Matching Items (8)
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- All Subjects: Unity
- Creators: Computing and Informatics Program
Description
Valley Fever, also known as coccidioidomycosis, is a respiratory disease that affects 10,000 people annually, primarily in Arizona and California. Due to a lack of gene annotation, diagnosis and treatment of Valley Fever is severely limited. In turn, gene annotation efforts are also hampered by incomplete genome sequencing. We intend to use proteogenomic analysis to reannotate the Coccidioides posadasii str. Silveira genome from protein-level data. Protein samples extracted from both phases of Silveira were fragmented into peptides, sequenced, and compared against databases of known and predicted proteins sequences, as well as a de novo six-frame translation of the genome. 288 unique peptides were located that did not match a known Silveira annotation, and of those 169 were associated with another Coccidioides strain. Additionally, 17 peptides were found at the boundary of, or outside of, the current gene annotation comprising four distinct clusters. For one of these clusters, we were able to calculate a lower bound and an estimate for the size of the gap between two Silveira contigs using the Coccidioides immitis RS transcript associated with that cluster's peptides \u2014 these predictions were consistent with the current annotation's scaffold structure. Three peptides were associated with an actively translated transposon, and a putative active site was located within an intact LTR retrotransposon. We note that gene annotation is necessarily hindered by the quality and level of detail in prior genome sequencing efforts, and recommend that future studies involving reannotation include additional sequencing as well as gene annotation via proteogenomics or other methods.
ContributorsSherrard, Andrew (Author) / Lake, Douglas (Thesis director) / Grys, Thomas (Committee member) / Mitchell, Natalie (Committee member) / Computing and Informatics Program (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The objective of this creative project was to gain experience in digital modeling, animation, coding, shader development and implementation, model integration techniques, and application of gaming principles and design through developing a professional educational game. The team collaborated with Glendale Community College (GCC) to produce an interactive product intended to supplement educational instructions regarding nutrition. The educational game developed, "Nutribots" features the player acting as a nutrition based nanobot sent to the small intestine to help the body. Throughout the game the player will be asked nutrition based questions to test their knowledge of proteins, carbohydrates, and lipids. If the player is unable to answer the question, they must use game mechanics to progress and receive the information as a reward. The level is completed as soon as the question is answered correctly. If the player answers the questions incorrectly twenty times within the entirety of the game, the team loses faith in the player, and the player must reset from title screen. This is to limit guessing and to make sure the player retains the information through repetition once it is demonstrated that they do not know the answers. The team was split into two different groups for the development of this game. The first part of the team developed models, animations, and textures using Autodesk Maya 2016 and Marvelous Designer. The second part of the team developed code and shaders, and implemented products from the first team using Unity and Visual Studio. Once a prototype of the game was developed, it was show-cased amongst peers to gain feedback. Upon receiving feedback, the team implemented the desired changes accordingly. Development for this project began on November 2015 and ended on April 2017. Special thanks to Laura Avila Department Chair and Jennifer Nolz from Glendale Community College Technology and Consumer Sciences, Food and Nutrition Department.
ContributorsNolz, Daisy (Co-author) / Martin, Austin (Co-author) / Quinio, Santiago (Co-author) / Armstrong, Jessica (Co-author) / Kobayashi, Yoshihiro (Thesis director) / Valderrama, Jamie (Committee member) / School of Arts, Media and Engineering (Contributor) / School of Film, Dance and Theatre (Contributor) / Department of English (Contributor) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Herberger Institute for Design and the Arts (Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Natural Language Processing and Virtual Reality are hot topics in the present. How can we synthesize these together in order to make a cohesive experience? The game focuses on users using vocal commands, building structures, and memorizing spatial objects. In order to get proper vocal commands, the IBM Watson API for Natural Language Processing was incorporated into our game system. User experience elements like gestures, UI color change, and images were used to help guide users in memorizing and building structures. The process to create these elements were streamlined through the VRTK library in Unity. The game has two segments. The first segment is a tutorial level where the user learns to perform motions and in-game actions. The second segment is a game where the user must correctly create a structure by utilizing vocal commands and spatial recognition. A standardized usability test, System Usability Scale, was used to evaluate the effectiveness of the game. A survey was also created in order to evaluate a more descriptive user opinion. Overall, users gave a positive score on the System Usability Scale and slightly positive reviews in the custom survey.
ContributorsOrtega, Excel (Co-author) / Ryan, Alexander (Co-author) / Kobayashi, Yoshihiro (Thesis director) / Nelson, Brian (Committee member) / Computing and Informatics Program (Contributor) / School of Art (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Last Hymn was created by the team of Tyler Pinho, Jefferson Le, and Curtis Spence with the desire to create an eccentric Role Playing Game focused on the exploration of a strange, dying world. Battles in the game are based off of rhythm games like Dance Dance Revolution using a procedural generation algorithm that makes every encounter unique. This is then complemented with the path system where each enemy has unique rhythm patterns to give them different types of combat opportunities. In Last Hymn, the player arrives on a train at the World's End Train Station where they are greeted by a mysterious figure and guided to the Forest where they witness the end of the world and find themselves back at the train station before they left for the Forest. With only a limited amount of time per cycle of the world, the player must constantly weigh the opportunity cost of each decision, and only with careful thought, conviction, and tenacity will the player find a conclusion from the never ending cycle of rebirth. Blending both Shinto architecture and modern elements, Last Hymn used a "fantasy-chic" aesthetic in order to provide memorable locations and dissonant imagery. As the player explores they will struggle against puzzles and dynamic, rhythm based combat while trying to unravel the mystery of the world's looping time. Last Hymn was designed to develop innovative and dynamic new solutions for combat, exploration, and mapping. From this project all three team members were able to grow their software development and game design skills, achieving goals like improved level design, improved asset pipelines while simultaneously aiming to craft an experience that will be unforgettable for players everywhere.
ContributorsPinho, Tyler (Co-author) / Le, Jefferson (Co-author) / Spence, Curtis (Co-author) / Nelson, Brian (Thesis director) / Walker, Erin (Committee member) / Kobayashi, Yoshihiro (Committee member) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.
Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).
ContributorsTollis, Marc (Author) / DeNardo, Dale F (Author) / Cornelius, John A (Author) / Dolby, Greer A (Author) / Edwards, Taylor (Author) / Henen, Brian T. (Author) / Karl, Alice E. (Author) / Murphy, Robert W. (Author) / Kusumi, Kenro (Author)
Created2017-05-31
Description
Cancer is a disease which can affect all animals across the tree of life. Certain species have undergone natural selection to reduce or prevent cancer. Mechanisms to block cancer may include, among others, a species possessing additional paralogues of tumor suppressor genes, or decreasing the number of oncogenes within their genome. To understand cancer prevention patterns across species, I developed a bioinformatic pipeline to identify copies of 545 known tumor suppressor genes and oncogenes across 63 species of mammals. I used phylogenetic regressions to test for associations between cancer gene copy numbers and a species’ life history. I found a significant association between cancer gene copies and species’ longevity quotient. Additional paralogues of tumor suppressor genes and oncogenes is not solely dependent on body size, but rather the balance between body size and longevity. Additionally, there is a significance association between life history traits and genes that are both germline and somatic tumor suppressor genes. The bioinformatic pipeline identified large tumor suppressor gene and oncogene copy numbers in the naked mole rat (Heterocephalus glaber), armadillo (Dasypus novemcinctus), and the two-fingered sloth (Choloepus hoffmanni). These results suggest that increased paralogues of tumor suppressor genes and oncogenes are these species’ modes of cancer resistance.
ContributorsSchneider-Utaka, Aika Kunigunda (Author) / Maley, Carlo C (Thesis advisor) / Wilson, Melissa A. (Committee member) / Tollis, Marc (Committee member) / Arizona State University (Publisher)
Created2019
Description
The instruction of students in computer science concepts can be enhanced by creating programmable simulations and games. ASU VIPLE, which is a framework used to control simulations, robots, and for IoT applications, can be used as an educational tool. Further, the Unity engine allows the creation of 2D and 3D games. The development of basic minigames in Unity can provide simulations for students to program. One can run the Unity minigame and their corresponding VIPLE script to control them over a network connection as well as locally. The minigames conform to the robot output and robot input interfaces supported by VIPLE. With this goal in mind, a snake game, a space shooter game, and a runner game have been created as Unity simulations, which can be controlled by scripts made using VIPLE. These games represent simulated environments that, with movement output and sensor input, students can program simply and externally from VIPLE to help learn robotics and computer science principles.
ContributorsChristensen, Collin Riley (Author) / Chen, Yinong (Thesis director) / Kobayashi, Yoshihiro (Committee member) / Computer Science and Engineering Program (Contributor) / Computing and Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The goal of this project was to determine if the chosen research and testing method would result in a game where students would practice math in the best way. This was done by creating a video game using Unity that followed key principles for designing a math game and for how students should practice math in general. Testing was done on participants to determine the strategies they used in order to play the game and these strategies were then defined and categorized based on their effectiveness and how well they met the learning principles. Also, the participants were asked a before and after question to determine if the game improved their overall attitude towards math to make sure the game was helping them learn and was not a hindrance. There was an overall increase in the participants’ feelings towards math after playing the game as well as beneficial strategies, so the research and testing method was overall a success.
ContributorsVaillancourt, Tyler (Author) / Kobayashi, Yoshihiro (Thesis director) / Amresh, Ashish (Committee member) / Barrett, The Honors College (Contributor) / Computing and Informatics Program (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-05