scholarly journals The ISOTILT software for discovering cooperative rigid-unit rotations in networks of interconnected rigid units

2021 ◽  
Vol 54 (6) ◽  
Author(s):  
Branton J. Campbell ◽  
Harold T. Stokes ◽  
Tyler B. Averett ◽  
Shae Machlus ◽  
Christopher J. Yost
Keyword(s):  
Null Space ◽  
Software Tool ◽  
Software Suite ◽  
Web Based ◽  
Linear System Of Equations ◽  
Displacement Vectors ◽  
Rigid Unit Modes ◽  
Value Decomposition ◽  
User Friendly ◽  
Symmetry Mode

A user-friendly web-based software tool called `ISOTILT' is introduced for detecting cooperative rigid-unit modes (RUMs) in networks of interconnected rigid units (e.g. molecules, clusters or polyhedral units). This tool implements a recently described algorithm in which symmetry-mode patterns of pivot-atom rotation and displacement vectors are used to construct a linear system of equations whose null space consists entirely of RUMs. The symmetry modes are first separated into independent symmetry-mode blocks and the set of equations for each block is solved separately by singular value decomposition. ISOTILT is the newest member of the ISOTROPY Software Suite. Here, it is shown how to prepare structural and symmetry-mode information for use in ISOTILT, how to use each of ISOTILT's input fields and options, and how to use and interpret ISOTILT output.

scholarly journals Design and development of a web-based application for structural shielding calculation of medical X-ray imaging facilities

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Cristian Sosa Vera ◽  
Pablo Andres
Keyword(s):  
Software Tool ◽  
Web Based ◽  
X Ray ◽  
Software Application ◽  
X Ray Imaging ◽  
Optimization Principle ◽  
Materials Used ◽  
Operating Potential ◽  
Comparison Of The Results ◽  
User Friendly

A user-friendly HTML-based open-source software has been developed for structural shielding design of medical X-ray imaging facilities. Based on values published by the NCRP Report N° 147 the software allows thickness calculations for different materials used in conventional X-ray rooms, mammography rooms and computed tomography rooms, diminishing errors resulting from the use of curves. The software focuses on the optimization principle by considering workload distributions instead of applying all the workload at a single high operating potential. The input data can be those recommended by the NCRP Report N° 147 or, if the facility has its own data, they can be used instead. With the implemented methodology, the code validation was performed by comparison of the results with a study case provided by the Report. The software application is available in two languages (English and Spanish) and provides the accuracy of the method presented, as well as assisting the physicist in shielding computations in a user-friendly manner. This software tool is available upon request to the corresponding author.

scholarly journals The BioCyc Metabolic Network Explorer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Suzanne Paley ◽  
Peter D. Karp
Keyword(s):  
Metabolic Network ◽  
Metabolic Networks ◽  
Dynamic Control ◽  
Software Tool ◽  
Ease Of Use ◽  
Network Visualization ◽  
Software Suite ◽  
Genome Database ◽  
Web Based ◽  
Visualization Tools

Abstract Background The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset of all possible metabolite connections, or the results will be visually overwhelming. Existing tools, even those that purport to show an organism’s full metabolic network, limit the set of displayed connections based on predefined pathways or other preselected criteria. We sought instead to provide a tool that would give the user dynamic control over which connections to follow. Results The Metabolic Network Explorer is an easy-to-use, web-based software tool that allows the user to specify a starting metabolite of interest and interactively explore its immediate metabolic neighborhood in either or both directions to any desired depth, letting the user select from the full set of connected reactions. Although, as for other tools, only a small portion of the metabolic network is visible at a time, that portion is selected by the user, based on the full reaction complement, and it is easy to switch among alternate paths of interest. The display is intuitive, customizable, and provides copious links to more detailed information pages. Conclusions The Metabolic Network Explorer fills a gap in the set of metabolic network visualization tools and complements other modes of exploration. Its primary strengths are its ease of use, diagrams that are intuitive to biologists, and its integration with the broader corpus of data provided by a BioCyc Pathway/Genome Database.

An algebraic approach to cooperative rotations in networks of interconnected rigid units

2018 ◽  
Vol 74 (5) ◽  
pp. 408-424 ◽  
Author(s):  
Branton Campbell ◽  
Christopher J. Howard ◽  
Tyler B. Averett ◽  
Thomas A. Whittle ◽  
Siegbert Schmid ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
Algebraic Approach ◽  
Functional Materials ◽  
Linear System Of Equations ◽  
Rotational Degrees Of Freedom ◽  
Rigid Unit Modes ◽  
Symmetry Mode ◽  
Entire Network

Crystalline solids consisting of three-dimensional networks of interconnected rigid units are ubiquitous amongst functional materials. In many cases, application-critical properties are sensitive to rigid-unit rotations at low temperature, high pressure or specific stoichiometry. The shared atoms that connect rigid units impose severe constraints on any rotational degrees of freedom, which must then be cooperative throughout the entire network. Successful efforts to identify cooperative-rotational rigid-unit modes (RUMs) in crystals have employed split-atom harmonic potentials, exhaustive testing of the rotational symmetry modes allowed by group representation theory, and even simple geometric considerations. This article presents a purely algebraic approach to RUM identification wherein the conditions of connectedness are used to construct a linear system of equations in the rotational symmetry-mode amplitudes.

Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes

2020 ◽  
Vol 111 (5) ◽  
pp. 486-490
Author(s):  
Manmohan Pandey ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
Prachi Srivastava ◽  
Suman Saroj ◽  
...  
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Web Browser ◽  
Web Based ◽  
Specific Data ◽  
Sequencing Technologies ◽  
Assembly Algorithms ◽  
User Friendly ◽  
Research Domains ◽  
Generation Sequencing

Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

scholarly journals ELIMU-MDx: a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data

BioTechniques ◽  
2020 ◽  
Vol 68 (1) ◽  
pp. 22-27 ◽  
Author(s):  
Silvan Krähenbühl ◽  
Fabian Studer ◽  
Etienne Guirou ◽  
Anna Deal ◽  
Philipp Mächler ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Tool ◽  
Turnaround Time ◽  
Storage Management ◽  
Quantitative Real Time Pcr ◽  
Web Browser ◽  
Web Based ◽  
Data Standard ◽  
User Friendly

The Electronic Laboratory Information and Management Utensil for Molecular Diagnostics (ELIMU-MDx) is a user-friendly platform designed and built to accelerate the turnaround time of diagnostic qPCR assays. ELIMU-MDx is compliant with Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines and has extensive data-import capabilities for all major qPCR instruments by using the RDML data standard. This platform was designed as an open-source software tool and can be accessed through the web browser on all major operating systems.

The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

2017 ◽  
Vol 1 (1) ◽  
pp. 44-49
Author(s):  
Nur Azizah ◽  
Dedeh Supriyanti ◽  
Siti Fairuz Aminah Mustapha ◽  
Holly Yang
Keyword(s):  
Financial Management ◽  
Accounting System ◽  
Bank Account ◽  
Web Based ◽  
Online System ◽  
Version 2.0 ◽  
User Friendly ◽  
The Impact ◽  
A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements.   Keywords:​Accounting Online System, Financial Management, Cash and Bank

Web-Based Peer and Self-Assessment System Design and Development for Elementary School Students

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Mehmet EMIN KORTAK
Keyword(s):  
Elementary School ◽  
Elementary School Students ◽  
Primary Schools ◽  
Peer Assessment ◽  
Assessment System ◽  
Assessment Process ◽  
School Students ◽  
Self Assessment ◽  
Web Based ◽  
User Friendly

This research aimed at designing and improving the web-based integrated peer and self- assessment. WesPASS (web-based peer-assessment system), developed in this research, allows students to assess their own or their peers’ performance and project assignments and to report about the result of these assessments so that they correct their assignments. This study employed design-based research. The participants included 102 fourth grade primary school students and their 4 teachers from 2 state and 2 private primary schools in Ankara, Kecioren (Turkey) who employed the system and were engaged in a questionnaire survey to assess its quality. The findings were analyzed through quantitative data analysis. The findings revealed that the system can be used by elementary school students for peer and self-assessment system. The participants stated that WesPASS is simple and user-friendly, and it accelerates the assessment process by employing information technology and allows to share opinions 

scholarly journals The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Julia Koblitz ◽  
Sabine Will ◽  
S. Riemer ◽  
Thomas Ulas ◽  
Meina Neumann-Schaal ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Point Of View ◽  
Use Cases ◽  
Mathematical Methods ◽  
State Behavior ◽  
Web Based ◽  
Research Fields ◽  
Balance Analysis ◽  
Metabolic Models ◽  
User Friendly

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

scholarly journals An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

2021 ◽  
pp. 193229682098557
Author(s):  
Alysha M. De Livera ◽  
Jonathan E. Shaw ◽  
Neale Cohen ◽  
Anne Reutens ◽  
Agus Salim
Keyword(s):  
Continuous Glucose Monitoring ◽  
Web Application ◽  
Diabetes Management ◽  
Glucose Monitoring ◽  
Epidemiological Studies ◽  
Interactive Software ◽  
Web Based ◽  
Software Applications ◽  
Visualization Of Data ◽  
User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

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