Submission information
Submission Number: 66
Submission ID: 97
Submission UUID: d4f1f6b0-d3d8-420f-837a-204bb8362219
Submission URI: /form/project
Created: Tue, 09/08/2020 - 17:42
Completed: Tue, 09/08/2020 - 17:55
Changed: Tue, 06/22/2021 - 15:25
Remote IP address: 67.176.36.130
Submitted by: Anita Schwartz
Language: English
Is draft: No
Webform: Project
| Project Title | Optimization of Mouse Social Behavior Data Analyses Pipeline |
|---|---|
| Program | CAREERS |
| Project Leader | Josh Neunuebel |
| jneun@udel.edu | |
| Mobile Phone | |
| Work Phone | 302-831-4811 |
| Mentor(s) | Josh Neunuebel, Anita Schwartz |
| Student-facilitator(s) | Joel Turk |
| Mentee(s) | |
| Project Description | The Neunuebel Neuroscience Lab research team in the Department of Psychological Brain Sciences at the University of Delaware is interested in the mechanisms that the nervous system uses to process and integrate information, specifically social cues, during innate behavior. To understand the neural basis of social communication, the research team has built a unique, non-commercially available system for simultaneously recording audio and behavioral data from freely socializing mice. The system generates massive data sets that require the use of high-performance computing to analyze. Moreover, we developed a fully functional data processing pipeline on the University of Delaware’s second Community Cluster (Farber), ideally positioning the laboratory to conduct innovative research from socially interacting groups of mice. While the pipeline on the Farber cluster has been highly productive and beneficial, the University has upgraded to a more efficient and effective computing cluster that has a significantly longer shelf life (Caviness). Recently, the research team invested in the Caviness cluster and we are now looking to train a highly motivated, enthusiastic student eager to immerse themselves in high-performance computing with the end goal of optimizing the laboratory’s data analysis pipeline for use on the Caviness cluster. |
| Project Deliverables | a. Scripting-convert the executable scripts developed to work on a grid engine job scheduling system (Farber) to the Slurm workload manager system used on Caviness b. Profiling-optimize resources such as memory, disk space, and processor cores to deliver peak performance on Caviness c. Testing-process four data sets using our data analysis pipelines (Motr only) on Farber and Caviness and then verify that the output in each data set is identical (vocalizations extracted, mouse trajectories, and sources of each vocalization) d. System Source Code and Documentation (google docs)-write clear and concise instructions so that members of the research team can process data on Caviness |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | One programming class |
| Mentee Programming Skill Level | |
| Project Institution | University of Delaware |
| Project Address | 210 South College Ave. Newark, Delaware. 19716 |
| Anchor Institution | CR-University of Delaware |
| Preferred Start Date | 12/14/2020 |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | 3 |
| Launch Presentation | |
| Launch Presentation Date | 01/13/2021 |
| Wrap Presentation | |
| Wrap Presentation Date | 04/14/2021 |
| Project Milestones |
|
| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | |
| What will the student learn? | a. Batch coding to control Slurm and Grid Engine job scheduling b. Cluster resource management c. Scripting in Matlab d. Scientific approach to analyzing complex mouse social behavior e. Data and statistical analyses |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | a. Access to Caviness and Farber cluster at University of Delaware b. Inclusion in Neunuebel workgroup on Caviness and Farber |
| Notes | This project will be funded by CAREERS for 2 months, and the remaining month will be funded by UD RA.. |
| What is the impact on the development of the principal discipline(s) of the project? | While the project might have been overly ambitious for the allotted time, we were able to transfer our tracking software to the new cluster. This made a strong, positive impact on the lab’s research and will help sustain the lab’s progress going forward. |
| What is the impact on other disciplines? | It made a positive impact on the field of social neuroscience and I imagine that it made a positive impact on the high performance computing field. The Singularity container will allow other researchers to set up similar environments regardless of the scheduler. |
| Is there an impact physical resources that form infrastructure? | N/A |
| Is there an impact on the development of human resources for research computing? | N/A |
| Is there an impact on institutional resources that form infrastructure? | N/A |
| Is there an impact on information resources that form infrastructure? | N/A |
| Is there an impact on technology transfer? | N/A |
| Is there an impact on society beyond science and technology? | The approach used by CAREERS has potential to facilitate learning across multiple fields, in particular, the student facilitator position. This was a great idea. |
| Lessons Learned | Learned about Grid Engine and Slurm job schedulers Specific details of tracking software functionality Process of setting up data analyses on a cluster Running jobs, fitting software together, writing scripts used to execute the programs Importance of documenting each step in the process Learned how research facilitation works enabling the student RCF to mentor future students wanting help with the process |
| Overall results | Funding was a bonus; helped expedite the project Mentor role important with knowledge about the project Hearing about other projects, being able to tell others about their project, and networking opportunities were an unexpected and valuable experience |