scholarly journals NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR

2021 ◽  
Vol 2 (2) ◽  
pp. 843-861
Author(s):  
Yulia Pustovalova ◽  
Frank Delaglio ◽  
D. Levi Craft ◽  
Haribabu Arthanari ◽  
Ad Bax ◽  
...  
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Formal Theory ◽  
Nonuniform Sampling ◽  
Data Sampling ◽  
Software Support ◽  
Computational Performance ◽  
Spectral Reconstruction ◽  
Weak Intensity ◽  
Quantitative Analyses

Abstract. Although the concepts of nonuniform sampling (NUS​​​​​​​) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective of determining best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals, and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses, and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a roadmap for continued community-driven development with the ultimate aim of providing best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.

scholarly journals NUScon: A community-driven platform for quantitative evaluation of nonuniform sampling in NMR

2021 ◽  
Author(s):  
Yulia Pustovalova ◽  
Frank Delaglio ◽  
D. Levi Craft ◽  
Haribabu Arthanari ◽  
Ad Bax ◽  
...  
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Formal Theory ◽  
Nonuniform Sampling ◽  
Data Sampling ◽  
Road Map ◽  
Computational Performance ◽  
Spectral Reconstruction ◽  
Weak Intensity ◽  
Quantitative Analyses

Abstract. Although the concepts of non-uniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge four decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and the increased data sampling demands imposed by higher magnetic fields. However, the identification of best practices still remains a significant and unmet challenge. Unlike the discrete Fourier transform, non-Fourier methods used to reconstruct spectra from NUS data are nonlinear, depend on the complexity and nature of the signals, and lack quantitative or formal theory describing their performance. Seemingly subtle algorithmic differences may lead to significant variabilities in spectral qualities and artifacts. A community-based critical assessment of NUS challenge problems has been initiated, called the “Nonuniform Sampling Contest” (NUScon), with the objective to determine best practices for processing and analyzing NUS experiments. We address this objective by constructing challenges from NMR experiments that we inject with synthetic signals and we process these challenges using workflows submitted by the community. In the initial rounds of NUScon our aim is to establish objective criteria for evaluating the quality of spectral reconstructions. We present here a software package for performing the quantitative analyses and we present the results from the first two rounds of NUScon. We discuss the challenges that remain and present a road-map for continued community-driven development with the ultimate aim to provide best practices in this rapidly evolving field. The NUScon software package and all data from evaluating the challenge problems are hosted on the NMRbox platform.

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

BLENDED LEARNING IN ELECTRONICS AND AUTOMATION ENGINEERING: A STUDY OF SOFTWARE SUPPORT AND BEST PRACTICES

2017 ◽  
Author(s):  
Guillermo Azuara ◽  
Jorge Delgado ◽  
Jesús Gallardo ◽  
Juan Carlos García ◽  
Eduardo Gil ◽  
...  
Keyword(s):  
Best Practices ◽  
Blended Learning ◽  
Software Support

Security Gaps in Databases

2011 ◽  
Vol 2 (3) ◽  
pp. 42-62
Author(s):  
Afonso Araújo Neto ◽  
Marco Vieira
Keyword(s):  
Best Practices ◽  
Operating Systems ◽  
Software Package ◽  
Web Applications ◽  
Gap Analysis ◽  
Database Security ◽  
Security Requirements ◽  
Management Systems ◽  
Software Products ◽  
Software Packages

When deploying database-centric web applications, administrators should pay special attention to database security requirements. Acknowledging this, Database Management Systems (DBMS) implement several security mechanisms that help Database Administrators (DBAs) making their installations secure. However, different software products offer different sets of mechanisms, making the task of selecting the adequate package for a given installation quite hard. This paper proposes a methodology for detecting database security gaps. This methodology is based on a comprehensive list of security mechanisms (derived from widely accepted security best practices), which was used to perform a gap analysis of the security features of seven software packages composed by widely used products, including four DBMS engines and two Operating Systems (OS). The goal is to understand how much each software package helps developers and administrators to actually accomplish the security tasks that are expected from them. Results show that while there is a common set of security mechanisms that is implemented by most packages, there is another set of security tasks that have no support at all in any of the packages.

scholarly journals Sharing Data from Molecular Simulations

2019 ◽  
Author(s):  
Mark J. Abraham ◽  
Rossen Apostolov ◽  
Jonathan Barnoud ◽  
Paul Bauer ◽  
Christian Blau ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Best Practices ◽  
Molecular Dynamics Simulations ◽  
Software Package ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Scientific Output ◽  
Level Of Detail ◽  
Simulation Data ◽  
Dynamics Simulations

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( <a href="https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/">https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/</a>). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.

scholarly journals Sharing Data from Molecular Simulations

2019 ◽  
Author(s):  
Mark J. Abraham ◽  
Rossen Apostolov ◽  
Jonathan Barnoud ◽  
Paul Bauer ◽  
Christian Blau ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Best Practices ◽  
Molecular Dynamics Simulations ◽  
Software Package ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Scientific Output ◽  
Level Of Detail ◽  
Simulation Data ◽  
Dynamics Simulations

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( <a href="https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/">https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/</a>). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.

A Primer on Survey Research

2021 ◽  
pp. 1-26
Author(s):  
Mary A. Hansen ◽  
Gaelebale Nnunu Tsheko
Keyword(s):  
Best Practices ◽  
Construct Validity ◽  
Survey Research ◽  
Validity Evidence ◽  
Design Development ◽  
Research Project ◽  
Quantitative Survey ◽  
Qualitative And Quantitative ◽  
Quantitative Analyses ◽  
Sampling Procedures

This chapter presents a summary of best practices for the design, development, and analysis of quantitative survey research. The authors provide an overview of sampling procedures, as well as a summary of considerations for researchers as they develop questionnaires. Additionally, they provide descriptions of both qualitative and quantitative analyses that should be used to provide content and construct validity evidence for questionnaires. Finally, they show examples of common descriptive and inferential procedures appropriate for survey research. The goal of the chapter is to summarize factors that survey researchers should consider at all stages of their research project, from design to analysis, in order to improve survey research in practice.

Examining the Outcomes of the InsideOut Dad Fatherhood Education Program for Incarcerated Minority Fathers

2020 ◽  
pp. 106648072097854
Author(s):  
Joshua J. Turner ◽  
Kay Bradford ◽  
Brian J. Higginbotham ◽  
Andrea Coppin
Keyword(s):  
Best Practices ◽  
Education Program ◽  
Well Being ◽  
Parenting Programs ◽  
Subjective Well Being ◽  
Mixed Methods Approach ◽  
Quantitative Analyses ◽  
Underserved Groups ◽  
Incarcerated Fathers ◽  
Qualitative Analyses

Using a mixed-methods approach, this study examined the outcomes and experiences of incarcerated minority fathers ( N = 713) who participated in InsideOut Dad, a widely used, corrections-based fatherhood education program. Quantitative analyses indicated decreases in partner conflict among participants and more positive perceptions of subjective well-being. Qualitative analyses revealed that the program was positively received, with participants noting the skills they developed. As a result of fatherhood education, incarcerated minority fathers reported being empowered and more confident in their roles as fathers and that they learned needed skills to be responsible and responsive fathers. Such findings may inform facilitators of corrections-based parenting programs on best practices for serving incarcerated fathers from historically underserved groups.

Laser fluorescence angiography reveals perfusion defects in retrograde cardioplegia

Perfusion ◽  
2011 ◽  
Vol 26 (6) ◽  
pp. 536-541 ◽  
Author(s):  
H Gorki ◽  
NC Patel ◽  
L Balacumaraswami ◽  
JB Pillai ◽  
VA Subramanian
Keyword(s):  
Software Package ◽  
Green Laser ◽  
Laser Fluorescence ◽  
Fluorescence Angiography ◽  
Retrograde Cardioplegia ◽  
Cardiac Veins ◽  
Perfusion Defects ◽  
Quantitative Analyses ◽  
The Right ◽  
Image Details

Background: Adequate perfusion of the right ventricle with retrograde cardioplegia has always been questioned. However, clinical studies suggested sufficient protection and, up to now, intraoperative assessment of cardioplegia distribution has been difficult. Methods: As a pilot study in 14 patients, we used indocyanine green laser fluorescence angiography (ICGLA) to assess vascular and myocardial perfusion of different areas of the right anterior ventricular wall. Regions of interest were analyzed quantitatively using a new software package. Results: ICGLA allowed rapid and reliable visualization of cardioplegic flow and distribution. Retrograde cardioplegia revealed perfusion defects in the territory of the right anterior cardiac veins when compared to antegrade delivery and to areas close to the left anterior descending vein(s), confirmed by quantitative analyses of maximal fluorescence intensity. Five patients were excluded from quantitative analyses. The learning curve, pitfalls, limitations and special image details are described. Conclusion: A larger study is necessary to examine the relevance of perfusion defects to metabolic changes in affected myocytes and to global right ventricular function.

Quantitative Data Gathering Techniques

2015 ◽  
Author(s):  
Babek Taheri ◽  
Catherine Porter ◽  
Nikolaos Valantasis-Kanellos
Keyword(s):  
Experimental Research ◽  
Quantitative Data ◽  
Research Question ◽  
Data Gathering ◽  
Data Sampling ◽  
Measurement Issues ◽  
Common Features ◽  
Key Issues ◽  
Quantitative Analyses

The role of managers and researchers is concerned with analysing and solving problems. These problems come in many forms with common features and often numerical information can be useful for analysis. In order to perform quantitative analyses, we need data. This chapter illustrates how to collect quantitative data: sampling and measurement issues, surveys and experimental research. In this chapter the tools that are needed for collecting quantitative data are introduced. In particular, the key issues that should be related to your research question are a) defining what are your dependent and independent variables b) how to sample your participants and c) how to design appropriate questions to elicit the data you need to answer your research question.

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