Scalable grid resource allocation for scientific workflows using hybrid metaheuristics

Grid infrastructure is a valuable tool for scientific users, but it is characterized by a high level of complexity which makes it difficult for them to quantify their requirements and allocate resources. In this paper, we show that resource trading is a viable and scalable approach for scientific users to consume resources. We propose the use of Grid resource bundles to specify supply and demand combined with a hybrid metaheuristic method to determine the allocation of resources in a market-based approach. We evaluate this through the application domain of scientific workflow execution on the Grid

Heuristic Solutions for Loading in Flexible Manufacturing Systems

Production planning in flexible manufacturing system deals with the efficient organization of the production resources in order to meet a given production schedule. It is a complex problem and typically leads to several hierarchical subproblems that need to be solved sequentially or simultaneously. Loading is one of the planning subproblems that has to addressed. It involves assigning the necessary operations and tools among the various machines in some optimal fashion to achieve the production of all selected part types. In this paper, we first formulate the loading problem as a 0-1 mixed integer program and then propose heuristic procedures based on Lagrangian relaxation and tabu search to solve the problem. Computational results are presented for all the algorithms and finally, conclusions drawn based on the results are discussed

Computational Protein Design Using AND/OR Branch-and-Bound Search

The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this paper, we propose a new protein design algorithm based on the AND/OR branch-and-bound (AOBB) search, which is a variant of the traditional branch-and-bound search algorithm, to solve this combinatorial optimization problem. By integrating with a powerful heuristic function, AOBB is able to fully exploit the graph structure of the underlying residue interaction network of a backbone template to significantly accelerate the design process. Tests on real protein data show that our new protein design algorithm is able to solve many prob- lems that were previously unsolvable by the traditional exact search algorithms, and for the problems that can be solved with traditional provable algorithms, our new method can provide a large speedup by several orders of magnitude while still guaranteeing to find the global minimum energy conformation (GMEC) solution.Comment: RECOMB 201

Rigidity and flexibility of biological networks

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of protein structures, as well as local flexibility measures of proteins and their applications in explaining allostery and thermostability is given. We also briefly discuss the network aspects of cytoskeletal tensegrity. Finally, we show the importance of the balance between functional flexibility and rigidity in protein-protein interaction, metabolic, gene regulatory and neuronal networks. Our summary raises the possibility that the concepts of flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl

Combinatorial optimisation of a large, constrained simulation model: an application of compressed annealing

Simulation models are valuable tools in the analysis of complex, highly constrained economic systems unsuitable for solution by mathematical programming. However, model size may hamper the efforts of practitioners to efficiently identify the most valuable configurations. This paper investigates the efficacy of a new metaheuristic procedure, compressed annealing, for the solution of large, constrained systems. This algorithm is used to investigate the value of incorporating a sown annual pasture, French serradella (Ornithopus sativa Brot. cv. Cadiz), between extended cropping sequences in the central wheat belt of Western Australia. Compressed annealing is shown to be a reliable means of considering constraints in complex optimisation problems in agricultural economics. It is also highlighted that the value of serradella to dryland crop rotations increases with the initial weed burden and the profitability of livestock production.combinatorial optimisation, crop rotation, simulated annealing, Research Methods/ Statistical Methods, C63, Q15,