As of version 2, simx can use SIMPUT files, and by default generates SIMPUT files as output if the input source is not a SIMPUT file.
The number of different consequences (or subsets) corresponds to the number of different concepts in K. Priorities of defaults, generated during the mapping of every NRDR concept (see Sect. "Mapping NRDR to default theories"), ensure mutual exclusion when applying defaults which have the same consequence.
A collection of formulae, regarded as a set of prerequisite-free normal defaults, generates a nonmonotonic inference relation through its Reiter skeptical extension.
The default protocol generated a large docking box and produced the binding pose with an RMSD from native of 13.9 Å.
This allows users to run these analyses on any number of feature layers (default or generated) present in the GIS-based tool.
While these parameters can be fit to data, using default values generated highly similar quantitative predictions as a previously constructed detailed biochemical model of the same pathway which used 88 parameters from literature [33,34].
User interface layout: the layout of the program invocation form and job result pages are by default automatically generated from the XML definition, but can be customized.
Although Newbler with default parameter generated an assembly with the largest N50, mean contig length and number of contig no less than 1,000 bp, it also produced the smallest summed length of contigs, and startlingly low total number of contigs.
MIRA with default parameter generated an assembly with the longest summed length of contigs and maximum total number of contigs, but it also produced the smallest N50 and mean contig length.
The mapped reads in BAM format for either sample and TE annotation were supplied to the compare_ND_TD module, which runs the main Jitterbug module on both sample BAMs (bin size set to 50,000,000 bp), filters the results according the default values generated on the fly, and calls somatic TEs as explained above.
