Matching Items (3)
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- All Subjects: Visualization
- Creators: Anbar, Ariel
- Creators: Bodford, Jessica
Description
The greatest barrier to understanding how life interacts with its environment is the complexity in which biology operates. In this work, I present experimental designs, analysis methods, and visualization techniques to overcome the challenges of deciphering complex biological datasets. First, I examine an iron limitation transcriptome of Synechocystis sp. PCC 6803 using a new methodology. Until now, iron limitation in experiments of Synechocystis sp. PCC 6803 gene expression has been achieved through media chelation. Notably, chelation also reduces the bioavailability of other metals, whereas naturally occurring low iron settings likely result from a lack of iron influx and not as a result of chelation. The overall metabolic trends of previous studies are well-characterized but within those trends is significant variability in single gene expression responses. I compare previous transcriptomics analyses with our protocol that limits the addition of bioavailable iron to growth media to identify consistent gene expression signals resulting from iron limitation. Second, I describe a novel method of improving the reliability of centroid-linkage clustering results. The size and complexity of modern sequencing datasets often prohibit constructing distance matrices, which prevents the use of many common clustering algorithms. Centroid-linkage circumvents the need for a distance matrix, but has the adverse effect of producing input-order dependent results. In this chapter, I describe a method of cluster edge counting across iterated centroid-linkage results and reconstructing aggregate clusters from a ranked edge list without a distance matrix and input-order dependence. Finally, I introduce dendritic heat maps, a new figure type that visualizes heat map responses through expanding and contracting sequence clustering specificities. Heat maps are useful for comparing data across a range of possible states. However, data binning is sensitive to clustering cutoffs which are often arbitrarily introduced by researchers and can substantially change the heat map response of any single data point. With an understanding of how the architectural elements of dendrograms and heat maps affect data visualization, I have integrated their salient features to create a figure type aimed at viewing multiple levels of clustering cutoffs, allowing researchers to better understand the effects of environment on metabolism or phylogenetic lineages.
ContributorsKellom, Matthew (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Elser, James (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2017
Description
Social media has become a direct and effective means of transmitting personal opinions into the cyberspace. The use of certain key-words and their connotations in tweets portray a meaning that goes beyond the screen and affects behavior. During terror attacks or worldwide crises, people turn to social media as a means of managing their anxiety, a mechanism of Terror Management Theory (TMT). These opinions have distinct impacts on the emotions that people express both online and offline through both positive and negative sentiments. This paper focuses on using sentiment analysis on twitter hash-tags during five major terrorist attacks that created a significant response on social media, which collectively show the effects that 140-character tweets have on perceptions in social media. The purpose of analyzing the sentiments of tweets after terror attacks allows for the visualization of the effect of key-words and the possibility of manipulation by the use of emotional contagion. Through sentiment analysis, positive, negative and neutral emotions were portrayed in the tweets. The keywords detected also portray characteristics about terror attacks which would allow for future analysis and predictions in regards to propagating a specific emotion on social media during future crisis.
ContributorsHarikumar, Swathikrishna (Author) / Davulcu, Hasan (Thesis director) / Bodford, Jessica (Committee member) / Computer Science and Engineering Program (Contributor) / Department of Information Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Elizabeth Grumbach, the project manager of the Institute for Humanities Research's Digital Humanities Initiative, shares methodologies and best practices for designing a digital humanities project. The workshop will offer participants an introduction to digital humanities fundamentals, specifically tools and methodologies. Participants explore technologies and platforms that allow scholars of all skills levels to engage with digital humanities methods. Participants will be introduced to a variety of tools (including mapping, visualization, data analytics, and multimedia digital publication platforms), and how and why to choose specific applications, platforms, and tools based on project needs.
ContributorsGrumbach, Elizabeth (Author)
Created2018-09-26