A widespread use of high-throughput gene expression analysis techniques enabled the biomedical research community to share a huge body of gene expression datasets in many public databases on the web. However, current ...
详细信息
A widespread use of high-throughput gene expression analysis techniques enabled the biomedical research community to share a huge body of gene expression datasets in many public databases on the web. However, current gene expression data repositories provide static representations of the data and support limited interactions. This hinders biologists from effectively exploring shared gene expression datasets. Responding to the growing need for better interfaces to improve the utility of the public datasets, we have designed and developed a new web-based visual interface entitled GeneShelf (hftp://***/GeneShelf). It builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. We applied GeneShelf to one of the largest microarray datasets generated to study the progression and recovery process of injuries at the spinal cord of mice and rats. We present a case study and a preliminary qualitative user study with biologists to show the utility and usability of GeneShelf.
A widespread use of high-throughput gene expression analysis techniques enabled the biomedical research community to share a huge body of gene expression datasets in many public databases on the web. However, current ...
详细信息
A widespread use of high-throughput gene expression analysis techniques enabled the biomedical research community to share a huge body of gene expression datasets in many public databases on the web. However, current gene expression data repositories provide static representations of the data and support limited interactions. This hinders biologists from effectively exploring shared gene expression datasets. Responding to the growing need for better interfaces to improve the utility of the public datasets, we have designed and developed a new web-based visual interface entitled GeneShelf (hftp://***/GeneShelf). It builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. We applied GeneShelf to one of the largest microarray datasets generated to study the progression and recovery process of injuries at the spinal cord of mice and rats. We present a case study and a preliminary qualitative user study with biologists to show the utility and usability of GeneShelf.
One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short sub-sequences produced by current technologies. The final stages of the genome assembly process inevit...
详细信息
One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short sub-sequences produced by current technologies. The final stages of the genome assembly process inevitably require manual inspection of data inconsistencies and could be greatly aided by visualization. This paper presents our design decisions in translating key data features identified through discussions with analysts into a concise visual encoding. Current visualization tools in this domain focus on local sequence errors making high-level inspection of the assembly difficult if not impossible. We present a novel interactive graph display, ABySS-Explorer, that emphasizes the global assembly structure while also integrating salient data features such as sequence length. Our tool replaces manual and in some cases pen-and-paper based analysis tasks, and we discuss how user feedback was incorporated into iterative design refinements. Finally, we touch on applications of this representation not initially considered in our design phase, suggesting the generality of this encoding for DNA sequence data.
One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short sub-sequences produced by current technologies. The final stages of the genome assembly process inevit...
详细信息
One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short sub-sequences produced by current technologies. The final stages of the genome assembly process inevitably require manual inspection of data inconsistencies and could be greatly aided by visualization. This paper presents our design decisions in translating key data features identified through discussions with analysts into a concise visual encoding. Current visualization tools in this domain focus on local sequence errors making high-level inspection of the assembly difficult if not impossible. We present a novel interactive graph display, ABySS-Explorer, that emphasizes the global assembly structure while also integrating salient data features such as sequence length. Our tool replaces manual and in some cases pen-and-paper based analysis tasks, and we discuss how user feedback was incorporated into iterative design refinements. Finally, we touch on applications of this representation not initially considered in our design phase, suggesting the generality of this encoding for DNA sequence data.
Biologists hope to address grand scientific challenges by exploring the abundance of data made available through microarray analysis and other high-throughput techniques. However, the impact of this large volume of da...
详细信息
Biologists hope to address grand scientific challenges by exploring the abundance of data made available through microarray analysis and other high-throughput techniques. However, the impact of this large volume of data is limited unless researchers can effectively assimilate the entirety of this complex information and integrate it into their daily research;interactive visualization tools are called for to support the effort. Specifically, typical studies of gene coexpression can make use of novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters and achieving data reduction. These tools should allow biologists to develop an intuitive understanding of the structure of biological networks and discover genes that reside in critical positions in networks and pathways. By using a graph as a universal data representation of correlation in gene expression data, our novel visualization tool employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene coexpression data integrates techniques such as graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by querying an optimized B-tree, dynamic level-of-detail graph abstraction, and template-based fuzzy classification using neural networks. We demonstrate our system using a real-world workflow from a large-scale systems genetics study of mammalian gene coexpression.
The influence of color on size and depth perception has been explored for a century, but there is very limited research on interventions that can reduce the color illusions. This study was motivated to identify interv...
详细信息
The influence of color on size and depth perception has been explored for a century,
but there is very limited research on interventions that can reduce the color illusions. This study was motivated to identify interventions and propose design guidelines for information
visualization, especially where size judgment is critical.
This study replicated the color size illusion and color depth illusion on an LCD
monitor and it was found that yellow is the smallest and farthest color among red, yellow,
green, and blue on a white background. Three types of interventions (background
brightness, border color, and background grid brightness) were tested to identify the
conditions that reduce the color illusions, but all of them were not statistically significant.
Based on the experiment results and literature survey, design guidelines were
proposed. To extend the guidelines to the bioinformatics field, design recommendations
were proposed and implementation examples were illustrated. Evaluations on design
implementations were evaluated by interviewing domain experts.
Additionally, the relationship between the color size illusion and the color depth
illusion was explored.
暂无评论