- Computer Models & Software Tools
- About the Computational Systems Biology Laboratory
For further information about the Computational Systems Biology Laboratory, contact Dr. Ranjan Dash.
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Computational modeling work at the Computational Systems Biology Laboratory is conducted using resources made available by the Marquette University and Medical College of Wisconsin (MCW) Department of Biomedical Engineering, the MCW Department of Physiology, and the MCW Research Computing Center. Major resources include wet lab and experimental equipment, as well as computer and computer-modeling resources.
The CSBL has recently established an experimental wet laboratory of approximately 400 sq. ft. and located in the wet-lab space of the second floor of MCW's Translational and Biomedical Research Center. This facility is designated for the performance of high-resolution respirometry (HRR) and spectrofluorometric measurements and reactive oxygen species in isolated mitochondria, isolated myocytes, and tissue homogenate from various tissues/organs using the Oxygraph-2k Equipment (Oroboros) and a PTI spectrofluorometer (Horiba Scientific).
The Oroboros Instruments Oxygraph-2k (O2k) for high-resolution respirometry with added Fluorometer module for spectrofluorometry is an assembled instrument that includes the O2k-Core, Titration-Injection microPump TIP2k-Module, O2k-Fluo LED2-Module, O2k-TPP+ ISE-Module, O2k-pH ISE-Module, and O2k-NO Amp-Module. This state-of-the-art equipment is ideal for performing high-resolution respirometry (HRR) for mitochondrial respiration (O2 consumption) and specific excitation and emission filter-based spectrofluorometric measurements of mitochondrial membrane potential and intramitochondrial and extramitochondrial cation (e.g., Ca2+, Mg2+, pH) concentrations and reactive oxygen species (ROS; e.g., O2-., H2O2) production in isolated mitochondria, cultured/isolated myocytes, and tissue homogenate from various tissues/organs. Data collected using this equipment is essential for the development and validation of integrated computational models of mitochondrial function/dysfunction.
PTI QuantaMasterTM 800 Spectrofluorometer
The PTI QuantaMasterTM 800 Spectrofluorometer from HORIBA Instruments Inc. is used to measure intracellular and intramitochondrial bioenergetics, Ca2+ dynamics, and ROS emission. The high-speed QuantaMaster spectrofluorometer uses the patented DeltaRAM X tunable excitation source and can select any wavelength within a millisecond. For the detection of dual-emission probes, a QM-800 second emission monochromator channel has been added to the system, which includes a second computer-controlled, autocalibrated coma aberration corrected, QuadraScopicTM 300 mm monochromator with triple grating turret for emission wavelength selection. In addition, the system contains a rapid temperature-controlled single sample holder K-155-C (instead of standard sample holder) for controlling temperature -40 degree C to +105 degree C, as well as individual stir, water circulator and software driver for FelixGX.
The CSBL's dry lab is equipped with several high-performance desktop and laptop computers (twelve total) loaded with high-performance scientific computing and visualization softwares (e.g., Visual Fortran, Maple, MATLAB, OriginLab, SPSS SigmaPlot and SigmaStat). The large-scale computations are conducted using the MCW Research Computing Center (RCC high-performance computing platforms (e.g., MATLAB Distributed Computing Cluster).
Researchers of the CSBL enjoy shared access to the Computer Core in MCW's Department of Physiology. The Computer Core is equipped with nine multiprocessor Windows servers and 3.2 Terabytes of Raid 5 disk storage with LTO2 tape libraries for backup; 18 Windows workstations; 35 mm slide imager and slide scanner; 2 flatbed scanners; HP8100 laser jet; HP4600DN color laser jet; 2 inkjet; and a 36” format Design Jet 1050C plotter. In addition, the Computer Core provides computer and application support for all users.