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Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical(More)
This paper discusses the semantics of the prialt construct in Handel-C[1]. The language is essentially a static subset of C, augmented with a parallel construct and channel communication, as found in CSP. All assignments and channel communication events take one clock cycle, with all updates synchronised with the clock edge marking the cycle end. The(More)
When some agents want to communicate through a media stream (for example voice or video), the Real Time Protocol (RTP) is used. This protocol does not provide encryption, so it is necessary to use Secure RTP (SRTP) to secure the communication. In order for this to work, the agents need to agree on key material and ZRTP provides them with a procedure to(More)
We present second steps in the construction of formal models of NAND flash memory, based on a recently emerged open standard for such devices. The model is intended as a key part of a pilot project to develop a verified file store system based on flash memory. The project was proposed by Joshi and Holzmann as a contribution to the Grand Challenge in(More)
We present first steps in the construction of formal models of NAND flash memory, based on a recently emerged open standard for such devices. The model is at a level of abstraction that captures the internal architecture of such a device, as well as the commands that are used to operate it. The model is intended as a key step in a plan to develop a verified(More)
We present a research roadmap for the second pilot project in the Verified Software Grand Challenge on formally verified POSIX file stores. The work is inspired by the requirements for NASA's forthcoming Mars Rover missions. The roadmap describes an integrated and comprehensive body of work, including current work, as well as further opportunities for(More)
This paper develops a language for reasoning about concurrent functional I/O. We assume that the API is specified as state-transformers on a single world state. We then prove that under certain conditions evaluation in this language is deterministic, and give some examples. All properties were machine-verified using the Sparkle proof-assistant and using(More)
We describe an operational semantics for the hardware compilation language Handel-C [7], which is a C-like language with channel communication and parallel constructs which compiles down to mainly synchronously clocked hardware. The work in this paper builds on previous work describing the semantics of the “prialt” construct within Handel-C [5] and a(More)