Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
In this experiment, a haptic glove with vibratory motors on the fingertips was tested against the standard HTC Vive controller to see if the additional vibrations provided by the glove increased immersion in common gaming scenarios where haptic feedback is provided. Specifically, two scenarios were developed: an explosion scene containing a small and large explosion and a box interaction scene that allowed the participants to touch the box virtually with their hand. At the start of this project, it was hypothesized that the haptic glove would have a significant positive impact in at least one of these scenarios. Nine participants took place in the study and immersion was measured through a post-experiment questionnaire. Statistical analysis on the results showed that the haptic glove did have a significant impact on immersion in the box interaction scene, but not in the explosion scene. In the end, I conclude that since this haptic glove does not significantly increase immersion across all scenarios when compared to the standard Vive controller, it should not be used at a replacement in its current state.
The process of learning a new skill can be time consuming and difficult for both the teacher and the student, especially when it comes to computer modeling. With so many terms and functionalities to familiarize oneself with, this task can be overwhelming to even the most knowledgeable student. The purpose of this paper is to describe the methodology used in the creation of a new set of curricula for those attempting to learn how to use the Dynamic Traffic Simulation Package with Multi-Resolution Modeling. The current DLSim curriculum currently relates information via high-concept terms and complicated graphics. The information in this paper aims to provide a streamlined set of curricula for new users of DLSim, including lesson plans and improved infographics.
This project is a video game implementation of the Filipino ruleset of Mahjong for the purpose of increasing awareness of the Mahjong game and Filipino culture. The game, titled Todas!, is built from scratch using various free resources and contains a Tutorial for teaching players the basics of the game and a Multiplayer mode that enables remote gameplay for up to four people.
For my Spring 2022-23 Barrett Honors College creative project, I designed and created my own analog game. The created game is a tile-management game for 2-4 players called Plash. Players collect tiles and manipulate the board to complete goals and win the game. The paper for this project details the inspirations and research done for the game’s design, the game's design journey, and detailed instructions on how to play.
My creative project is an extension of my Computer Science capstone project, a Tamagotchi-style game in which the user takes care of an ocean animal. It focuses specifically on expanding upon two of the project’s design goals: improving user retention and fostering a bond between the user and the virtual character they are taking care of. The project consists of researching Human Computer Interaction principles, selecting an assortment that are most relevant to my project, and integrating them into the design of mechanics for the game. The goal of this project is to demonstrate how integrating HCI design principles into game design can foster new ideas and improve the experience of the game for its users.
NASA has partnered with multiple colleges, including ASU, on a mission to study an asteroid called Psyche. Psyche is the first asteroid discovered made of metal, mostly iron, that is close enough for us to study and could give insight into what Earth’s core is like. The mission plans and research documents on how the various measurement tools work are not engaging to those without a background in STEM. This serves as inspiration to make a web-based game in order to make the information more engaging to the player. This web-based game will take the user through the Psyche mission going from the assembly of the measurement tools all the way to when the satellite is orbiting the asteroid. The creative project consisted of creating a simulation for a young audience, between ages 10 and 18, to experience what the mission could look like once the satellite is at the Psyche asteroid and what the data collected could mean. The asteroid could have been formed through a process called the dynamo process or it could be a piece of a larger parent body. It could be made mostly of metal or silicates, which will be determined during the mission. These are some of the results that will be generalized and relayed to the player. This creative project includes the four main sections of the orbit phase of the mission in which the users will perform tasks to collect some data in order to see some of the generalized possible results of the study of Psyche. Some of the data collected would be the amount of metal making up the asteroid and figuring out what the gravitational pull is. The first main section will use the magnetometer, the second section will use the multispectral imager, the third section will use X-Band Radio Waves, and the fourth section will use the gamma ray and neutron spectrometer.