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Case Study

RCDS Power User: The SeNSE Lab

About the Research

RCDS Power User: The SeNSE Lab

Mitra Hartmann is a professor of biomedical and mechanical engineering at the McCormick School of Engineering, where she studies the sense of touch using a rodent whisker system as a model. Understanding this problem has applications for the development of complex robotic systems and could ultimately help people disabled by stroke or brain injury. 

Research Challenge

Hartmann and her team—The Sensory and Neural Systems Engineering (SeNSE) Lab—capture high-speed videos of rats and mice performing different tasks to study how animals perceive their environment through movement and sensory input from their whiskers. The data collection necessary to address this research question presents a challenge in data management. As part of this research, they have generated nearly 150 terabytes of data consisting of thousands of video files collected by several lab members.  

Throughout their research, the SeNSE Lab encountered several challenges that Northwestern IT Research Computing and Data Services (RCDS) helped address, including: 

  • Creating models that accurately represent the geometry of the whiskers of multiple animal species  
  • Harnessing enough computational power to run dynamic simulations to quantify how whiskers interact with objects 
  • Sharing their data within their research group after migrating their data from Box to SharePoint 

Hartmann’s group worked with consultants from all three RCDS teams to solve these issues.  

Solution

Hartmann’s group came to RCDS with a data science problem: how to model the geometry of whiskers across multiple animal species; the geometry is important in determining the sensory input that the animal receives when the whisker interacts with its surroundings. Testing several different model types in collaboration with RCDS data scientists allowed them to see the pros and cons of each approach and publish an article, “On the intrinsic curvature of animal whiskers,” that informs their future work.  

Running dynamic simulations of how whiskers will interact with objects to generate tactile signals requires significant computational power. So, the team also sought RCDS help using the Quest High-Performance Computing cluster. Research Computing consultants introduced the team to Quest features like using project folders for shared software and Quest OnDemand as a user-friendly interface to run Quest jobs. They also helped the team build and run WHISKiT Physics, a 3D dynamical model that allows them to simulate the mechanical signals generated at the base of each whisker in an array, on Quest. The ability to run many of these complex simulations in parallel saved them significant time compared to running them sequentially on their local machines.   

RCDS data management consultants also brought fresh eyes. They provided the SeNSE Lab with suggestions on how best to organize their data in SharePoint for long-term management as part of the Box Transition effort.

For most users, the automatic migration of data from Box to SharePoint was seamless; however, the volume of data stored in Box, combined with the differences between the Box and SharePoint platforms, made the transition challenging for this group. The data was migrated into multiple, separate "document libraries" due to storage quota restrictions, making access more complicated. SharePoint also places restrictions on the number of files that can be shared simultaneously within these document libraries.  

To overcome this limitation, data management consultants recommended storing and sharing similar data, such as the research output from a former graduate student, in a separate document library to overcome the sharing restrictions. Hartmann affectionately refers to these document libraries as “lab time capsules” and shares them with incoming graduate students when they agree to pick up a former student’s project.  

In addition to assisting with the Box to SharePoint migration, members of the SeNSE Lab have also attended RCDS workshops on various research computing and data-related topics. 

Impact

The combination of services and support RCDS provided has enabled SeNSE Lab to continue its impactful research, including the publication of “On the intrinsic curvature of animal whiskers.” 

The RCDS team is a great sounding board and thought partner. They’ve helped point us in the right direction multiple times and have been instrumental in the success of our work.”

Mitra Hartmann
Professor of Biomedical and Mechanical Engineering
McCormick School of Engineering

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