High-performance computing service in the Health Science and Human Services Library at University of Maryland Baltimore
Creators: name: Mayo, Alexa
name: Courneya, Jean-Paul
Publisher: name: F1000 Research Limited
Year: 2018

description: The majority of biomedical investigators seem to agree that their capacity to perform contemporary computationally heavy tasks lags compared to their wet bench-based advancements.  To address this deficiency, University of Maryland Health Sciences and Human Services Library set out to build infrastructure to support analysis of high-throughput data from global molecular profiling experiments by offering a Bioinformatics and Data Science High Performance Workstation (HPW) with open source software, combined with expert Bioinformationist support.  The audience for this new service are faculty, staff, and students for whom the use of the University’s large scale, CORE computational resources are not warranted because such resources exceed the needs of smaller projects. In the Library’s approach, users are empowered to analyze high-throughput data at the level that exceeds the depth and complexity of analyses available on a basic lab computer.  <br><br>We consulted with campus bioinformatics experts to identify the ideal computing hardware and open source bioinformatics software, to provide analysis options for experimental data such as complex scientific images, high-throughput sequence reads, and flow cytometry files. Registration for the service is managed via an online calendar and users are able to select four-hour blocks to compute, which accommodate their schedules. Information describing the service, the computer, as well as policies and guidelines of use are available on a landing page for the high performance computer hosted on the library’s main website. To promote and enhance user experience, workshops and one-on-one consultation are offered covering topics related to bioinformatics and data science relevant to using the open-source software available on the high performance computer. While implementing this project, we realized that abundant practice was key to developing solid coding skills and computer literacy after receiving focused instruction on high tech topics. To close the loop between learning and practice, we developed self-guided learning materials for users to practice performing tasks such as reference genome-based RNA sequence data analysis or retrieving raw sequence reads from the NCBI Sequence Read Archive SRA. The HPW allows for researchers to apply the data analysis techniques learned in the classroom in an ideal computing environment.<br><br>The initial users for the service have been students and faculty members, and the popularity of this new service on our campus is growing. We have already had instances in which a faculty member would use the HPW for about 5 days straight, for more than 5 hours each day, analyzing RNA-Seq data. In another example, a PhD student had the chance to prepare CT data of mice for presentation at a scientific conference, a task they were unable to perform due to insufficient memory on the labs computer to work with 3D image stacks.   The feedback we have gotten from our users has been very positive. We anticipate that as campus users become aware of the service, the numbers of users will continue increasing. To help this process, there will be focused advertisements as well as a cross-campus promotion within departments.