Simulation and visualization of multiple KEGG pathways using BioNSi

Motivation: Many biologists are discouraged from using network simulation tools because these require manual, often tedious network construction. This situation calls for building new tools or extending existing ones with the ability to import biological pathways previously deposited in databases and analyze them, in order to produce novel biological insights at the pathway level. Results: We have extended a network simulation tool (BioNSi), which now allows merging of multiple pathways from the KEGG pathway database into a single, coherent network, and visualizing its properties. Furthermore, the enhanced tool enables loading experimental expression data into the network and simulating its dynamics under various biological conditions or perturbations. As a proof of concept, we tested two sets of published experimental data, one related to inflammatory bowel disease condition and the other to breast cancer treatment. We predict some of the major observations obtained following these laboratory experiments, and provide new insights that may shed additional light on these results. Tool requirements: Cytoscape 3.x, JAVA 8 Availability: The tool is freely available at http://bionsi.wix.com/bionsi, where a complete user guide and a step-by-step manual can also be found.

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CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows

F1000Research ◽

10.12688/f1000research.4410.2 ◽

2014 ◽

Vol 3 ◽

pp. 145 ◽

Cited By ~ 11

Author(s):

Lilit Nersisyan ◽

Ruben Samsonyan ◽

Arsen Arakelyan

Keyword(s):

Systems Biology ◽

Protein Interaction ◽

Kegg Pathway ◽

Computer Assisted ◽

Pathway Database ◽

Protein Protein Interaction ◽

Kegg Pathways ◽

Kegg Pathway Database ◽

Context Specific ◽

Biological Context

The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app (http://apps.cytoscape.org/apps/cykeggparser) for Cytoscape 3 that allows manipulation with KEGG pathway maps. Along with basic functionalities for pathway retrieval, visualization and export in KGML and BioPAX formats, the app provides unique features for computer-assisted adjustment of inconsistencies in KEGG pathway KGML files and generation of tissue- and protein-protein interaction specific pathways. We demonstrate that using biological context-specific KEGG pathways created with CyKEGGParser makes systems biology analysis more sensitive and appropriate compared to original pathways.

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KPGminer: A tool for retrieving pathway genes from KEGG pathway database

10.1101/416131 ◽

2018 ◽

Cited By ~ 1

Author(s):

A. K. M. Azad

Keyword(s):

Pathway Analysis ◽

Kegg Pathway ◽

Single Mode ◽

Computational Systems Biology ◽

Pathway Database ◽

Batch Mode ◽

Kegg Pathways ◽

Kegg Pathway Database ◽

Crucial Component ◽

Computational Systems

AbstractPathway analysis is a very important aspect in computational systems biology as it serves as a crucial component in many computational pipelines. KEGG is one of the prominent databases that host pathway information associated with various organisms. In any pathway analysis pipelines, it is also important to collect and organize the pathway constituent genes for which a tool to automatically retrieve that would be a useful one to the practitioners. In this article, I present KPGminer, a tool that retrieves the constituent genes in KEGG pathways for various organisms and organizes that information suitable for many downstream pathway analysis pipelines. We exploited several KEGG web services using REST APIs, particularly GET and LIST methods to request for the information retrieval which is available for developers. Moreover, KPGminer can operate both for a particular pathway (single mode) or multiple pathways (batch mode). Next, we designed a crawler to extract necessary information from the response and generated outputs accordingly. KPGminer brings several key features including organism-specific and pathway-specific extraction of pathway genes from KEGG and always up-to-date information. Thus, we hope KPGminer can be a useful and effective tool to make downstream pathway analysis easier and faster. KPGminer is freely available for download from https://sourceforge.net/projects/kpgminer/.

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Academic Use of Commercial Network Simulation Tools

International Journal of Electrical Engineering Education ◽

10.7227/ijeee.37.2.3 ◽

2000 ◽

Vol 37 (2) ◽

pp. 136-145 ◽

Cited By ~ 2

Author(s):

G. B. Jones ◽

E. Stipidis ◽

E. T. Powner

Keyword(s):

Teaching And Learning ◽

Network Simulation ◽

Simulation Tools ◽

Computer Assistance ◽

Network Communications ◽

Commercial Network ◽

Fast Evolution

The paper describes the use of computer assistance in teaching communications engineering. Today, the fast evolution of network communications makes teaching and learning a huge task. Commercial packages such as COMNET III greatly ease this aspect of learning and allow the student to experiment with ‘change and play’ scenarios.

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Network Simulation Tools for Supporting Teaching in Computer Networks

Simulation in Computer Network Design and Modeling ◽

10.4018/978-1-4666-0191-8.ch023 ◽

2012 ◽

pp. 479-489 ◽

Cited By ~ 1

Author(s):

Shao Ying Zhu ◽

Gerald Schaefer

Keyword(s):

Student Performance ◽

Computer Networks ◽

Network Simulation ◽

Computer Networking ◽

Actual Performance ◽

Simulation Tools ◽

Virtual Computer ◽

Network Administrators ◽

Interactive Feedback ◽

Different Levels

Computer networks have evolved dramatically in recent years and consequently qualified and experienced network administrators are highly sought after, which in turn has led to the development of specialised computer networking courses at many universities. In this chapter, the authors investigate the use of network simulation tools as an alternative to be employed in computer networking laboratories. Network simulation tools provide students with the opportunity to freely experiment with virtual computer networks and equipment without the expensive costs associated with real networking hardware. The results of their research show that students appreciate the use of network simulators and see them as an effective approach to learning computer networking concepts and gaining the relevant experience. This was also confirmed by the actual performance of students who experienced different levels of exposure to networks simulators during their studies. The authors furthermore investigate the use of interactive, electronically assessed lab sessions, where students get immediate and interactive feedback while they are going through lab exercises. Their research shows that this approach not only releases the lecturer from less demanding students to better support weaker students, but that this will also lead to improved student performance and better student retention.

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Development and feasibility of a telemonitoring tool with full integration in the electronic medical record: a proof of concept study for patients with inflammatory bowel disease in remission on biological therapy

Scandinavian Journal of Gastroenterology ◽

10.1080/00365521.2020.1735506 ◽

2020 ◽

Vol 55 (3) ◽

pp. 287-293

Author(s):

Sofie Coenen ◽

Egon Nijns ◽

Ellen Weyts ◽

Patricia Geens ◽

Bart Van den Bosch ◽

...

Keyword(s):

Inflammatory Bowel Disease ◽

Medical Record ◽

Electronic Medical Record ◽

Bowel Disease ◽

Biological Therapy ◽

Proof Of Concept ◽

Concept Study ◽

Inflammatory Bowel

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TargeTALE: A Web Resource to Identify TALEs in Xanthomonas Genomes and Their Respective Targets

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-08-19-0227-a ◽

2019 ◽

Vol 32 (12) ◽

pp. 1577-1580

Author(s):

Frederico Schmitt Kremer ◽

Amanda Munari Guimarães ◽

Christian Domingues Sanchez ◽

Luciano da Silva Pinto

Keyword(s):

Target Genes ◽

Economic Value ◽

Gram Negative Bacteria ◽

Expression Data ◽

Proof Of Concept ◽

Host Gene Expression ◽

Transcription Activator ◽

Gram Negative ◽

Web Resource ◽

Concept Validation

The Xanthomonas genus, comprises more than 30 species of gram-negative bacteria, most of which are pathogens of plants with high economic value, such as rice, common bean, and maize. Transcription activator-like effectors (TALEs), which act by regulating the host gene expression, are some of the major virulence factors of these bacteria. We present a novel tool to identify TALE genes in the genome of Xanthomonas strains and their respective targets. The analysis of the results obtained by TargeTALE in a proof-of-concept validation demonstrate that, at optimum setting, approximately 93% of the predicted target genes with available expression data were confirmed as upregulated during the infection, indicating that the tool might be useful for researchers in the field.

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