The visual display of quantitative information
The visual display of quantitative information
Seeing the forest for the trees: hierarchical displays of hypertext structures
COCS '88 Proceedings of the ACM SIGOIS and IEEECS TC-OA 1988 conference on Office information systems
Finding usability problems through heuristic evaluation
CHI '92 Proceedings of the SIGCHI Conference on Human Factors in Computing Systems
Pad++: a zooming graphical interface for exploring alternate interface physics
UIST '94 Proceedings of the 7th annual ACM symposium on User interface software and technology
Usability engineering: scenario-based development of human-computer interaction
Usability engineering: scenario-based development of human-computer interaction
Graph Visualization and Navigation in Information Visualization: A Survey
IEEE Transactions on Visualization and Computer Graphics
Cognitive measurements of graph aesthetics
Information Visualization
PathwayFinder: paving the way towards automatic pathway extraction
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
An Insight-Based Methodology for Evaluating Bioinformatics Visualizations
IEEE Transactions on Visualization and Computer Graphics
Proceedings of the Working Conference on Advanced Visual Interfaces
An Insight-Based Methodology for Evaluating Bioinformatics Visualizations
IEEE Transactions on Visualization and Computer Graphics
An Insight-Based Longitudinal Study of Visual Analytics
IEEE Transactions on Visualization and Computer Graphics
An assessment of the role of computing in systems biology
IBM Journal of Research and Development - Systems biology
Visual data mining of multimedia data for social and behavioral studies
Information Visualization
Glycobrowser: a tool for contextual visualization of biological data and pathways using ontologies
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Human-centered visualization environments
Human-centered visualization environments
Comparing benchmark task and insight evaluation methods on timeseries graph visualizations
Proceedings of the 3rd BELIV'10 Workshop: BEyond time and errors: novel evaLuation methods for Information Visualization
A novel grid-based visualization approach for metabolic networks with advanced focus&context view
GD'09 Proceedings of the 17th international conference on Graph Drawing
A comparison of benchmark task and insight evaluation methods for information visualization
Information Visualization - Special issue on Evaluation for Information Visualization
Visualizing genome expression and regulatory network dynamics in genomic and metabolic context
EuroVis'08 Proceedings of the 10th Joint Eurographics / IEEE - VGTC conference on Visualization
Navigation and exploration of interconnected pathways
EuroVis'08 Proceedings of the 10th Joint Eurographics / IEEE - VGTC conference on Visualization
Pathway preserving representation of metabolic networks
EuroVis'11 Proceedings of the 13th Eurographics / IEEE - VGTC conference on Visualization
Domain specific vs generic network visualization: an evaluation with metabolic networks
AUIC '11 Proceedings of the Twelfth Australasian User Interface Conference - Volume 117
Guiding the interactive exploration of metabolic pathway interconnections
Information Visualization
Semi-automatic drawing of metabolic networks
Information Visualization - Special issue on Best Papers of Visual Analytics Science and Technology (VAST) 2010
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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.