Web-Based Genomic-Scale Metabolic Pathways Comparative of Two Actinobacillus pleuropneumoniae Strains

2010 ◽  
Author(s):  
Ren-Feng Li ◽  
Xue-Bin Li ◽  
Kun Zhao ◽  
San-Hu Wang
Keyword(s):  
Metabolic Pathways ◽  
Actinobacillus Pleuropneumoniae ◽  
Web Based ◽  
Genomic Scale

scholarly journals MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 288
Author(s):  
Julia Koblitz ◽  
Dietmar Schomburg ◽  
Meina Neumann-Schaal
Keyword(s):  
Experimental Data ◽  
Systems Biology ◽  
Metabolic Pathways ◽  
Common Knowledge ◽  
Numerical Data ◽  
Omics Data ◽  
Web Based ◽  
Ongoing Research ◽  
Complex Interactions ◽  
Biology Research

Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.

scholarly journals Design, Implementation and Maintenance of a Model Organism Database forArabidopsis thaliana

2004 ◽  
Vol 5 (4) ◽  
pp. 362-369 ◽  
Author(s):  
Danforth Weems ◽  
Neil Miller ◽  
Margarita Garcia-Hernandez ◽  
Eva Huala ◽  
Seung Y. Rhee
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Metabolic Pathways ◽  
Model Organism ◽  
Information Resource ◽  
Model Organism Database ◽  
Software Developers ◽  
Web Based ◽  
Model Plant ◽  
Community Information

TheArabidopsisInformation Resource (TAIR) is a web-based community database for the model plantArabidopsis thaliana. It provides an integrated view of genes, sequences, proteins, germplasms, clones, metabolic pathways, gene expression, ecotypes, polymorphisms, publications, maps and community information. TAIR is developed and maintained by collaboration between software developers and biologists. Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software. Software developers design, implement and test the database and software. In this review, we briefly describe how TAIR was built and is being maintained.

WinBEST-KIT: WINDOWS-BASED BIOCHEMICAL REACTION SIMULATOR FOR METABOLIC PATHWAYS

2006 ◽  
Vol 04 (03) ◽  
pp. 621-638 ◽  
Author(s):  
TATSUYA SEKIGUCHI ◽  
MASAHIRO OKAMOTO
Keyword(s):  
Metabolic Pathways ◽  
Time Course ◽  
System Analysis ◽  
Competitive Inhibition ◽  
Reaction Scheme ◽  
Mass Action ◽  
Biochemical Reaction ◽  
Engineering System ◽  
Web Based ◽  
Mathematical Equations

We have implemented an efficient, user-friendly biochemical reaction simulator called Web-based BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing large-scale nonlinear networks such as metabolic pathways. Users can easily design and analyze an arbitrary reaction scheme through the Internet and an efficient graphical user interface without considering the mathematical equations. The reaction scheme can include several reaction types, which are represented by both the mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state, such as Michaelis-Menten, Hill cooperative, Competitive inhibition. However, since all modules in Web-based BEST-KIT have been developed in Java™ applet style, users cannot optionally make use of original mathematical equations in addition to the prepared equations. In the present study, we have developed a new version of BEST-KIT (for Microsoft® Windows® called WinBEST-KIT) to allow users to define original mathematical equations and to customize these equations very easily as user-defined reaction symbols. The following powerful system-analytical methods are prepared for system analysis: time-course calculation, parameter scanning, estimation of the values of unknown kinetic parameters based on experimentally observed time-course data of reactants, dynamic response of reactants against virtual external perturbations, and real-time simulation (Virtual Dry Lab).

Web-Based Bioinformatics Analysis of TbpB from Actinobacillus pleuropneumonie L20 Strain

2012 ◽  
Vol 466-467 ◽  
pp. 256-261
Author(s):  
Ren Feng Li ◽  
Xiang Qin Tian ◽  
Kun Zhao ◽  
Jin Qing Jiang ◽  
San Hu Wang
Keyword(s):  
Membrane Protein ◽  
Bioinformatics Analysis ◽  
Binding Protein ◽  
Iron Acquisition ◽  
Protein A ◽  
Actinobacillus Pleuropneumoniae ◽  
Biological Characterization ◽  
Web Based

The transferring(Tf) receptor from Actinobacillus pleuropneumoniae (App) is comprised of a surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), both of which are essential for survival in the host, and TbpB is required for the iron acquisition process in vivo. In this study. We analyzed the salient features of the TbpB gene and encoded protein of App L20 strain by bioinformatics tools and highlighted its important biological characterization, which. providing insights into the mechanism of Tf binding and the role of TbpB,

scholarly journals BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 4
Author(s):  
Caroline Gaud ◽  
Bebiana C. Sousa ◽  
An Nguyen ◽  
Maria Fedorova ◽  
Zhixu Ni ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Biological Sample ◽  
Biosynthetic Pathways ◽  
Single Experiment ◽  
Web Based ◽  
Lipid Molecular Species ◽  
Large Numbers ◽  
Mammalian Tissues ◽  
Biological Differences ◽  
Multiple Categories

Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample.  As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment.  Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways.  As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging.  BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways.  BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

scholarly journals MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 288 ◽  
Author(s):  
Julia Koblitz ◽  
Dietmar Schomburg ◽  
Meina Neumann-Schaal
Keyword(s):  
Experimental Data ◽  
Systems Biology ◽  
Metabolic Pathways ◽  
Common Knowledge ◽  
Numerical Data ◽  
Omics Data ◽  
Web Based ◽  
Ongoing Research ◽  
Complex Interactions ◽  
Biology Research

Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.

scholarly journals BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 4
Author(s):  
Caroline Gaud ◽  
Bebiana C. Sousa ◽  
An Nguyen ◽  
Maria Fedorova ◽  
Zhixu Ni ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Biological Sample ◽  
Biosynthetic Pathways ◽  
Single Experiment ◽  
Web Based ◽  
Lipid Molecular Species ◽  
Large Numbers ◽  
Mammalian Tissues ◽  
Biological Differences ◽  
Multiple Categories

Lipidomics increasingly describes the quantitation using mass spectrometry of all lipids present in a biological sample.  As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment.  Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways.  As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging.  BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways.  BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.

The PBL-Evaluator: a web-based tool for assessment in tutorials

1998 ◽  
Vol 62 (9) ◽  
pp. 671-674
Author(s):  
JF Chaves ◽  
JA Chaves ◽  
MS Lantz
Keyword(s):  
Web Based

Using Popular Mobile Devices in Voice Therapy

2013 ◽  
Vol 23 (3) ◽  
pp. 82-87 ◽  
Author(s):  
Eva van Leer
Keyword(s):  
Exercise Behavior ◽  
Voice Therapy ◽  
Pure Oxygen ◽  
Mobile Platforms ◽  
Self Monitoring ◽  
Web Based ◽  
Motivational Messages ◽  
Related Information ◽  
Health Related ◽  
Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

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