Submission information
Submission Number: 121
Submission ID: 214
Submission UUID: b6d1b5ba-965f-4bdf-8b71-7baea0c98291
Submission URI: /form/project
Created: Wed, 10/13/2021 - 14:08
Completed: Wed, 10/13/2021 - 14:22
Changed: Wed, 10/13/2021 - 14:22
Remote IP address: 74.78.188.196
Submitted by: Bruce Segee
Language: English
Is draft: No
Webform: Project
| Project Title | Computational model of interphase chromosome territories in a simulated cell nucleus |
|---|---|
| Program | Northeast |
| Project Leader | Andre Khalil |
| andre.khalil@maine.edu | |
| Mobile Phone | |
| Work Phone | |
| Mentor(s) | Larry Whitsel |
| Student-facilitator(s) | |
| Mentee(s) | |
| Project Description | This project started in the mid 2000s during our work centered on the development of a novel image segmentation approach called the Wavelet Transform Modulus Maxima (WTMM) segmentation method. Our first application on the segmentation and analysis of fluorescence microscopy images of chromosome territories (CTs) from interphase mouse lymphocytes (Khalil et al. 2007 DOI:doi.org/10.1007/s10577-007-1172-8). As an accompaniment to the segmentation approach, the biological analysis motivated us to develop a computational (in silico) random model to which the empirical observations could be compared to. In this model, CTs are modeled as ellipsoids having similar geometrical attributes as the empirical data (in terms of volume, diameter, and surface area), except that they are randomly rotated and randomly positioned within a simulated cell nucleus that is also based on empirical observations. For each realization, measurements such as inter-CT distance, radial distance, relationship between CT size and eccentricity vs. their position within the nucleus, etc., are made and compared to the empirical data obtained from the fluorescence microscopy images. The overall purpose of this computational model is to provide a randomized numerical version of the empirical observations of chromosome territories, to help demonstrate and quantify their non-random (preferential) position. The biomedical context is that in a disease state (e.g. cancer), the shape and position of some CTs are known to be altered, which motivates the development of potential early diagnosis computational approaches. In our most recent work (https://digitalcommons.library.umaine.edu/etd/3416) we used the numerical model to show that a subset of CTs from mouse lymphocytes were closer to the periphery of the cell nucleus when compared random positioning. However, due to computational constraints (both in terms of coding efficiency and computing power), the work was limited in two ways: only one measurement was made (the radial distance) and only one CT was simulated at a time. The computing time for the program to converge when placing several CTs increases greatly with increasing number of CTs. Placing at least four CTs is our goal, so that we can also include inter-CT measurements. |
| Project Deliverables | Our two project deliverables are to 1) extend the model so that it can handle more than one CT at a time (at least four is our goal) and 2) with the addition of more CTs, implement the calculation of additional measurements such as inter-CT distances, etc. |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | Ideally a proficient programmer with experience in monte-carlo methods |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Practical applications |
| Mentee Programming Skill Level | |
| Project Institution | University of Maine |
| Project Address | 5708 Barrows Hall Orono, Maine. 04469 |
| Anchor Institution | NE-University of Maine |
| Preferred Start Date | |
| Start as soon as possible. | Yes |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | 2 |
| Launch Presentation | |
| Launch Presentation Date | |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
|
| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | The measurements obtained from this parallelized program will allow us to complete a manuscript for publication in a peer reviewed journal. These data are eagerly anticipated and will complement the computational analysis presented in the last student who participated in this project (https://digitalcommons.library.umaine.edu/etd/3416). |
| What will the student learn? | The student will learn about the biological context (cell nucleus architecture), the geometrical measurements being made, C++ memory allocation and overall programming, parallelization and implementation on a supercluster. |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | The contributions to the program are likely to be the exposure to the biological application (e.g. chromosome territories and their altered positions and morphologies in disease states). |
| HPC resources needed to complete this project? | Sufficient resources are available. |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |