Genetic Algorithms, Operators, and DNA Fragment Assembly
Machine Learning - Special issue on applications in molecular biology
A Taxonomy of Hybrid Metaheuristics
Journal of Heuristics
Evolutionary Optimization Techniques on Computational Grids
ICCS '02 Proceedings of the International Conference on Computational Science-Part I
Trie-Based Data Structures for Sequence Assembly
CPM '97 Proceedings of the 8th Annual Symposium on Combinatorial Pattern Matching
An Enabling Framework for Master-Worker Applications on the Computational Grid
HPDC '00 Proceedings of the 9th IEEE International Symposium on High Performance Distributed Computing
Grid Computing: Making the Global Infrastructure a Reality
Grid Computing: Making the Global Infrastructure a Reality
Condor-G: A Computation Management Agent for Multi-Institutional Grids
HPDC '01 Proceedings of the 10th IEEE International Symposium on High Performance Distributed Computing
Exact and Heuristic Algorithms for the DNA Fragment Assembly Problem
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
A grid-oriented genetic algorithm framework for bioinformatics
New Generation Computing - Grid systems for life sciences
Implementation and utilisation of a Grid-enabled problem solving environment in Matlab
Future Generation Computer Systems - Special section: Complex problem-solving environments for grid computing
Mega process genetic algorithm using grid MP
LSGRID'04 Proceedings of the First international conference on Life Science Grid
LSGRID'04 Proceedings of the First international conference on Life Science Grid
Parallelism and evolutionary algorithms
IEEE Transactions on Evolutionary Computation
A decision support approach for assigning reviewers to proposals
Expert Systems with Applications: An International Journal
Customizable execution environments for evolutionary computation using BOINC + virtualization
Natural Computing: an international journal
Benchmark datasets for the DNA fragment assembly problem
International Journal of Bio-Inspired Computation
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In this paper we propose a genetic algorithm (GA) for solving the DNA fragment assembly problem in a computational grid. The algorithm, which is named GrEA, is a steady-state GA which uses a panmitic population, and it is based on computing parallel function evaluations in an asynchronous way. We have implemented GrEA on top of the Condor system, and we have used it to solve the DNA assembly problem. This is an NP-hard combinatorial optimization problem which is growing in importance and complexity as more research centers become involved on sequencing new genomes. While previous works on this problem have usually faced 30K base pairs (bps) long instances, we have tackled here a 77K bps long one to show how a grid system can move research forward. After analyzing the basic grid algorithm, we have studied the use of an improvement method to still enhance its scalability. Then, by using a grid composed of up to 150 computers, we have achieved time reductions from tens of days down to a few hours, and we have obtained near optimal solutions when solving the 77K bps long instance (773 fragments). We conclude that our proposal is a promising approach to take advantage of a grid system to solve large DNA fragment assembly problem instances and also to learn more about grid metaheuristics as a new class of algorithms for really challenging problems.