George W. Shiflet

An Introduction to Agent-based Modeling for Undergraduates

Abstract Agent-based modeling (ABM) has become an increasingly important tool in computational science. Thus, in the final week of the 2013 fall semester, Wofford Colleges undergraduate Modeling and Simulation for the Sciences course (COSC/MATH 201) considered ABM using the NetLogo tool. The students explored existing ABMs and completed two tutorials that developed models on unconstrained growth and the average distance covered by a random walker. The models demonstrated some of the utility of ABM and helped illustrate the similarities and differences between agent-based modeling and previously discussed techniques— system dynamics modeling, empirical modeling, and cellular automaton simulations. Improved test scores and questionnaire results support the success of the goals for the week.

Gene Expression, DNA Synthesis and Protein Synthesis in Cells from Dissociated Sea Urchin Embryos

DNA synthesis, protein synthesis, and the accumulation of two tissue‐specific transcripts were examined in cultures of sea urchin embryos that were completely dissociated during early cleavage stages and raised in Ca2+ ‐free sea water for 24 hr. In Strongylocentrotus purpuratus, both DNA and protein synthesis were severely reduced by dissociation treatment. Previous studies using this species indicated that aboral ectoderm‐specific transcript accumulation is severely reduced while mesenchyme‐specific transcripts generally accumulate more normally (11, 17). We therefore examined the accumulation of tissue‐specific transcripts in another specific of sea urchin (Lytechinus pictus) whose DNA and protein synthetic rates were found to be less affected by dissociation. We find that accumulation of an aboral ectoderm‐specific transcript (Spec 1) is also extremely low in L. pictus while a primary measenchyme‐specific transcript (LSM) accumulates to normal levels. When DNA synthesis was restored to 77% of normal by keeping dissociatesd cells apposed with the fertilization membranes, Spec 1 accumulation was not improved. Adding Ca2+ to the sea water 8 hours after fertilization and allowing cells to reassociate into small, tight clusters restored Spec 1 accumulation to 70% of controls. Hence, there is no direct correlation between the reduced metabolic acitivities and lowered Spec 1 accumulation in dispersed cell cultures.

An Undergraduate Computational Science Curriculum

Wofford College instituted one of the first undergraduate programs in computational science, the Emphasis in Computational Science (ECS). Besides programming, data structures, and calculus, ECS students take two computational science courses (Modeling and Simulation for the Sciences, Data and Visualization) and complete a summer internship involving computation in the sciences. Materials written for the modeling and simulation course and developed with funding from National Science Foundation served as a basis the first textbook designed specifically for an introductory course in the computational science and engineering curriculum. The successful ECS has attracted a higher percentage of females than in most computer science curricula. The SIAM Working Group on Undergraduate Computational Science and Engineering Education summarized features of Woffords ECS and other computational science programs. Besides its established curriculum, Wofford has incorporated computational science in other courses, such as in a sequence of three microbiology laboratories on modeling the spread of disease.

Undergraduate Module on Computational Modeling: Introducing Modeling the Cane Toad Invasion☆

Abstract “Modeling an ‘Able’ Invader—the ‘Cane’ Toad” is an educational computational science module developed by the authors for the NSF funded Blue Waters Undergraduate Petascale Education Program. The module considers the fundamentals of a grid-based individual-based simulation and develops such a model for an invasive species, the cane toad, to study the effect of fencing artificial water points on the adults invasion. Besides serial implementations in MATLAB and C, a parallel program in C/MPI accompanies the module. Moreover, the module considers a serial algorithm and an approach to parallelizing, speedup, and scalability. This paper describes the module and details experiences using the material in an undergraduate course on Modeling Biological Networks at Wofford College.

Introducing Life Science Doctoral Students in Oz to the Wizardry of Computational Modeling: Introducing Computational Thinking with CellDesigner™

Abstract A five-day, hands-on workshop was held at Monash University to introduce doctoral students in the life sciences to computational applications for research. Although three software tools were employed (CellDesigner™, MATLAB™ including the Parallel Computing Toolbox, and Nimrod), this paper reports on the use of CellDesigner in teaching computational thinking and modeling, including system dynamics and regulatory networks. Each session included a series of brief orientations to the tool, followed with illustrative, practical projects for participants to implement. From written evaluations and various forms of anecdotal evidence (e.g., oral communications, participation, project/assignment performance), we conclude CellDesigner to be a suitable tool for use in such a workshop.

Educational Module on Genomic Sequence Alignment Using HPC

Aligning Sequences-Sequentially and Concurrently,” an educational computational science module by the authors and available online, develops a sequential algorithm to determine the highest similarity score and the alignments that yield this score for two DNA sequences. Moreover, the module considers several approaches to parallelization and speedup. Besides a serial implementation in C, a parallel program in C/MPI is available. This paper describes the module and details experiences using the material in a bioinformatics course at University “Magna Græcia” of Catanzaro, Italy. Besides being appropriate for such a course, the module can provide a meaningful application for a high performance computing or a data structures class. CCS Concepts • Social and professional topics~Computing education • Theory of computation~Parallel algorithms • Theory of computation~Dynamic programming • Applied computing~Bioinformatics

Making connections: Modeling epidemiological networks in mathematical modeling and HPC courses

Abstract Significant applications that demonstrate fundamental concepts and techniques are vital in computational science education. In this paper, we discuss development of simulations involving social networks and individual-based epidemiology that are appropriate for modeling and simulation, mathematical modeling, and high performance computing courses. Consideration of the computational graph theory concepts in this context can empower students to develop similar models for other applications. Moreover, execution of the model with massive amounts of data can illustrate and motivate the need for high performance computing in computational science. The module, “Getting the ‘Edge’ on the Next Flu Pandemic: We Should’a ‘Node’ Better,” which was developed by the authors as an Undergraduate Petascale Education Program (UPEP) Curriculum Module, used for instruction in two course and evaluated by class participants, is available at http://computationalscience.org/upep/curriculum. The module provides the biological background necessary to understand the application, the mathematical background needed to develop models, example solutions in Mathematica to help with implementation, quick review questions with answers to provide immediate feedback, and projects for further exploration.

Simulating the formation of biofilms in an undergraduate modeling course

Abstract Meaningful applications that illustrate fundamental concepts and techniques are crucial in computational science education. In this paper, we discuss development of a simulation on the structural growth of a biofilm that is appropriate for modeling, simulation, or high performance computing courses. Consideration of cellular automaton simulations, boundary conditions, and diffusion in this context can empower students to develop similar simulations for other applications. Moreover, extensions of the basic model can illustrate and motivate the need for high performance computing in computational science. The module, “Biofilms: United They Stand, Divided They Colonize,” used for instruction and developed by the authors as an Undergraduate Petascale Education Program (UPEP) Curriculum Module is available at http://computationalscience.org/upep/curriculum .

Spread-of-Disease Modeling in a Microbiology Course

Microbiology is the study of microorganisms. Most college courses in microbiology emphasize the biology of bacteria and viruses, including those that are human pathogens. One challenging aspect of the course is to introduce students to epidemiology, which considers the causes, dispersal, and control of disease. Although disease transmission models have helped develop successful strategies for managing epidemics, most science students are unaware of their advantages and complexities. To address this challenge, the microbiology course at Wofford College has incorporated a sequence of three or four laboratories on modeling the spread of disease. Emphasis in Computational Science students who have studied modeling and simulation in depth serve as laboratory assistants and mentors. Evidence from test scores and self-assessment support the hypothesis that the sequence of laboratories has improved student understanding of human disease dynamics and demonstrated the utility of computational models.