NCSI: Making the Computational Microscope Accessible to Blind Researchers

Status	Completed
Mentor Name	Jodi Hadden-Perilla
Mentor's XSEDE Affiliation	Research 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 a large-scale molecular dynamics simulation project aimed at the study of a complex protein system. Over the course of the project, the student will develop computational tools as needed that enable them to carry out the work using only the technology readily available to a blind researcher to interface with the supercomputer, namely screen-readers and Braille displays. The student will assess the accessibility of XSEDE resources, as well as widely-used computational chemistry and molecular visualization software, and identify strategies to adapt these for effective use by blind researchers. Using the tools and strategies they develop, the student will not only complete an impactful scientific study of an important protein system as part of a multi-university collaboration, but also produce a toolkit aimed at making the computational microscope (i.e., all-atom MD simulations) accessible to the blind. 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 Research Allocation on Comet and Bridges to perform molecular dynamics simulations of a complex protein system, including trajectory analysis. Access to the supercomputer is essential for identifying strategies that will improve accessibility of the resource for blind researchers.
Contribution to Community
Position Type	Learner
Training Plan	The student will learn to utilize supercomputers to carry out molecular dynamics simulations through hands-on training, working closely with a faculty mentor with over twelve years of experience in the field. The student will gain experience in coding and software development and work in tandem with an experimental collaborator. The student will also collaborate with local disability services to access tactile graphics machines and 3D printers to support their research. Every month, a remote meeting will be arranged with a member of the blind computational chemists community to provide additional learning opportunities and mentoring for the student. The student will prepare and submit a manuscript on their work in response to an invited article for the Journal of Science Education for Students with Disabilities. The student will present their work at the Spring 2020 Meeting of the American Chemical Society and the 2020 IsLAND conference on STEM accessibility.
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	02/10/2020
End Date	05/04/2020