UROP Research Mentor Project Submission Portal: Submission #507

Submission information
Submission Number: 507
Submission ID: 8806
Submission UUID: 32a423f3-d863-45b6-be9f-addc4b8021ea

Created: Sun, 08/20/2023 - 05:18 PM
Completed: Sun, 08/20/2023 - 05:35 PM
Changed: Mon, 08/21/2023 - 11:24 AM

Remote IP address: 73.42.41.179
Submitted by: Anonymous
Language: English

Is draft: No
Primary Research Mentor Name Scott Stagg
Research Mentor Preferred Pronouns
When potential research assistants are reaching out via email, what is your preferred honorific?
Contact Email (FSU Email if affiliated) sstagg@fsu.edu
Position Title Faculty
FSU College (if applicable) Arts and Sciences
FSU Department or Non-FSU Organization Affiliation Biological Sciences / Institute of Molecular Biophysics
Headshot (optional) C11DBD71-06FC-4064-B139-2C4F1DD6D493_edited.jpg
Research Assistant Supervisor (if different from above) Behdad Khoshbin
Research Assistant Supervisor Preferred Pronouns
Research Assistant Supervisor Preferred Honorific?
Contact Email (FSU Email if affiliated) bk22n@fsu.edu
Name of Other Faculty/Collaborator(s) (if applicable)
Other Faculty/Collaborator(s) Preferred Pronouns
Other Faculty/Collaborator(s) Preferred Honorific?
Contact Email (FSU Email if affiliated)
Title of the Project Magellon: A next generation software package for automated cryo-EM data collection and processing
Project Keywords computer science, biochemistry, workflows
Are you currently looking for research assistants? Yes
Number of Research Assistants Needed 3
Relevant Research Assistant Major(s) Computer Science, Biochemistry, Engineering
Project Location: On FSU Main Campus
If the project location is off campus, does the research assistant(s) need to provide their own transportation?
Please select the choice that most accurately describes your expectations for the research assistant(s): Partially Remote
Approximately how many hours a week would the research assistant(s) need to work? 10
Roughly what time frame do you expect research assistant(s) to work? Flexible schedule (Combination of business and outside of business. TBD between student and research mentor.)
Overall Research Project Description We are developing the next generation of software for automated data collection and processing for cryo-electron microscopy (cryo-EM). Cryo-EM is now a widely established and indispensable method for determining the high-resolution structures of biomedically important molecules. The pioneering software packages Leginon and Appion demonstrated the power of automated data acquisition and real-time processing, and there are now numerous programs for automated data acquisition and real-time processing. Despite advances in automation, data collection and processing still require a good deal of manual involvement of an expert electron microscopist. Building on the foundations of Leginon and Appion, we are developing the next generation software package that we call “Magellon”. Magellon will overcome existing bottlenecks and provide an avenue toward fully automated data acquisition that bypasses need for user input during data collection. Importantly, this software will support the computational infrastructure to enable real-time image processing results to inform on and modify the ongoing data collection regime by learning where to acquire images in regions that will yield the highest resolution structures. Using machine learning and the new industry standard tools for distributed processing, we will develop new fast image assessment routines, and provide an application programming interface to enable the incorporation of extensions and plugins from developers in the community.
Research Tasks Students will work with a team of programmers and biochemists to develop new tools for data collection and processing. The overall goals of the project have been modularized so that individual team members can work on a discrete task that contributes to the overall project. There are many potential tasks available depending on the interests of the student. Examples include: 1) adapting existing code to build backend tools that interface with the electron microscopes to drive data collection from the web, 2) using machine learning tools to automatically identify good areas of the sample for data collection, 3) developing front end web tools to interface with the instruments, 4) developing and testing deployment strategies for the software
Skills that research assistant(s) may need: We can take most any student with a computational mindset. Students should have at least one skill in the following list: Python, MySQL, Web development, HTML, Javascript, RESTful programming
Mentoring Philosophy My philosophy is to provide students with the information and resources they need to be successful. Additionally, I assign a peer mentor who has experience on the project. We have weekly group meetings where I check in on their project and help them problem solve any issues with their research. My goal is to promote independent, research minded students who will thrive in dynamic cooperative team environment.
Please provide a link to your publications, a video clip, or a website for your research project (if applicable): https://www.stagglab.com
Please add any additional information here (if applicable):
Roundtable times and Zoom links Thursday, 9/7 4:00-5:00 - https://fsu.zoom.us/j/97609646320
Friday, 9/8 4:00-5:00 - https://fsu.zoom.us/j/97609646320
Mentor Handbook, FAQs, and Communication Yes
UROP Performance Evaluation Yes
Materials Grant Yes
UROP Poster Presentation Yes
Year 2023
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