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Author: Ketil Malde

Affiliation: Institute of Marine Research, Norway

ISBN: 978-989-8565-35-8

Keyword(s): Software Transactional Memory, Genome Assembly.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering

Abstract: Parallel programs are key to exploiting the performance of modern computers, but traditional facilities for synchronizing threads of execution are notoriously difficult to use correctly, especially for problems with a non-trivial structure. Software transactional memory is a different approach to managing the complexity of interacting threads. By eliminating locking, many of the complexities of concurrency is eliminated, and the resulting programs are composable, and thus simplifies refactoring and other modifications. Here, we investigate STM in the context of genome assembly, and demonstrate that a program using STM is able to successfully parallelize the genome scaffolding process with a near linear speedup.

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Paper citation in several formats:
Malde, K. (2013). Can Software Transactional Memory Make Concurrent Programs Simple and Safe?.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 223-228. DOI: 10.5220/0004326702230228

@conference{bioinformatics13,
author={Ketil Malde.},
title={Can Software Transactional Memory Make Concurrent Programs Simple and Safe?},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={223-228},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004326702230228},
isbn={978-989-8565-35-8},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - Can Software Transactional Memory Make Concurrent Programs Simple and Safe?
SN - 978-989-8565-35-8
AU - Malde, K.
PY - 2013
SP - 223
EP - 228
DO - 10.5220/0004326702230228

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