scholarly journals XRD Data Visualization, Processing and Analysis with d1Dplot and d2Dplot Software Packages

Proceedings ◽  
2020 ◽  
Vol 62 (1) ◽  
pp. 9
Author(s):  
Oriol Vallcorba ◽  
Jordi Rius
Keyword(s):  
Data Analysis ◽  
Data Visualization ◽  
X Ray Diffraction ◽  
Specific Data ◽  
X Ray ◽  
Software Packages ◽  
Compound Database ◽  
Synchrotron Light ◽  
User Friendly ◽  
Transformation Processes

The d1Dplot and d2Dplot computer programs have been developed as user-friendly tools for the inspection and processing of 1D and 2D X-ray diffraction (XRD) data, respectively. d1Dplot provides general tools for data processing and includes the ability to generate comprehensive 2D plots of multiple patterns to easily follow transformation processes. d2Dplot is a full package for 2D XRD data. Besides general processing tools, it includes specific data analysis routines for the application of the through-the-substrate methodology [Rius et al. IUCrJ 2015, 2, 452–463]. Both programs allow the creation of a user compound database for the identification of crystalline phases. The software can be downloaded from the ALBA Synchrotron Light Source website and can be used free of charge for non-commercial and academic purposes.

scholarly journals AUSPEX: a graphical tool for X-ray diffraction data analysis

2017 ◽  
Vol 73 (9) ◽  
pp. 729-737 ◽  
Author(s):  
Andrea Thorn ◽  
James Parkhurst ◽  
Paul Emsley ◽  
Robert A. Nicholls ◽  
Melanie Vollmar ◽  
...  
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Software Tool ◽  
Data Conversion ◽  
Data Sets ◽  
X Ray Diffraction ◽  
X Ray ◽  
Pixel Detectors ◽  
Graphical Tool ◽  
Data Acquisition And Processing

In this paper,AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated howAUSPEXcan be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected byAUSPEX.

IDATENandG-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA

2014 ◽  
Vol 21 (6) ◽  
pp. 1378-1383 ◽  
Author(s):  
Yuki Sekiguchi ◽  
Masaki Yamamoto ◽  
Tomotaka Oroguchi ◽  
Yuki Takayama ◽  
Shigeyuki Suzuki ◽  
...  
Keyword(s):  
User Interfaces ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Custom Made ◽  
Sample Position ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
User Friendly ◽  
Ccd Detectors

Using our custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors, cryogenic coherent X-ray diffraction imaging experiments have been undertaken at the SPring-8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user-friendly graphical user interfaces have been developed. The first is a program suite namedIDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI-1, loading a flash-cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI-1, adjusting the sample position with respect to the X-ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X-ray pulses. NamedG-SITENNO, the other suite is an automated version of the originalSITENNOsuite, which was designed for processing diffraction data. These user-friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.

D-67 High-Resolution X-ray Diffraction Data Analysis From The Partly Relaxed Semiconductor Structures

2009 ◽  
Vol 24 (2) ◽  
pp. 171-171
Author(s):  
A. Ulyanenkov ◽  
A. Benediktovitch ◽  
I. Feranchuk ◽  
B. He ◽  
H. Ress
Keyword(s):  
Data Analysis ◽  
High Resolution ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Semiconductor Structures

scholarly journals MetumpX—a metabolomics support package for untargeted mass spectrometry

2019 ◽  
Vol 36 (5) ◽  
pp. 1647-1648 ◽  
Author(s):  
Bilal Wajid ◽  
Hasan Iqbal ◽  
Momina Jamil ◽  
Hafsa Rafique ◽  
Faria Anwar
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Small Molecules ◽  
Software Package ◽  
Life Sciences ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Software Packages ◽  
Develop Software ◽  
User Friendly

Abstract Motivation Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and scripting of software that are mostly not user friendly and lack basic GUIs. As the researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines truly speeding up the learning curve to build software workstations. Therefore, this paper aims to provide MetumpX, a software package that eases in the installation of 103 software by automatically resolving their individual dependencies and also allowing the users to choose which software works best for them. Results MetumpX is a Ubuntu-based software package that facilitate easy download and installation of 103 tools spread across the standard metabolomics pipeline. As far as the authors know MetumpX is the only solution of its kind where the focus lies on automating development of software workstations. Availability and implementation https://github.com/hasaniqbal777/MetumpX-bin. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals COVID19-world: a shiny application to perform comprehensive country-specific data visualization for SARS-CoV-2 epidemic

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cristian Tebé ◽  
Joan Valls ◽  
Pau Satorra ◽  
Aurelio Tobías
Keyword(s):  
Data Visualization ◽  
Web Application ◽  
Case Fatality ◽  
Epidemiological Surveillance ◽  
Fatality Rate ◽  
Specific Data ◽  
User Friendly ◽  
And Control ◽  
Shiny Application ◽  
Country Specific

Abstract Background Data analysis and visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance. Results Data on COVID-19 diagnosed cases and mortality, from January 1st, 2020, onwards is collected automatically from the European Centre for Disease Prevention and Control (ECDC). We have developed a Shiny application for data visualization and analysis of several indicators to follow the SARS-CoV-2 epidemic using ECDC data. A country-specific tool for basic epidemiological surveillance, in an interactive and user-friendly manner. The available analyses cover time trends and projections, attack rate, population fatality rate, case fatality rate, and basic reproduction number. Conclusions The COVID19-World online web application systematically produces daily updated country-specific data visualization and analysis of the SARS-CoV-2 epidemic worldwide. The application may help for a better understanding of the SARS-CoV-2 epidemic worldwide.

scholarly journals Practical Aspects of the SAMPL Challenge: Providing an Extensive Experimental Data Set for the Modeling Community

2009 ◽  
Vol 14 (10) ◽  
pp. 1245-1250 ◽  
Author(s):  
Janet Newman ◽  
Vincent J. Fazio ◽  
Tom T. Caradoc-Davies ◽  
Kim Branson ◽  
Thomas S. Peat
Keyword(s):  
Evaluation Study ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Software Application ◽  
X Ray Crystallography ◽  
Software Packages ◽  
Structure Solution ◽  
Fragment Library ◽  
Extensive Experimental Data

To provide an experimental basis for a comprehensive molecular modeling evaluation study, 500 fragments from the Maybridge fragment library were soaked into crystals of bovine pancreatic trypsin and the structures determined by X-ray crystallography. The soaking experiments were performed in both single and pooled aliquots to determine if combination of fragments is an appropriate strategy. A further set of data was obtained from co-crystallizing the pooled fragments with the protein. X-ray diffraction data were collected on approximately 1000 crystals at the Australian Synchrotron, and these data were subsequently processed, and the preliminary analysis was performed with a custom software application (Jigsaw), which combines available software packages for structure solution and analysis.

scholarly journals Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals

2012 ◽  
Vol 46 (1) ◽  
pp. 108-119 ◽  
Author(s):  
Simon W. M. Tanley ◽  
Antoine M. M. Schreurs ◽  
John R. Helliwell ◽  
Loes M. J. Kroon-Batenburg
Keyword(s):  
Diffraction Data ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Noticeable Effect ◽  
Raw Data ◽  
X Ray ◽  
Data Comparison ◽  
Data Processing Software ◽  
Software Packages ◽  
Lysozyme Crystals

The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies andBfactors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed withEVAL. A systematic comparison shows that the largest differences in the occupancies andBfactors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets availableviaa local depository, it is possible for the diffraction community to make their own evaluation as they may wish.

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