Howdy! My name is Ogenna Esimai. I attend the University of Texas at Arlington (UTA) where my major is Computer Science in the Department of Computer Science and Engineering. I just completed my sophomore year and plan to graduate in two years. For the summer I shall be carrying out research under Dr. Nancy Amato, my faculty research mentor, and Hsin-Yi (Cindy) Yeh, my graduate student mentor.
Dr. Amato is Unocal Professor, Department of Computer Science and Engineering, Texas A&M University (TAMU), College Station, an endowed professorship she has held since 2011. Dr. Amato is also Interim Head of the Computer Science and Engineering Department and co-directs the Parasol Lab. Her research focuses on motion planning and robotics, computational biology and geometry, and parallel and distributed computing. Dr. Amato is a speaker for the ACM (Association for Computing Machinery) Distinguished Speakers Program.
Cindy is a Ph.D. student at TAMU Department of Computer Science and Engineering. Her research focuses on Uniform Obstacle-Based Probabilistic Roadmap Method (UOBPRM) which she developed recently.
Cindy (Hsin-Yi) Yeh, Ph.D. Student
ACM Distinguished Speakers Program
Research Project:
Introduction: In the broad field of motion planning, we are interested in designing algorithms that produce a path for a robot to get from a beginning phase (called the start configuration) to an end phase (called the goal configuration) without colliding with any present obstacles. A new motion planning algorithm, Uniform Obstacle-Based Probabilistic Roadmap Method (UOBPRM) [3], is able to produce a path that not only biases the robot configurations near the obstacles which is advantageous to help the robot navigate narrow passageways, but also generates configurations that are spread out in the space near obstacles in a uniform manner and without increased computational cost. The project is an application of motion planning generally and UOBPRM specifically to a current problem in computational biology/biochemistry.
Motivation: Pharmaceutical companies when developing new drugs often go through a process of testing many candidates to determine which show the most promise. The selected candidates then undergo further, more rigorous testing until hopefully, a few are obtained that can be used in trials to establish their more practical characteristics as potential drugs, for example, their toxicity. The testing process is costly and by conducting a part of it computationally the cost burden is reduced [2]. Reduced cost helps in drug manufacturing and may lead to a faster discovery of drugs that are helpful for fighting numerous diseases. An effective drug molecule acting as a ligand will need to bind to the active site of a protein (typically an enzyme) in order to cause the protein to undergo a change that will enable it carry out a desired effect that fights disease. This binding process is sometimes referred to as docking. The ligand may have to overcome obstacles to reach the active (binding) site of the protein making motion planning applicable to this scenario [1]. This protein-ligand interaction is the area on which the project focuses.
Goals: Approximating ligands to robots and proteins to obstacles, the project aims to develop an algorithm to test the affinity between each of several ligands and a protein molecule and rank the ligands based on their affinity. Likewise, the project aims for the developed algorithm to test the affinity between each of several protein molecules and an individual ligand and rank the proteins based on their affinity. In both situations, the conditions shall be static.
Conclusion: The research project plans to develop an algorithm which by experimentation can produce protein-ligand pairs that are top-ranked based on the strength of their affinity. Such an algorithm may have practical significance in the pharmaceutical industry and clinical significance in the treatment of diseases.
References:
[1] O. B. Bayazit, G. Song, and N. M. Amato. Ligand Binding with OBPRM and User Input. In Proc. IEEE Int. Conf. Robotics and Systems (ICRA), IEEE/RSJ Int. Conf., pages 954 – 959, 2001.
[2] H. Choset, K. M. Lynch, S. Hutchinson, G. Kantor, W. Burgard, L. E. Kavraki, and S. Thrun, Sampling-Based Algorithms, in Principles of Robot Motion: Theory, Algorithms, and Implementations. Cambridge, MA: MIT Press, 2005, ch. 7, sec. 7.5.6, pp. 262-267.
[3] H.-Y. Yeh, S. Thomas, D. Eppstein, and N. M. Amato. UOBPRM: A Uniformly Distributed Obstacle-Based PRM. In Intelligent Robots and Automation (IROS), IEEE/RSJ Int. Conf., pages 2655 – 2662, 2012.
Week One:
For undergraduate students at the Parasol Lab, the first four weeks are scheduled for completing the Crash Course, a course aimed at introducing motion planning and the lab generally, in preparation for working directly on a research project. Jory Denny and Read Sandstrom are Ph.D. students in the lab who lead the Crash Course. I completed Lessons 0, 1, and 2 of the Crash Course. It was exciting to see and use concepts I had learned in class only last semester during the exercises for this first week. On Thursday, we had a session to discuss the questions at the end of Lesson 1. I started learning C++. C++ is the programming language used for coding in the Parasol Lab. There are over ten undergraduate or high school students in the lab this summer and it has been a great experience interacting with them and also with graduate students supervising the Crash Course. We had a campus tour this week. The main TAMU campus is huge compared to my home campus (the University has a number of branch campuses). We had a welcome BBQ dinner hosted by the Office of Honors and Undergraduate Research for summer student researchers on campus, for example, all REU students. TAMU has many REU programs that host students over the summer. The attendance looked to be in the several hundreds. It was great to get to know other members of the lab better during this event.
Week Two:
This week I completed Lesson 3 of the Crash Course and started Lesson 4. We had a session to discuss the questions at the end of Lesson 2. I continued learning C++. We had a meeting of the Parasol Computational Biology Group and a Brown Bag lunch where Drs. Schaefer, Klappenecker, and Walker presented their research. We also attended a seminar where Dr. Becky Petitt, the Associate Vice President for Diversity at TAMU, gave a talk titled “Getting the Most out of your REU Experience.” I really enjoyed the content of this seminar. It contained information that I believe will apply not only this summer but beyond. In addition, it was an opportunity to meet REU students from other Departments. It was exciting to learn what project I shall be working on for the summer (it is described above before the entry for Week One). I read two papers for my project that Cindy gave me. They were interesting and provided a background for the project as well as an introduced to tools that the project will use. On Saturday, there was a picnic put together by the CSE Graduate Students Association (CSEGSA). The picnic was a lot of fun and it was great to meet several graduate students. There were different games. I got to work on a 700-piece puzzle with other students and it was gratifying that the puzzle was completed. Dr. Amato came to the picnic which was nice. She even took a panorama picture of us around the completed puzzle.
Week Three:
This week I completed more of Lesson 4 of the Crash course and we discussed Lesson 3 questions. I also updated three lab header files according to lab documentation standards and completed an online training program on research ethics. This week I wrote an abstract for the research project. Cindy reviewed it and gave me suggestions on what I might modify and we repeated this process. I also completed a literature survey and submitted the articles to Cindy. We met and discussed two papers that contribute to the protein-ligand affinity project on which we are working. I continued to learn C++. As part of the summer program, we students got to hear from a panel of graduate students who spoke with us in an REU Scholars meeting. We also had a noon Brown Bag session by Dr. Keyser that covered research ethics.
Week Four:
This week I worked more on the coding for Lesson 4 and completed Lesson 5 except for the coding. I also started reading papers from the literature survey and updated the project abstract several times after getting input from two of my peers and again from Cindy. I studied more of the C++ textbook. We had an REU Scholars program by Dr. Sumana Datta, Executive Director of Honors and Undergraduate Research at TAMU, that dealt with inter-cultural interactions and related concepts. I learned a lot from it. We also had an Undergraduate Research program titled "National Fellowships" by Jamaica Afiya Pouncy and a noon Brown Bag session by Dr. Keyser that covered presentation skills that were both useful.
Week Five:
It is amazing how quickly time has flown. This week I read a couple of papers for my research project. I met with Cindy and got detailed and helpful guidance on deliverables I can work on now for the project and also wrote pseudocode for an algorithm for the project that determines the binding affinity between a protein and its ligand and submitted the pseudocode to her. Cindy also introduced me to the part of the lab's code that is used for working with proteins. I am also searching for protein-ligand complexes we might choose to use for the project and found a couple so far. I completed the coding for Lesson 4 and got through compiling but it is not running yet, so I am debugging. For Lesson 6 of the Crash Course, I completed the literature survey and wrote up a LaTeX document. In addition, I completed more of the C++ textbook. We had an REU Scholars program on financing graduate education by Dr. Samuel Merriweather and Ms. Shaine Marsden, an Undergraduate Research program on preparing for graduate school by Ms. Shaine Marsden, and a noon Brown Bag session with a Graduate Student panel which were all helpful. This was the "Camera! Lights! Fireworks!" week. July 4th was a great day.
Week Six:
This week I debugged code for Lesson 4 of the Crash Course, completed coding for Lesson 5, and prepared and delivered final presentations for the Course. We each made our presentations to Jory and Read as well as to our peers and this meeting officially concluded the Course. Overall, the Crash Course was an effective way to become familiar with motion planning and the Parasol Lab. For my research project, I searched further for protein-ligand pairs to use and found several more and also read a paper for the project. We had helpful talks - an REU Scholars Program titled “How to Best Position Yourself for Acceptance and Funding for Graduate School, (Along with Expectations After Being Accepted)” by Mr. Edward Tarlton and a Noon Brown Bag focused on work-life balance by Drs. Welch and Williams.
Week Seven:
This week for my project, I carried out file conversions of the proteins and ligands to formats more suitable for the project. I read a paper for the project as well. We had interesting talks - an REU Scholars Program on leadership by Dr. C. J. Woods, Assistant Vice President for Student Affairs at TAMU, and a Noon Brown Bag where representatives from industry, specifically Chevron and Schlumberger, spoke about their companies and also about research careers.
Week Eight:
This week I implemented code for the project using a framework Cindy sent me. Three of the protein-ligand complexes had behaved differently from all the others during file conversion, so I did troubleshooting and noted the cause. I worked on the research poster and more on the research paper.
Week Nine:
We will be using a different metric for our algorithm for the research project, so this week I wrote part of the new code. I also ran and analyzed the experiments for the project. Shawna Thomas, a post-doc in the lab, Cindy, and I went over the poster a couple of times and I made changes. After that, Cindy went over it some more and I made more changes. These were helpful for improving the poster. This week we also presented our posters at the Noon Brown Bag and got reviews by CSE graduate students. We also presented our posters at our Motion Planning lab meeting. It was helpful to hear thoughts from lab members and make changes accordingly. Cindy also reviewed the paper and I made changes to that as well.
Week Ten:
This week Cindy and I iterated over the paper several more times. I completed it and the poster. We presented our posters at the first Annual CSE Poster Session. We also presented our posters at the Annual USRG Poster Session. The poster sessions were both fun and educative. It was bittersweet getting to say byes to everyone but at the same being excited to get to go home after a rewarding ten-week research experience.
Here are the paper and the poster for my project this summer as well as my resume.