SInC: An accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data

We report SInC (SNV, Indel and CNV) simulator and read generator, an open-source tool capable of simulating biological variants taking into account a platform-specific error model. SInC is capable of simulating and generating single- and paired-end reads with user-defined insert size with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes. Sinc can be downloaded from https://sourceforge.net/projects/sincsimulator/

Interface Simulation Distances

The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, and that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.Comment: In Proceedings GandALF 2012, arXiv:1210.202

Regression-free Synthesis for Concurrency

While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in for repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs.Comment: for source code see https://github.com/thorstent/ConRepai

Comments on "New hypergeometric identities arising from Gauss’s second summation theorem"

In 1997, Exton [J. Comput. Appl. Math. 88 (1997) 269–274] obtained a general transfor- mation involving hypergeometric functions by elementary manipulation of series. A number of hypergeometric identities not previously recorded in the literature were then deduced by application of Gauss’ second summation theorem and other known hypergeometric summa- tion theorems. However, many of the results stated by Exton contain errors. It is the purpose of this note to present the corrected forms of these hypergeometric identities