Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.

BACKGROUND: Computational models in systems biology are becoming more important with the advancement of experimental techniques to query the mechanistic details responsible for leading to phenotypes of interest. In particular, Boolean models are well fit to describe the complexity of signaling networks while being simple enough to scale to a very large number of components. With the advance of Boolean model inference techniques, the field is transforming from an artisanal way of building models of moderate size to a more automatized one, leading to very large models. In this context, adapting the simulation software for such increases in complexity is crucial. RESULTS: We present two new developments in the continuous time Boolean simulators: MaBoSS.MPI, a parallel implementation of MaBoSS which can exploit the computational power of very large CPU clusters, and MaBoSS.GPU, which can use GPU accelerators to perform these simulations. CONCLUSION: These implementations enable simulation and exploration of the behavior of very large models, thus becoming a valuable analysis tool for the systems biology community.

Superparamagnetic iron oxide (SPIO) labeling efficiency and subsequent MRI tracking of native cell populations pertinent to pulmonary heart valve tissue engineering studies.

The intimal and medial linings of the pulmonary artery consist largely of vascular endothelial cells (VECs) and vascular smooth muscle cells (VSMCs), respectively. The migration of these cell types to a potential tissue-engineered pulmonary valve (TEPV) implant process is therefore of interest in understanding the valve remodeling process. Visualization and cell tracking by MRI, which employs hypointense contrast achievable through the use of superparamagnetic iron oxide (SPIO) microparticles to label cells, provides a method in which this can be studied. We investigated the SPIO labeling efficiency of human VECs and VSMCs, and used two- and three-dimensional gradient echo sequences to track the migration of these cells in agar gel constructs. Protamine sulfate (4.5 µg/mL) was used to enhance SPIO uptake and was found to have no influence on cell viability or proliferation. MRI experiments were initially performed using a 9.4-T scanner. The results demonstrated that the spatial positions of hypointense spots were relatively unchanged over 12 days. Subsequent MR experiments performed at 7 T demonstrated that three-dimensional imaging provided the best spatial resolution to assess cell fate. R(2)* maps were bright in SPIO cell-encapsulated gels in comparison with unlabeled counterparts. Signal voids were ruled out as hypointense regions owing to the smooth exponential decay of T(2)* in these voxels. As a next step, we intend to use the SPIO cell labeling and MR protocols established in this study to assess whether hemodynamic stresses will alter the vascular cell migratory patterns. These studies will shed light on the mechanisms of vascular remodeling after TEPV implantation.

Toward a comprehensive hybrid physical-virtual reality simulator of peripheral anesthesia with ultrasound and neurostimulator guidance.

We are developing a simulator of peripheral nerve block utilizing a mixed-reality approach: the combination of a physical model, an MRI-derived virtual model, mechatronics and spatial tracking. Our design uses tangible (physical) interfaces to simulate surface anatomy, haptic feedback during needle insertion, mechatronic display of muscle twitch corresponding to the specific nerve stimulated, and visual and haptic feedback for the injection syringe. The twitch response is calculated incorporating the sensed output of a real neurostimulator. The virtual model is isomorphic with the physical model and is derived from segmented MRI data. This model provides the subsurface anatomy and, combined with electromagnetic tracking of a sham ultrasound probe and a standard nerve block needle, supports simulated ultrasound display and measurement of needle location and proximity to nerves and vessels. The needle tracking and virtual model also support objective performance metrics of needle targeting technique.