Alba Cristina M. A. de Melo
Professor at the Department of
Computer Science, UnB
CNPq Fellow Researcher Level 1D
University of Brasilia -
Department of Computer Science, office 8
Campus Darcy Ribeiro – Predio
CEP 70910-900 - Brasilia, DF - Brazil
Phone: +55 61 31073679 Fax: +55 61 33073214
Interests | Academic
Background | Students
| Selected Publications(2014-2010) |
Courses | Links
Algorithms for Bioinformatics Applications: cluster, grid, FPGA, GPU
and/or IBM Cell/BE solutions
Parallel Programming Environments: Unified Programming Environment with
Shared Memory and Message Passing, Dynamic Load Balancing, Multi and Manycore architectures
Shared Memory: Memory Consistency Models, Memory Coherence Protocols
Publications (2016-2010) - Full Papers in Journals [top]
Sandes, E. F. O.; Miranda, G. ; Ayguade, E. ; Martorell, X.; Teodoro, G. ;
Melo, Alba C. M. A.. CUDAlign 4.0: incremental speculative traceback for exact chromosome-wide alignment in GPU
clusters. IEEE Transactions on
Parallel and Distributed Systems, v. 27, n.10, p. 2838-2850, 2016.
Sundfeld, D.; Havgard,
J. H. ; Melo, A. C. M. A. ; Gorodkin, J. . Foldalign
2.5: multithreaded implementation for pairwise structural RNA alignment. Bioinformatics, v. 32, p.
- (2016) Sandes,
E. F. O.; Miranda, G. ; Ayguade,
E. ; Martorell, X.; Teodoro,
G. ; Melo, Alba C. M. A. . MASA: A Multiplatform Architecture for
Sequence Aligners with Block Pruning. ACM Transactions on Parallel Computing, v. 2, p. 1-31, 2016.
- (2016) Sandes,
E. F. O.; Boukerche, A. ;
Melo, A. C. M. A. . Parallel Optimal Pairwise
Biological Sequence Comparison. ACM Computing Surveys, v. 48, p.
- (2014) Sandes,
E. F. O.; Ralha, C. G.; Melo,
A. C. M. A. An Agent-Based Solution for Dynamic Multi-Node Wavefront Balancing in Biological Sequence Comparison.
Expert Systems with Applications, v. 41, n.10, p. 4929-4938.
- (2014) Guimaraes, F. P.;
Celestin, P.; Batista, D. M.; Rodrigues, G. N.; Melo,
A. C. M. A. .A Framework for Adaptive Fault-Tolerant Execution of
Workflows in the Grid: Empirical and Theoretical Analysis. Journal of
Grid Computing, v. 12, n.1, p. 127-151.
- (2013) Sandes,
E. F. O.; Melo, A. C. M. A. .
Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. IEEE
Transactions on Parallel and Distributed Systems, v. 24, n. 5, p.
- (2013) Hamidouche,
K. ; Mendonca, F. M. ; Falcou, J. ; Melo, A. C. M.
A. ; Etiemble, D.. Parallel Smith-Waterman
Comparison on Multicore and Manycore Computing
Platforms with BSP++. International Journal of Parallel Programming,
v. 41, n. 1, p. 111-136.
- (2013) Macedo,
E. A; Melo, A. C. M. A. ;
Pfitscher, G. H. ; Boukerche,
A. Multiple biological sequence alignment in heterogeneous multicore
clusters with user-selectable task allocation policies. The Journal of
Supercomputing, v. 63, n. 3, p. 740-756.
- (2012) Boukerche,
A. ; Batista, R. B. ; Melo,
A. C. M. A. ; Scarel, F. B. ; Souza, L. A. B. C.
. Exact Parallel Alignment of Megabase Genomic
Sequences with Tunable Work Distribution. International Journal of
Foundations of Computer Science, v. 23, p. 407-429.
- (2012) Eusse,
J. F. ; Moreano, N. ; Melo, A. C. M. A. ; Jacobi, R. P. . A Protein Sequence
Analysis Hardware Accelerator Based on Divergences. International
Journal of Reconfigurable Computing (Print), v. 2012, p. 1-19.
- (2012) Leite,
A. F. ; Mendes, H. C. ; Weigang,
L. ; Melo, Alba C. M. A. ; Boukerche,
A. . An architecture for P2P bag-of-tasks
execution with multiple task allocation policies in desktop grids. Cluster
Computing, v. 15, p. 351-361,
- (2010) BOUKERCHE, A., CORREA, J. M.,
MELO, Alba C. M. A, JACOBI, R. P., "A Hardware Accelerator for Fast Retrieval
of DIALIGN Biological Sequence Alignments in Linear Space", IEEE
Transactions on Computers v.59, n.6, pp. 808-821.
- (2010) SOUSA, Marcelo S., MELO, Alba
C. M. A, BOUKERCHE, Azzedine, "An Adaptive
Multi-Policy Grid Service for Biological Sequence Comparison", Journal
of Parallel and Distributed Computing v.70, n.2, pp. 160-172.
- (2010) SANDES, E. F. O., MELO, Alba C.
M. A, "CUDAlign: Using GPU to Accelerate
the Comparison of Megabase Genomic
Sequences", ACM SIGPLAN Notices v.45, n.5, pp. 137-146.
Graduate Students [top]
- (MsC) Simone Cintra Chagas. Visualizing Memory Consistency Models. Concluded
in June 1999.
- (MsC) Cicero R. O. Galdino: Memory
Coherence Protocols for Eficient DSM Systems.
Concluded in December 2000.
- (MsC) Nilo S. L. Barros. Visualizing
Hybrid Memory Consistency Models. Concluded in May 2000.
- (MsC) Jan M. Correa. Using a Classifier System for
Dynamic Load Balancing. Concluded in November 2001.
- (MsC) Glaucia Dias. Integrating
Optimistic Virtual Synchrony to a CORBA Object Group Service, Concluded
in October 2002.
- (MsC) Gustavo J. Portela. Load
Balancing Task Scheduling for Grid Computing Environments. Concluded
in June 2004.
- (MsC) Jeferson G. Koch. Coordinated
Checkpointing Mechanism for DSM Systems. Concluded
in July 2004.
- (MsC) Marcelo S. Sousa. PackageBLAST:
An Adaptive Grid Service with Multiple Task Allocation Policies for
Biological Sequence Comparison, Concluded in September 2005.
- (MsC) Tania G. Ramos. An Extensible Resource
Discovery Mechanism for Grid Computing Environments. Concluded in November, 2005.
- (MsC) Rodolfo B. Batista, Parallel Exact Biological
Sequence Comparison with User-Restricted memory Usage. Concluded in April, 2006.
- (MsC) Glauber Scorsatto, GrAMoS:
A Grid Service for Monitoring Agreements in Grids. Concluded in September, 2007.
Jan M. Correa, Hardware Accelerators for Biological Sequence Comparison
Applications. Concluded in May, 2008.
- (MsC) Lidia A. Miranda,Parallel Strategy for Multiple
Sequence Alignment with a Parallel Injection Island Algorithm. Concluded
in September, 2009.
- (MsC) Alessandro F. Leite.A
P2P Framework for Bag-of-Tasks Applications with Multiple Allocation
Policies. Concluded in June, 2010.
- (MsC) Emerson A. Macedo.Distributed
Strategy for Biological Sequence Comparison with DIALIGN-TX in
Heterogeneous Multicore Clusters. Concluded October,
- (MsC) Felipe P. Guimaraes.A
Framework for Adaptive and Fault Tolerant Execution of Workflows in Grids.
Concluded October, 2010.
- (MsC) Edans F. O. Sandes. Parallel Exact Alignment of Whole
Chromosomes in GPUs. Concluded June 2011.
- (MsC) Alisson W. A. Silva, A
Mechanism for Negotiation of QoS Auditors in
Grid with WS-Agreements, Concluded in July 2011.
- (MsC) Daniel S. Lima, Parallel Strategy for Exact
Multiple Sequence Alignment in GPU, Concluded in August 2012.
- (MsC) Fernando M. Mendonca, Parallel
Biological Sequence Comparison in Hybrid High Performance Computing
Platforms, Concluded in January 2013.
Alessandro F. Leite, A User-Centered and
Autonomic Multi-Cloud Architecture for High-Performance Computing
Applications, Concluded in December 2014.
- (MsC) Marco A. Figueredo, Exact
Parallel Sequence Alignment in OpenCL,
Concluded in August 2015.
- (PhD) Edans F. O. Sandes, CUDAlign: Obtaining the Smith-Waterman
Alignment of Megabase Biological Sequence in
Multiple High-Performance Computing Platforms, Concluded in September
- (MsC) Gabriel H. G. Silva, Fickett-CUDAlign: Parallel Sequence Comparison with Multiple Blocks and Adjustable
Bands, Concluded in March 2016.
Emerson A. Macedo: Parallel Protein Folding
Algorithms for Heterogeneous Platforms, expected conclusion in March
Daniel S. Lima, Primary and Secondary Multiple Sequence Alignment in High
Performance Computing Platforms, expected conclusion in February 2017.
Detailed CV (full list of publications)