NCSI: Making the Computational Microscope Accessible to Blind Researchers

Status	Completed
Mentor Name	Jodi Hadden-Perilla
Mentor's XSEDE Affiliation	Education Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Making the Computational Microscope Accessible to Blind Researchers
Summary	Develop the computational tools necessary to enable a blind researcher to setup, run, and analyze molecular dynamics simulations of proteins, including scripts that improve accessibility of running calculations on national supercomputers through the interfaces of screen-readers and Braille displays. Develop strategies for visualization and conceptualization of protein structure and dynamics through data analysis and presentation techniques that do not depend on the sense of sight.
Job Description	The student will participate in the development of a computational toolkit aimed at increasing accessibility of the fields of computational chemistry and biophysics for researchers who are blind. The student will write code to support the tactile visualization, automated textual description, and data sonification strategies utilized by the toolkit to present protein structures in a medium through which individuals who are blind can analyze them. The student will use XSEDE resources to perform molecular dynamics simulations to generate data for testing features of the toolkit aimed at characterizing protein dynamics. Through their access to the supercomputer, the student will identify existing barriers for computational research on national resources that exist for individuals who are blind and develop strategies to overcome these barriers using assistive technology such as screen-readers, Braille displays, and electronic refreshable tactile graphics displays. The student will employ the toolkit and code they develop to carry out meaningful scientific analysis of a small protein system as part of a multi-university research collaboration. Through their efforts, the student will be in a position to provide valuable feedback to XSEDE that will support inclusion of disabled researchers in the XSEDE user community in the future.
Computational Resources	The student will have access to XSEDE resources through our Education Allocation targeted toward her project to perform molecular dynamics simulations and analysis of small biomolecular systems. Access to the supercomputer is essential for identifying strategies that will improve accessibility of the resource for bind researchers.
Contribution to Community
Position Type	Intern
Training Plan	The student will learn to utilize supercomputers to carry out molecular dynamics simulations and analysis through hands-on training, working closely with a faculty mentor with over twelve years of experience in the field. The student will require basic programming skills and will gain experience in coding and software development and work in tandem with an experimental collaborator. The student will have access to an electronic refreshable tactile display prototype (Graphiti) through a non-disclosure agreement with Orbit Research, and will be guided by an expert in biomolecular visualization to leverage the device for tactile visualization and analysis. The student will present their work at the 2020 ISLAND conference on STEM accessibility and prepare a manuscript describing their work to the Journal of Science Education for Students with Disabilities.
Student Prerequisites/Conditions/Qualifications	Interest in computational chemistry, interest in STEM accessibility and inclusion, Braille literacy, working knowledge of assistive technology for the blind
Duration	Semester
Start Date	09/01/2020
End Date	12/15/2020