An occam Style Communications System for UNIX Networks

This document describes the design of a communications system which provides occam style communications primitives under a Unix environment, using TCP/IP protocols, and any number of other protocols deemed suitable as underlying transport layers. The system will integrate with a low overhead scheduler/kernel without incurring significant costs to the execution of processes within the run time environment. A survey of relevant occam and occam3 features and related research is followed by a look at the Unix and TCP/IP facilities which determine our working constraints, and a description of the T9000 transputer's Virtual Channel Processor, which was instrumental in our formulation. Drawing from the information presented here, a design for the communications system is subsequently proposed. Finally, a preliminary investigation of methods for lightweight access control to shared resources in an environment which does not provide support for critical sections, semaphores, or busy waiting, is made. This is presented with relevance to mutual exclusion problems which arise within the proposed design. Future directions for the evolution of this project are discussed in conclusion

Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

Efficient computation of aerodynamic influence coefficients for aeroelastic analysis on a transputer network

Aeroelastic analysis is multi-disciplinary and computationally expensive. Hence, it can greatly benefit from parallel processing. As part of an effort to develop an aeroelastic capability on a distributed memory transputer network, a parallel algorithm for the computation of aerodynamic influence coefficients is implemented on a network of 32 transputers. The aerodynamic influence coefficients are calculated using a 3-D unsteady aerodynamic model and a parallel discretization. Efficiencies up to 85 percent were demonstrated using 32 processors. The effect of subtask ordering, problem size, and network topology are presented. A comparison to results on a shared memory computer indicates that higher speedup is achieved on the distributed memory system

Symmetric and Synchronous Communication in Peer-to-Peer Networks

Motivated by distributed implementations of game-theoretical algorithms, we study symmetric process systems and the problem of attaining common knowledge between processes. We formalize our setting by defining a notion of peer-to-peer networks(*) and appropriate symmetry concepts in the context of Communicating Sequential Processes (CSP), due to the common knowledge creating effects of its synchronous communication primitives. We then prove that CSP with input and output guards makes common knowledge in symmetric peer-to-peer networks possible, but not the restricted version which disallows output statements in guards and is commonly implemented. (*) Please note that we are not dealing with fashionable incarnations such as file-sharing networks, but merely use this name for a mathematical notion of a network consisting of directly connected peers "treated on an equal footing", i.e. not having a client-server structure or otherwise pre-determined roles.)Comment: polished, modernized references; incorporated referee feedback from MPC'0

Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

Transputer-based robot controller

A cost-effective architecture for the control of robot manipulators based on functional decomposition of the equations of motion is described. The Lagrange-Euler( LE) and the Newton-Euler( NE) formulations are used for decomposition. According to real-time control criterion, the LE equations are not suitable for implementation using currently available hardware because the required number of computations is too high, even after taking the inherent parallelism into account. However, the recursive nature of the Newton-Euler equations of motion lend themselves to being decomposed to terms used to generate the recursive forward and backward formulations. A special architecture implemented on a network of transputers is proposed which takes advantage of both the parallelism and seriallism of the NE equations and the ease of building communication channel provided by the transputers and Occam language. This proposed controller model can be best defined as a macro level pipeline. Based on this model, both floating point computation and fixed point computation results are presented for performance comparison