Biomedical Engineering Reference
In-Depth Information
states that a small portion of the program that cannot be parallelized
will limit the overall speed-up available from parallelization. A program
solving a large mathematical or engineering problem will typically consist
of several parallelizable parts and several non-parallelizable (sequential)
parts. If is the fraction of running time a sequential program spends
on non-parallelizable parts, then S =
1
is the maximum speed-up with
parallelization of the program. Gustafson's law is another law in comput-
ing, closely related to Amdahl's law. It states that the speed-up with P
processors is S(P) = P(P1). Amdahl's law assumes a xed problem
size and that the running time of the sequential section of the program is
independent of the number of processors, whereas Gustafson's law does
not make these assumptions.
Phosphate buffered saline (PBS): A water-based salt solution contain-
ing sodium chloride, sodium phosphate, and, in some formulations, potas-
sium chloride and potassium phosphate. The buer's phosphate groups
help to maintain a constant pH. The osmolarity and ion concentrations
of the solution usually match those of the human body
PKH26GL: Red fluorescent cell linker Kit for general cell membrane label-
ing.
Plug-ins: Energy functions, lattice monitors, or stored user-assigned data
that CompuCell3D uses internally to initially configure the simulation.
Examples are plug-ins dening objects' types, biophysical properties, or
location and amplitude of external constant forces.
Rac: A subfamily of the Rho family of GTPases that regulates a wide range
of cellular functions including migration and cytoskeletal reorganization.
RPMI: A series of media utilizing a bicarbonate buffering system and alter-
ations in the amounts of amino acids and vitamins used for the culture of
human normal and neoplastic leukocytes. RPMI, when properly supple-
mented, has demonstrated wide applicability for supporting the growth
of many other types of cultured cells also.
Spin flip: Change in lattice configuration.
Steppables: CompuCell3D modules that are called every Monte Carlo Step
(MCS). More precisely, they are called after all the spin copy attempts
performed in a given MCS have been carried out. The steppables modules
employ all functions that need to be done every MCS, such as updating
the lattice conguration and recalculating the objects' attributes.
Student's t-test: Any statistical hypothesis test in which the test statistic
follows a Student's t distribution if the null hypothesis is supported. It
is most commonly applied when the test statistic would follow a normal
distribution if the value of a scaling term in the test statistic were known.
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