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 Modeling the Differences in Biochemical Capabilities ofPseudomonasSpecies by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences?

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Parizad Babaei ◽  
Tahereh Ghasemi-Kahrizsangi ◽  
Sayed-Amir Marashi
Keyword(s):  
In Silico ◽  
Metabolic Networks ◽  
Closely Related Species ◽  
Systematic Analysis ◽  
Reconstruction Process ◽  
Flux Balance ◽  
Wide Range ◽  
Balance Analysis ◽  
Metabolic Models ◽  
Genome Scale

To date, several genome-scale metabolic networks have been reconstructed. These models cover a wide range of organisms, from bacteria to human. Such models have provided us with a framework for systematic analysis of metabolism. However, little effort has been put towards comparing biochemical capabilities of closely related species using their metabolic models. The accuracy of a model is highly dependent on the reconstruction process, as some errors may be included in the model during reconstruction. In this study, we investigated the ability of threePseudomonasmetabolic models to predict the biochemical differences, namely, iMO1086, iJP962, and iSB1139, which are related toP. aeruginosaPAO1,P. putidaKT2440, andP. fluorescensSBW25, respectively. We did a comprehensive literature search for previous works containing biochemically distinguishable traits over these species. Amongst more than 1700 articles, we chose a subset of them which included experimental results suitable forin silicosimulation. By simulating the conditions provided in the actual biological experiment, we performed case-dependent tests to compare thein silicoresults to the biological ones. We found out that iMO1086 and iJP962 were able to predict the experimental data and were much more accurate than iSB1139.

scholarly journals Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks

2020 ◽  
Vol 48 (W1) ◽  
pp. W427-W435 ◽  
Author(s):  
Archana Hari ◽  
Daniel Lobo
Keyword(s):  
Metabolic Pathways ◽  
Web Application ◽  
Metabolic Networks ◽  
Metabolic Flux ◽  
Scale Model ◽  
Balance Analysis ◽  
Systems Biology Markup Language ◽  
User Friendly ◽  
Genome Scale ◽  
Genome Scale Model

Abstract Next-generation sequencing has paved the way for the reconstruction of genome-scale metabolic networks as a powerful tool for understanding metabolic circuits in any organism. However, the visualization and extraction of knowledge from these large networks comprising thousands of reactions and metabolites is a current challenge in need of user-friendly tools. Here we present Fluxer (https://fluxer.umbc.edu), a free and open-access novel web application for the computation and visualization of genome-scale metabolic flux networks. Any genome-scale model based on the Systems Biology Markup Language can be uploaded to the tool, which automatically performs Flux Balance Analysis and computes different flux graphs for visualization and analysis. The major metabolic pathways for biomass growth or for biosynthesis of any metabolite can be interactively knocked-out, analyzed and visualized as a spanning tree, dendrogram or complete graph using different layouts. In addition, Fluxer can compute and visualize the k-shortest metabolic paths between any two metabolites or reactions to identify the main metabolic routes between two compounds of interest. The web application includes >80 whole-genome metabolic reconstructions of diverse organisms from bacteria to human, readily available for exploration. Fluxer enables the efficient analysis and visualization of genome-scale metabolic models toward the discovery of key metabolic pathways.

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 

Learning from metabolic networks: current trends and future directions for precision medicine.

2020 ◽  
Vol 28 ◽  
Author(s):  
Ilaria Granata ◽  
Mario Manzo ◽  
Ari Kusumastuti ◽  
Mario R Guarracino
Keyword(s):  
Systems Biology ◽  
Precision Medicine ◽  
Metabolic Networks ◽  
Information Modeling ◽  
Model Systems ◽  
Specific Information ◽  
Important Indicator ◽  
Predictive Values ◽  
Metabolic Systems ◽  
Metabolic Models

Purpose: Systems biology and network modeling represent, nowadays, the hallmark approaches for the development of predictive and targeted-treatment based precision medicine. The study of health and disease as properties of the human body system allows the understanding of the genotype-phenotype relationship through the definition of molecular interactions and dependencies. In this scenario, metabolism plays a central role as its interactions are well characterized and it is considered an important indicator of the genotype-phenotype associations. In metabolic systems biology, the genome-scale metabolic models are the primary scaffolds to integrate multi-omics data as well as cell-, tissue-, condition-specific information. Modeling the metabolism has both investigative and predictive values. Several methods have been proposed to model systems, which involve steady-state or kinetic approaches, and to extract knowledge through machine and deep learning. Method: This review collects, analyzes, and compares the suitable data and computational approaches for the exploration of metabolic networks as tools for the development of precision medicine. To this extent, we organized it into three main sections: "Data and Databases", "Methods and Tools", and "Metabolic Networks for medicine". In the first one, we have collected the most used data and relative databases to build and annotate metabolic models. In the second section, we have reported the state-of-the-art methods and relative tools to reconstruct, simulate, and interpret metabolic systems. Finally, we have reported the most recent and innovative studies which exploited metabolic networks for the study of several pathological conditions, not only those directly related to the metabolism. Conclusion: We think that this review can be a guide to researchers of different disciplines, from computer science to biology and medicine, in exploring the power, challenges and future promises of the metabolism as predictor and target of the so-called P4 medicine (predictive, preventive, personalized and participatory).

scholarly journals Patient’s point of view on the use of telemedicine in multiple sclerosis: a web-based survey

2021 ◽  
Author(s):  
Doriana Landi ◽  
Marta Ponzano ◽  
Carolina Gabri Nicoletti ◽  
Gaia Cola ◽  
Gianluca Cecchi ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Point Of View ◽  
Physical Parameters ◽  
Chronic Medical Conditions ◽  
Socioeconomic Conditions ◽  
Web Based ◽  
Healthcare Facilities ◽  
Advantages And Disadvantages ◽  
Disease Characteristics ◽  
Degree Of Disability

AbstractRestrictions in the access to healthcare facilities during COVID-19 pandemic have raised the need for remote monitoring of chronic medical conditions, including multiple sclerosis (MS). In order to enable the continuity of care in these circumstances, many telemedicine applications are currently tested. While physicians’ preferences are commonly investigated, data regarding the patients’ point of view are still lacking. We built a 37 items web-based survey exploring patients’ propensity, awareness, and opinions on telemedicine with the aim to evaluate the sustainability of this approach in MS. Analysing 613 questionnaires out of 1093 that were sent to persons with MS followed at the Multiple Sclerosis Center of Tor Vergata University, Rome, we found that more than half of respondents (54%) were open to having a televisit. Propensity toward telemedicine significantly depended on having a higher income (p = 0.037), living farther from the center (p = 0.038), using computer and tablet (p = 0.010) and using the Internet for other remote activities (p < 0.001), conversely it was not influenced by any specific disease characteristics (i.e. degree of disability). The main advantages and disadvantages of televisit reported by participants were respectively saving time (70%) and impossibility to measure physical parameters (71%). Although the majority of respondents are in favour of televisit, so far this approach is restricted to those displaying better socioeconomic conditions and higher familiarity with technology. Implications of the study are that telemedicine platforms should be better tailored to patients’ demands in order to spread the use of telemedicine, to enhance usability and to increase patients’ adherence.

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.

scholarly journals A New Measure of Complementarity in Market Basket Data

2021 ◽  
Vol 16 (4) ◽  
pp. 670-681
Author(s):  
Radosław Puka ◽  
Stanislaw Jedrusik
Keyword(s):  
Large Data ◽  
Point Of View ◽  
Detailed Data ◽  
Market Basket ◽  
Economic Theories ◽  
Empirical Verification ◽  
Preliminary Results ◽  
Research Fields ◽  
It Systems ◽  
Real Market

Modern IT systems collect detailed data on each activity, transaction, forum entry, conversation and many other areas. The availability of large data volumes in the business, industry and research fields opens up new opportunities for the empirical verification of various economic theories and laws. The analysis of big datasets in turn allows us to look at many issues from a new point of view and see the dependencies that are otherwise difficult to derive. In this paper, we propose a new measure for dependencies between goods in market basket data. The introduced measure was inspired by the well-known microeconomic concept of complementarity. Due to its similar properties to those of complementarity, the new measure was called basket complementarity (b-complementarity). B-complementarity not only measures the strength of dependencies between goods but also measures the direction of these dependencies. The values of the proposed measure can be relatively easily calculated using market basket data. This paper also presents a simple example illustrating this new concept, areas of possible application (e.g., in e-commerce) and preliminary results of searching for goods that meet the criteria of basket complementarity in real market basket data.

CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation

2020 ◽  
Vol 36 (12) ◽  
pp. 3913-3915
Author(s):  
Hemi Luan ◽  
Xingen Jiang ◽  
Fenfen Ji ◽  
Zhangzhang Lan ◽  
Zongwei Cai ◽  
...  
Keyword(s):  
False Positive ◽  
Supplementary Information ◽  
Liquid Chromatography Mass Spectrometry ◽  
Targeted Metabolomics ◽  
Metabolomics Data ◽  
Web Based ◽  
Tremendous Amount ◽  
Chromatographic Peaks ◽  
User Friendly

Abstract Motivation Liquid chromatography–mass spectrometry-based non-targeted metabolomics is routinely performed to qualitatively and quantitatively analyze a tremendous amount of metabolite signals in complex biological samples. However, false-positive peaks in the datasets are commonly detected as metabolite signals by using many popular software, resulting in non-reliable measurement. Results To reduce false-positive calling, we developed an interactive web tool, termed CPVA, for visualization and accurate annotation of the detected peaks in non-targeted metabolomics data. We used a chromatogram-centric strategy to unfold the characteristics of chromatographic peaks through visualization of peak morphology metrics, with additional functions to annotate adducts, isotopes and contaminants. CPVA is a free, user-friendly tool to help users to identify peak background noises and contaminants, resulting in decrease of false-positive or redundant peak calling, thereby improving the data quality of non-targeted metabolomics studies. Availability and implementation The CPVA is freely available at http://cpva.eastus.cloudapp.azure.com. Source code and installation instructions are available on GitHub: https://github.com/13479776/cpva. Supplementary information Supplementary data are available at Bioinformatics online.

A Test Sheet Optimization Approach to Supporting Web-based Learning Diagnosis Using Group Testing Methods

2017 ◽  
Vol 7 (4) ◽  
pp. 1-23
Author(s):  
Chu-Fu Wang ◽  
Chih-Lung Lin ◽  
Gwo-Jen Hwang ◽  
Sheng-Pin Kung ◽  
Shin-Feng Chen
Keyword(s):  
Test Item ◽  
Group Testing ◽  
Diagnostic System ◽  
Point Of View ◽  
Optimization Approach ◽  
Exposure Rate ◽  
Web Based ◽  
Item Exposure ◽  
Test Items ◽  
Doubling Method

Assessment can help teachers to examine the effectiveness of teaching and to diagnose the unfamiliar basic concepts (or attributes) of students within the testing scope. A web-based adaptive testing and diagnostic system can achieve the above objective efficiently and correctly. From a diagnostic point of view, the major concerns are to diagnose whether or not an examinee has learned each basic concept well in the testing scope, while also limiting the number of test items used (the testing length) to as few as possible, which will be directly related to the patience of the examinee. In this paper, we consider a test item selecting optimization diagnostic problem to reveal the mastery profile of an examinee (that is, to diagnose each basic concept's learning status (well learned/unfamiliar) in the testing scope) with a short testing length and a limited test item exposure rate. This paper uses the techniques of Group Testing theory for the design of our test item selecting algorithm. Two test item selecting strategies, the bisecting method and the doubling method, are proposed. The effectiveness of the proposed methods was evaluated by experimental simulations. The results show that both of the proposed algorithms use fewer test items and a limited test item exposure rate compared to the conventional methods.

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