Doerschuk’s research group develops, validates, and uses mathematical models of primarily biological and medical systems, mostly with the goal of understanding experimental data. The range of problems has been broad, e.g., ethanol pharmacokinetics in human subjects based on breath-analyzer data to the 4-D spatial-temporal dynamics of virus particles based on single-particle cryo electron microscopy images. Most of the work is in collaboration with a domain expert whose research group performs the experiments. Most of the work is of a statistical character. The most successful work often involves systems where something is understood about the physical – chemical basis of the system and/or the measurement process. Some of the problems are “big data” problems, e.g., 100,000 images in single-particle cryo electron microscopy. The group’s two goals are to develop new interesting ideas in modeling and inference and to solve our collaborators’ problems!
Much of the group’s work involves custom solutions to challenges posed by collaborators. Such solutions are often a mix of symbolic components and computational components. Applying the ideas at relevant scales often involves substantial computations and the group has extensive experience with practical computing up to the level of writing software systems for distributed-memory cluster computing with C/C++/OpenMP/CUDA/MPI and Python. The group’s primary computers are currently two identical compute servers and one file server:
Compute servers (two identical machines) in a 4U form factor:
- Dual Intel Xeon E5 2670 microprocessors (2.6GHz, 8 cores, 20MB Cache).
- 256GB memory.
- Two nVidia Tesla K20X general-purpose GPUs each with 6GB memory.
- A RAID 6 disk array that acts as backup to the file server.
File server in a 2U form factor:
- Dual Intel Xeon E5 2650 microprocessors (2GHz, 8 cores, 20MB Cache).
- 32GB memory.
- 8 Seagate 3TB SATA drives configured as a RAID 6 array.
A photograph of the machines as installed in one of the Electrical and Computer Engineering server rooms. The two compute servers occupy rack positions 12-15 and 8-11, the file server occupies rack positions 6-7, and the battery backup occupies rack positions 1-5.