

Physician experience with speech recognition software in psychiatry: usage and perspective.

The purpose of this paper is to extend a previous study by evaluating the use of a speech recognition software in a clinical psychiatry milieu. Physicians (n = 55) at a psychiatric hospital participated in a limited implementation and were provided with training, licenses, and relevant devices. Post-implementation usage data was collected via the software. Additionally, a post-implementation survey was distributed 5 months after the technology was introduced.

Importance of software version for measurement of arterial stiffness: Arteriograph as an example.

Current guidelines recommend the measurement of arterial stiffness in terms of aortic pulse wave velocity (PWV) as an important cardio-vascular risk marker. Both aortic PWV and the aortic augmentation index (AIxao) can be measured using different techniques, e.g., the Arteriograph and SphygmoCor. A new version of the software for the Arteriograph (v., TensioMed, Budapest, Hungary; Arteriograph II) is now available. We wanted to determine whether this improved software differs from the previous versi...

ChromaWizard: An open source image analysis software for multicolor fluorescence in situ hybridization analysis.

Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex fluorescence in situ hybridization (M-FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse karyotypes, for which species sophisticated software and analysis tools are available, other organisms and species are less well...

Evaluating Mammographer Acceptance of MammoRisk Software.

To evaluate mammographers' acceptance of the breast cancer risk assessment software tool MammoRisk (Statlife) in the clinical setting.

A new method of mark detection for software-based optical mark recognition.

Software optical mark recognition (SOMR) is the process whereby information entered on a survey form or questionnaire is converted using specialized software into a machine-readable format. SOMR normally requires input fields to be completely darkened, have no internal labels, or be filled with a soft pencil, otherwise mark detection will be inaccurate. Forms can also have print and scan artefacts that further increase the error rate. This article presents a new method of mark detection that improves over e...

Anatomy learning from prosected cadaveric specimens versus three-dimensional software: A comparative study of upper limb anatomy.

modern, three-dimensional (3D) anatomy software is a promising teaching method, though few studies examine its effectiveness on upper limb and musculoskeletal anatomy learning. The purpose of this study is to investigate which method is associated with a better outcome, as assessed by students' performance on examinations, when comparing learning with prosections to the use of 3D software.

SATrans: New Free Available Software for Annotation of Transcriptome and Functional Analysis of Differentially Expressed Genes.

Recent technological advances have made next-generation sequencing (NGS) a popular and financially accessible technique allowing a broad range of analyses to be done simultaneously. A huge amount of newly generated NGS data, however, require advanced software support to help both in analyzing the data and biologically interpreting the results. In this article, we describe SATrans (Software for Annotation of Transcriptome), a software package providing fast and robust functional annotation of novel sequences...

FluxPyt: a Python-based free and open-source software for C-metabolic flux analyses.

C-Metabolic flux analysis (MFA) is a powerful approach to estimate intracellular reaction rates which could be used in strain analysis and design. Processing and analysis of labeling data for calculation of fluxes and associated statistics is an essential part of MFA. However, various software currently available for data analysis employ proprietary platforms and thus limit accessibility. We developed FluxPyt, a Python-based truly open-source software package for conducting stationary C-MFA data analysis. T...

Changes in perceived scientific consensus shift beliefs about climate change and GM food safety.

Despite an overwhelming scientific consensus, a sizable minority of people doubt that human activity is causing climate change. Communicating the existence of a scientific consensus has been suggested as a way to correct individuals' misperceptions about human-caused climate change and other scientific issues, though empirical support is mixed. We report an experiment in which psychology students were presented with consensus information about two issues, and subsequently reported their perception of the le...

Evaluation of Multimedia Medication Reconciliation Software: A Randomized Controlled, Single-Blind Trial to Measure Diagnostic Accuracy for Discrepancy Detection.

 The Veterans Affairs Portland Healthcare System developed a medication history collection software that displays prescription names and medication images.

The betaboost package-a software tool for modelling bounded outcome variables in potentially high-dimensional epidemiological data.

To provide an integrated software environment for model fitting and variable selection in regression models with a bounded outcome variable.

Software for convenient correction of artifacts in sonomicrometry.

Sonomicrometry is widely applied in biomechanics and physiology to measure precise distances with high temporal resolution. Although commonly used, its usefulness is often limited by the presence of artifacts that require correction. Unfortunately, procedures reported in the literature for artifact correction are often unclear. Furthermore, currently available tools for artifact correction require significant manual manipulations, the consistency of which takes painstaking effort to verify. To improve the e...

Entrepreneurship, intrapreneurship and scientific mobility: The Spanish case.

Scientific mobility can stimulate entrepreneurship and intrapreneurship, acting as a catalyst for reducing imbalances between local and global science and the resulting socio-economic damage. This study evaluates both whether scientific mobility effectively promotes these concepts and the fundamental reasons to articulate effective policies for scientific mobility. Toward this end, a survey has been prepared following the methodology of Global Entrepreneurship Monitor (GEM) and current scientific literature...

A comparison of two different software packages for the analysis of body composition using computed tomography images.

The analysis of body composition from computed tomography (CT) imaging has become widespread. However, the methodology used is far from established. Two main software packages are commonly used for body composition analysis, with results used interchangeably. However, the equivalence of these has not been well established. The aim of this study was to compare the results of body composition analysis performed using the two software packages to assess their equivalence.

Scientific production of the Brazilian Council for Scientific and Technological Development (CNPq) researchers in the field of Oral Medicine and Oral Pathology granted with a scientific productivity fellowship.

Validation of instrument to assess software of patients' risk classification.

Validate the content of an instrument that assesses the quality of a software applied to the risk classification of patients.

Performance evaluation of oil spill software systems in early fate and trajectory of oil spill: comparison analysis of OILMAP and PISCES 2 in Mersin bay spill.

The aim of this study is to evaluate the performance level of two advanced oil spill software systems in early transport and fate of oil spill through algorithms accepted in oil spill literature. To do this, the performance level of software systems mostly used in real cases have been compared. OILMAP (the oil spill prediction modeling system) and PISCES 2 (potential incident simulation, control and evaluation system) have been used for spill trajectory in the light of four spill scenarios. The findings rev...

The Dat Project, an open and decentralized research data tool.

Today's scientific data are primarily stored and accessed via centralized Web-based infrastructure. Centralization has advantages but also carries risks such as link rot and content drift, which can hinder scientific progress. It is time to ask whether traditional, centralized Web architecture aligns with scholarly priorities and values, and to collaboratively move towards new approaches that do.

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