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.

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 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.

Development of a Web-Based Interactive Compressible Flow Solver

2005 ◽  
Author(s):  
H. Eletem ◽  
F. Young ◽  
K. Aung
Keyword(s):  
User Interface ◽  
Compressible Flow ◽  
Programming Language ◽  
Graphical User Interface ◽  
Mechanical Engineering ◽  
Software Tool ◽  
Ease Of Use ◽  
Web Based ◽  
Flow Solver ◽  
Java Programming

Compressible flow is an important subject in aerospace and mechanical engineering disciplines. This paper describes the development of a web-base interactive compressible flow solver using Java programming language. The main objective of the solver is to provide students with a software tool than can be used in the compressible flow course offered in the Department of Mechanical Engineering at Lamar University. The solver has a graphical user interface (GUI) for ease of use and interactivity. The solver was developed with the intention of free distribution to the educational community and other interested users.

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 ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Facilitators and barriers to the utilization of the ACT SMART Implementation Toolkit in community-based organizations: a qualitative study

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Aksheya Sridhar ◽  
Amy Drahota ◽  
Kiersten Walsworth
Keyword(s):  
Technology Acceptance ◽  
Technology Acceptance Model ◽  
Autism Spectrum ◽  
Ease Of Use ◽  
Science Literature ◽  
Community Based ◽  
Web Based ◽  
Community Based Organizations ◽  
Facilitators And Barriers ◽  
Acceptance Model

Abstract Background Evidence-based practices (EBPs) have been shown to improve behavioral and mental health outcomes for children diagnosed with autism spectrum disorder (ASD). Research suggests that the use of these practices in community-based organizations is varied; however, the utilization of implementation guides may bridge the gap between research and practice. The Autism Community Toolkit: Systems to Measure and Adopt Research-Based Treatments (ACT SMART) Implementation Toolkit is a web-based implementation toolkit developed to guide organization-based implementation teams through EBP identification, adoption, implementation, and sustainment in ASD community-based organizations. Methods This study examined the facilitators and barriers (collectively termed “determinants”) to the utilization of this toolkit, based on the perspectives of implementation teams at six ASD community-based organizations. Two independent coders utilized the adapted EPIS framework and the Technology Acceptance Model 3 to guide qualitative thematic analyses of semi-structured interviews with implementation teams. Results Salient facilitators (e.g., facilitation teams, facilitation meetings, phase-specific activities) and barriers (e.g., website issues, perceived lack of ease of use of the website, perceived lack of resources, inner context factors) were identified, highlighting key determinants to the utilization of this toolkit. Additionally, frequent determinants and determinants that differed across adapted EPIS phases of the toolkit were noted. Finally, analyses highlighted two themes: (a) Inner Context Determinants to use of the toolkit (e.g., funding) and (b) Innovation Determinants (e.g., all website-related factors), indicating an interaction between the two models utilized to guide study analyses. Conclusions Findings highlighted several factors that facilitated the utilization of this implementation guide. Additionally, findings identified key areas for improvement for future iterations of the ACT SMART Implementation Toolkit. Importantly, these results may inform the development, refinement, and utilization of implementation guides with the aim of increasing the uptake of EBPs in community-based organizations providing services to children with ASD and their families. Finally, these findings contribute to the implementation science literature by illustrating the joint use of the EPIS framework and Technology Acceptance Model 3 to evaluate the implementation of a web-based toolkit within community-based organizations.

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.

Systematic Investigation of Mouse Models of Parkinson’s Disease by Transcriptome Mapping on a Brain-Specific Genome-Scale Metabolic Network

2021 ◽  
Author(s):  
Ecehan Abdik ◽  
Tunahan Cakir
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Metabolic Network ◽  
Mouse Models ◽  
Mus Musculus ◽  
Metabolic Networks ◽  
Systematic Investigation ◽  
Omics Data ◽  
Metabolic Alterations ◽  
Genome Scale

Genome-scale metabolic networks enable systemic investigation of metabolic alterations caused by diseases by providing interpretation of omics data. Although Mus musculus (mouse) is one of the most commonly used model...

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