scholarly journals KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Hugo Mochão ◽  
Pedro Barahona ◽  
Rafael S Costa
Keyword(s):  
Experimental Data ◽  
Metabolic Networks ◽  
Model Simulation ◽  
Web Interface ◽  
Concentration Data ◽  
Web Based ◽  
Share Data ◽  
Visualization Tools ◽  
Filter Mechanism ◽  
Machine Readable

Abstract The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  www.kimosys.org

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.

eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

2019 ◽  
Author(s):  
Ruslan N. Tazhigulov ◽  
James R. Gayvert ◽  
Melissa Wei ◽  
Ksenia B. Bravaya
Keyword(s):  
Web Application ◽  
Shortest Paths ◽  
Coarse Grained ◽  
Decay Parameter ◽  
Electron Hole ◽  
Web Based ◽  
Aromatic Amino Acid Residue ◽  
Pathways Model ◽  
Visualization Tools ◽  
Effective Decay

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one effective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be specified by the users. The software searches for the shortest paths connecting the user-specified electron/hole source to either all surface-exposed ETA residues or to the user-specified target. The identified pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>

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 Simultaneous Parameters Identifiability and Estimation of anE. coliMetabolic Network Model

2015 ◽  
Vol 2015 ◽  
pp. 1-21 ◽  
Author(s):  
Kese Pontes Freitas Alberton ◽  
André Luís Alberton ◽  
Jimena Andrea Di Maggio ◽  
Vanina Gisela Estrada ◽  
María Soledad Díaz ◽  
...  
Keyword(s):  
Experimental Data ◽  
Escherichia Coli ◽  
Metabolic Networks ◽  
Initial Conditions ◽  
Model Fit ◽  
Real Problem ◽  
Kinetic Rates ◽  
K 12 ◽  
Procedure Model

This work proposes a procedure for simultaneous parameters identifiability and estimation in metabolic networks in order to overcome difficulties associated with lack of experimental data and large number of parameters, a common scenario in the modeling of such systems. As case study, the complex real problem of parameters identifiability of theEscherichia coliK-12 W3110 dynamic model was investigated, composed by 18 differential ordinary equations and 35 kinetic rates, containing 125 parameters. With the procedure, model fit was improved for most of the measured metabolites, achieving 58 parameters estimated, including 5 unknown initial conditions. The results indicate that simultaneous parameters identifiability and estimation approach in metabolic networks is appealing, since model fit to the most of measured metabolites was possible even when important measures of intracellular metabolites and good initial estimates of parameters are not available.

A Web-Based Tool for Visualization of Biomolecular Network Comparison

2014 ◽  
Vol 556-562 ◽  
pp. 5482-5487
Author(s):  
Hui Ran Zhang ◽  
Xiao Long Shen ◽  
Jiang Xie ◽  
Dong Bo Dai
Keyword(s):  
Open Source ◽  
Undirected Graphs ◽  
Web Based ◽  
Network Comparison ◽  
Biomolecular Networks ◽  
Biomolecular Network ◽  
Visualization Tools ◽  
Similarities And Differences ◽  
Adaptive Visualization

Analyzing similarities and differences between biomolecular networks comparison through website intuitively could be a convenient and effective way for researchers. Although several network comparison visualization tools have been developed, none of them can be integrated into websites. In this paper, a web-based tool kit named dynamically adaptive Visualization of Biomolecular Network Comparison (Bio-NCV) is designed and developed. The proposed tool is based on Cytyoscape.js – a popular open-source library for analyzing and visualizing networks. Bio-NCV integrates arjor.js which including the Barnes-Hut algorithm and the Traer Physics library for processing in order to express the dynamically adaptive initialization. In addition, in order to maintain consistency, the counterparts in other networks will change while the nodes and edges in one of the compared networks change. Furthermore, Bio-NCV can deal with both directed and undirected graphs.

scholarly journals THE CENSUS OF SMS GATEWAY BASED WEB BASED KOTO LUAR PAUH DISTRICTS PADANG CITY

2016 ◽  
Vol 1 (2) ◽  
pp. 169
Author(s):  
Danyl Mallisza
Keyword(s):  
Short Message Service ◽  
Government Performance ◽  
Population Census ◽  
Short Message ◽  
Web Interface ◽  
Web Based ◽  
The World ◽  
Message Service ◽  
Multi Level ◽  
Computerized System

short message service (SMS) plays an important role in the field of IT in the future, SMS GATEWAY can be used as a mobile device for collecting data in the population census in achieving the availability and effectiveness. This research is about the development of software based on short message service (SMS) system to send messages via SMS gateway. The main objective of the proposed system is to provide a multi-level local authentication services to the SMS gateway. This service can be implemented in multi-departmental organizations where SMS service is used for system notifications. The proposed system has a web interface and encryption methods to provide services. Census information system that uses a computerized system is an effort to help smooth in the world of government so that the data obtained more precise and accurate. It can be expected to facilitate the penyensusan population in Koto village of Padang Pauh Subdistrict Affairs effectively, efficiently and accurately to improve government performance.

Web-Based Geospatial Services

2010 ◽  
pp. 281-297
Author(s):  
Iftikhar U. Sikder ◽  
Aryya Gangopadhyay ◽  
Nikhil V. Shampur
Keyword(s):  
Web Services ◽  
Environmental Planning ◽  
Simulation Models ◽  
Web Based ◽  
Web Mapping ◽  
Collaborative Modeling ◽  
Visualization Tools ◽  
Geospatial Services ◽  
Core Functionality

This chapter characterizes the requirements of Geographic Information Systems (GIS) middleware and its components for dynamic registering and discovering of spatial services specifically for collaborative modeling in environmental planning. The chapter explores the role of Web services with respect to implementation standard and protocols and identifies implementation features for exposing distributed GIS business logic and components via Web services. In particular, the chapter illustrates applications of the interoperability specifications of Open GIS Consortium’s (OGC) Web Mapping Service and (WMS), Web Processing Standards (WPS) with respect to implementation feature. The chapter demonstrates a prototype implementation of collaborative environmental decision support systems (GEO-ELCA- Exploratory Land Use Change Assessment) where Web service-enabled middleware adds core functionality to a Web mapping service. The application demonstrates how individual workspace-based namespaces can be used to perform Web mapping functionality (such as spatial analysis in visualization) through the integration of environmental simulation models to explore collective planning scenario. Built on OGC compliant connector and supports WMS and WPS, the system includes interactive supports for geospatial data query, mapping services and visualization tools for multi-user transactions.

Physical Activity Surveillance Using Wearable Activity Monitors: Are US Adults Willing to Share Their Data?

2020 ◽  
Vol 34 (6) ◽  
pp. 672-676 ◽  
Author(s):  
Eric T. Hyde ◽  
John D. Omura ◽  
Janet E. Fulton ◽  
Andre Weldy ◽  
Susan A. Carlson
Keyword(s):  
Public Health ◽  
Physical Activity ◽  
Health Agency ◽  
Cross Sectional ◽  
Physically Active ◽  
Web Based ◽  
Activity Monitors ◽  
Share Data ◽  
Using Data ◽  
National Physical Activity

Purpose: Wearable activity monitors (wearables) have generated interest for national physical activity (PA) surveillance; however, concerns exist related to estimates obtained from current users willing to share data. We examined how limiting data to current users who are willing to share data associated with PA estimates in a nationwide sample. Design: Cross-sectional web-based survey. Setting: US adults. Subjects: In total, 942 respondents. Measures: The 2018 Government & Academic Omnibus Survey assessing current wearable use, willingness to share data with various people or organizations, and PA levels. Analysis: Estimated the prevalence of current wearable use; current users’ willingness to share data with various people or organizations; and PA levels overall, among current users, and among current users willing to share their data. Results: Overall, 21.7% (95% confidence interval [CI]: 19.1-24.5) of US adults reported currently using a wearable. Among current users, willingness to share ranged from 40.1% with a public health agency to 76.3% with their health-care provider. Overall, 62.2% (95% CI: 58.9-65.3) of adults were physically active. These levels were similar between current users (75.0%, 95% CI: 68.3-80.7) and current users willing to share their data (75.3%, 95% CI: 67.9-81.5). Conclusion: Our findings suggest that using data from wearable users may overestimate PA levels, although reported willingness to share the data may not compound this issue.

Delivering Web-Based Education

2011 ◽  
pp. 647-653
Author(s):  
Kathryn A. Marold
Keyword(s):  
Online Teaching ◽  
Course Delivery ◽  
Good Thing ◽  
College Courses ◽  
Web Interface ◽  
Web Based ◽  
State Of Affairs ◽  
Faculty And Administrators ◽  
In The Beginning ◽  
Web Based Education

A decade of hindsight allows us to examine the phenomenon of Web-based course delivery and evaluate its successes and failures. When Web-delivered courses mushroomed from campuses in the 1990s, they were embraced by students, faculty, and administrators alike. The prospect of “electronic tutelage” (Marold, 2002), which allowed students through Web interface to take college courses for credit any time, any place (ATAP), was immediately popular with students. The interruptions of job and schedule changes, relocation, childbirth, failed transportation to campus, and so forth no longer necessitated an interruption in progress toward a degree. Likewise, faculty saw online teaching as an opportunity to disseminate knowledge and assess student progress according to their personal preferences, and to communicate personally with their students, albeit virtually. Administrators saw the revenue without physical classroom allocations as an immediate cash cow. In the beginning, there was satisfaction all around. Although this state of affairs was not necessarily universal, generally it could be concluded that Web-based education was a very good thing.

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