The BioHPC team, led by Liqiang Wang, supports all of the computing and storage hardware, software and web services that make up BioHPC. With a variety of backgrounds we have expertise that spans various aspects of computing and biological research, allowing us to recognize the needs of our users.
LOCATIONS: The BioHPC team is housed in the new facilities for the Lyda Hill Department of Bioinformatics, on South Campus, Room E4.350 (please enter from Library internal staircase or South elevators; there is no entry into Bioinformatics from the Faculty Club). The main office phone is x51745.
For in-person consultation, a help desk is also staffed on North Campus, Monday thru Friday, 10 AM to 5 PM in room NL5.120P.
NOTE - Please email BioHPC inquiries to firstname.lastname@example.org as all staff monitor this address.
Liqiang Wang, M.S., received his master’s degree in computer science from University of New Orleans in 2009 and a bachelor’s degree in computer science from Huazhong Normal University, China. For the past 9 years Liqiang has been working in High Performance Computing (HPC) from IBM SP, P5 and P5+ supercomputing systems to large-scale beowulf clusters, and providing scientific computing consultation to researchers in science and engineering. He has received certifications from 15 industrial companies, including Cisco Certified Internetwork Expert, Microsoft Certified Systems Engineer, Linux Professional Institute and Oracle Certified professional. While working for the Louisiana Optical Network Initiative (LONI), a state-wide supercomputing infrastructure for academic research, he provided scientific computing and applications support, supercomputing system deployment and administration of over 300 TFlops total computing capacity. He participated in multiple LONI projects, including Cybertools and HPCOPS. Wang developed an MPI-MapReduce cloud platform for the digital forensics research funded by the FBI in New Orleans.
Since its inception, the UT Southwestern Biomedical High Performance Computing infrastructure has thrived under Liqiang's leadership. As Director, he designed and built BioHPC Cloud, the first cloud HPC resource at UT Southwestern, designed with long-term scalability of storage and compute power, incorporating cloud storage, computing and apps. He works closely with the BioHPC user advisory council and steering committee and is responsible for the day-to-day activity, operation and management of the HPC team and leads the development of proposals to expand or extend the HPC system based on needs articulated by BioHPC member entities.
Email: Liqiang.Wang@UTSouthwestern.edu Phone: 214-645-1638
Ross Bateman recieved his bachelor's degree from Texas Christian University, and has been at UT Southwestern for three years. He joined the BioHPC team in 2015 to provide system administration and technical support. Ross has had experience in various IT roles, including higher education support, for 10 years.
Yingfei Chen received her Ph.D. degree in Chemical and Biological Engineering from Iowa State University. She is interested in solving biological problems using computational methods, and thus her research focused on bioinformatics, mentored by distinguised professor Dr. Peter Reilly. She studied protein sequences and tertiary structures for caborxyl ester hydrolases and enzymes in fatty acid and polyketide synthesis, classified them, and created the enzyme databases CASTLE and ThYme for these proteins. For those projects she wrote scripts to automate steps and analyze data. She also has data mining experience through a project that worked to to reveal insights on conditions under which protein crystallization occurs and has published 8 research papers.
Yingfei joined the BioHPC team in November 2016, and looks forward to providing UT Southwestern researchers with great computational services.
Murat Atis received his Ph.D. in Physics, Turkey in 2005. In his research, Murat investigated structural, thermodynamic, magnetic, spectral properties (FT-IR, Raman, NMR, UV) and hydrogen storage capabilities of nano structures by computational methods like molecular dynamics, quantum mechanical calculations, stochastic search algorithm, Monte Carlo and genetic algorithms. He not only used these methods but also is interested in developing and parallelization of programs using these methods. He joined UT Austin in 2016 as a visiting scientist for one year to investigate HIV Reverse Transcriptase by using a milestoning algorithm. He has published more than 20 journal papers, participated in six research projects, advised one Ph.D. and five M.S. theses. He joined the BioHPC team in 2017.
Daniel Moser graduated from Indiana State University in the spring of 2012 with a B.S. in Physics. Afterwards, he began his graduate studies in Atmospheric Sciences at Purdue University before transferring to the University of Illinois in Urbana-Champaign where he was awarded his Ph.D. For his dissertation, Daniel participated in the Convective Precipitation Experiment in the United Kingdom, an airborne field campaign that observed convective cloud development in situ. Daniel recreated these clouds in extensive high-resolution simulations on the Yellowstone and Blue Waters HPC systems, focusing on the turbulent exchanges between clouds and their surrounding environment, an important factor in determining how much rain may fall from a cloud. His Ph.D. research has contributed to the publication of five published papers in American Meteorological Society journals, of which two were first-authored.
Outside of academia Daniel is a certified private pilot and contributes to the growing flight simulation scene by developing and maintaining one of the largest 3-D global terrain datasets for Lockheed Martin and Microsoft line of flight simulators. He is also an avid ice hockey fan, monitors severe weather, and loves to chat about early 20th century history.
Paniz Karbasi graduated with a Ph.D. in electrical and computer engineering from Baylor University in August 2018. Her Ph.D. research was mainly focused on proton computed tomography (pCT) and high performance computing (HPC) leading to development of sparse robust iterative solvers and distributed multi-GPU based image reconstruction algorithms with the goal of generating real-time and accurate pCT images resulting in several published and soon to be published papers. During the Ph.D. program, Paniz collaborated with several national and international proton CT research institutes including the Loma Linda University Medical School, which is the world's first hospital-based Proton Therapy Center. After graduating from Baylor University, Paniz joined the BioHPC team at UTSW to start her career as a computational scientist at the Bioinformatics department.
Zengxing is an alumnus from the University of Texas at Arlington, where he attained a Master’s degree in Biomedical Engineering and a Bachelor’s degree in Biology in August of 2018. While in academia, he conducted his thesis research on Light Reflectance Spectroscopy (LRS) and its application in identifying positive surgical margins during Radical Prostatectomy. Utilizing elements from instrumentation, mechanical design, and user-end feedback, Zengxing created a handheld LRS prototype device intended for clinical settings. He was also a member of the university math modeling research team in ecology, in which he and his colleagues simulated the effects of global warming and overfishing on coral reefs.
Intrigued by High Performance Computing’s significant impact on biomedical sciences, Zengxing joined BioHPC in December 2018. With the aim of contributing to BioHPC’s growing relevance in Biomedicine, he is actively training to become familiarized with BioHPC’s infrastructure and service platform.
I’m a 3rd-year Biomedical Engineering graduate student, in the Biomedical and Molecular Imaging track, with a specialty in Computational and Systems Biology. I received my B.S. in Biomedical Engineering- Imaging and Instrumentation from UT Austin in 2015. My research primarily focuses on the use of multispectral imaging methods for the assessment of tumor hypoxia and hemodynamics.
Jinxin is a postdoctoral researcher in the Meeks lab, Dept. Neuroscience. He started a 12 month BioHPC fellowship in 2019, working with BioHPC to develop workflows for mouse behavioural analysis.
Daniela Ferreira Daniel has a degree in Control and Automation Engineering from Federal University of Santa Catarina (UFSC, 2012), and a Master's degree in Computer Engineering from the Aeronautics Institute of Technology (ITA, 2019). She has worked in the aeronautical industry for more than 7 years. Her research focuses on HPC and Performance Portability. She's moved to the US to join BioHPC and start a career as a computational scientist. She aims to apply her programming skills to support the research community at UT Southwestern.
Davide Vanzo graduated from University of Bologna (Italy) in Materials Chemistry and Photochemistry before receiving his PhD in Computational Chemistry from the same institution after working on the investigation of liquid crystal nanodrops using GPU accelerated molecular dynamics simulations. After two postdoc appointments at Virginia Commonwealth University and Princeton University, since 2015 he has been working as a Sr HPC Research Scientist at Vanderbilt University Advanced Computing Center for Research and Education (ACCRE). His primary responsibilities included maintaining the HPC cluster software stack, user support and performing benchmarks for performance bottlenecks detection and resolution, especially for parallel applications. He was also in charge of designing, optimizing and managing the GPU accelerated cluster resources. In addition, he also spread his passion for HPC by teaching an Advanced High Performance Computing semester-long course.
Peng Lian finished the joint training at the University of Tennessee and received his Ph.D. in Biomedical Engineering (Bioinformatics) from Shanghai Jiao Tong University in 2013. Later, he joined Professor Jeremy C. Smith's lab at the University of Tennessee/Oak Ridge National Laboratory (UT/ORNL). His research interests include Structural Bioinformatics, High-Performance Computing (HPC), Computer-Aided Drug Design (CADD), Molecular Biophysics, Computational Chemistry, and Machine Learning. He has published more than 30 papers in peer-reviewed journals or as book chapters. He developed HPC pipelines for drug discovery, deep learning, biomacromolecule modeling, molecular dynamics (MD) simulation, quantum mechanics/molecular mechanics (QM/MM) calculation, free energy sampling, and multiscale environmental science modeling etc. In one of the UT/ORNL projects, he led the establishment of the AQUA-MER database (https://aquamer.ornl.gov/). He also built several Linux HPC clusters from scratch in the past years. To work with scientists from biomedical areas to take full advantage of high-performance computing, he joined the BioHPC team at UT Southwestern Medical Center in November 2019.
Hossein earned his doctorate degree while working in the Mechanics, Uncertainty, and Simulations in Engineering (MUSE) division of the CAEE department at UT Austin. Hossein has over 5 years of professional software development experience with various roles and applications. His involvement in these applications have included the design and development of software leveraging computational methods for the solution of I/BVPs in the time and frequency domain and model implementation and integration in commercial solvers.