scholarly journals A Dashboard Component for Pathway Visualization

2020 ◽  
Vol 40 (156) ◽  
pp. 8-13
Author(s):  
Kozo NISHIDA ◽  
Kazunari KAIZU ◽  
Koichi TAKAHASHI
Keyword(s):  
Pathway Visualization

Metabolic pathway visualization in living yeast by DNP-NMR

2011 ◽  
Vol 7 (10) ◽  
pp. 2834 ◽  
Author(s):  
Sebastian Meier ◽  
Magnus Karlsson ◽  
Pernille R. Jensen ◽  
Mathilde H. Lerche ◽  
Jens Ø. Duus
Keyword(s):  
Metabolic Pathway ◽  
Pathway Visualization

Visualizing Biological Pathways: Requirements Analysis, Systems Evaluation and Research Agenda

2005 ◽  
Vol 4 (3) ◽  
pp. 191-205 ◽  
Author(s):  
Purvi Saraiya ◽  
Chris North ◽  
Karen Duca
Keyword(s):  
Pathway Analysis ◽  
Research Agenda ◽  
Biological Organization ◽  
Levels Of Abstraction ◽  
Pathway Visualization ◽  
Domain Experts ◽  
Biologically Relevant ◽  
Data Intensive ◽  
Complex Interactions ◽  
Visualization Systems

Pathway diagrams are used by life scientists to represent complex interactions at the molecular level in living cells. The recent shift towards data-intensive bioinformatics and systems-level science has created a strong need for advanced pathway visualizations that support exploratory analysis. This paper presents a comprehensive list of requirements for pathway visualization systems, based on interviews conducted to understand life scientists' needs for pathway analysis. A variety of existing pathway visualization systems are examined, to analyze common approaches by which the contemporary systems address these requirements. A heuristic evaluation, by biology domain experts, of five popular pathway visualization systems is conducted to analyze the end-user perception of these systems. Based on these studies, a research agenda is presented concerning five critical requirements for pathway visualization systems. If addressed effectively, these requirements can prove to be most helpful in supporting exploratory pathway analysis. These include: (1) automated construction and updating of pathways by searching literature databases, (2) overlaying information on pathways in a biologically relevant format, (3) linking pathways to multi-dimensional data from high-throughput experiments such as microarrays, (4) overviewing multiple pathways simultaneously with interconnections between them, (5) scaling pathways to higher levels of abstraction to analyze effects of complex molecular interactions at higher levels of biological organization.

scholarly journals Pathview Web: user friendly pathway visualization and data integration

2017 ◽  
Vol 45 (W1) ◽  
pp. W501-W508 ◽  
Author(s):  
Weijun Luo ◽  
Gaurav Pant ◽  
Yeshvant K. Bhavnasi ◽  
Steven G. Blanchard ◽  
Cory Brouwer
Keyword(s):  
Data Integration ◽  
Pathway Visualization ◽  
User Friendly

scholarly journals Reactome enhanced pathway visualization

2017 ◽  
Vol 33 (21) ◽  
pp. 3461-3467 ◽  
Author(s):  
Konstantinos Sidiropoulos ◽  
Guilherme Viteri ◽  
Cristoffer Sevilla ◽  
Steve Jupe ◽  
Marissa Webber ◽  
...  
Keyword(s):  
Pathway Visualization

Algorithmic Basis for Pathway Visualization

2008 ◽  
pp. 67-102 ◽  
Author(s):  
Sergey Simakov ◽  
Iaroslav Ispolatov ◽  
Sergei Maslov ◽  
Alexander Nikitin
Keyword(s):  
Pathway Visualization
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