title: Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine--an implementation perspective.
abstract: BACKGROUND
  RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly uses highly coupled Dynamic Programming (DP) solutions. The problem scale and complexity become embarrassingly humungous to handle as sequence size increases. This makes the case for parallelization. Parallelization can be achieved by way of networked platforms (clusters, grids, etc) as well as using modern day multi-core chips.
  
  
  METHODS
  In this paper, we exploit the parallelism capabilities of the IBM Cell Broadband Engine to parallelize an existing Dynamic Programming (DP) algorithm for RNA secondary structure prediction. We design three different implementation strategies that exploit the inherent data, code and/or hybrid parallelism, referred to as C-Par, D-Par and H-Par, and analyze their performances. Our approach attempts to introduce parallelism in critical sections of the algorithm. We ran our experiments on SONY Play Station 3 (PS3), which is based on the IBM Cell chip.
  
  
  RESULTS
  Our results suggest that introducing parallelism in DP algorithm allows it to easily handle longer sequences which otherwise would consume a large amount of time in single core computers. The results further demonstrate the speed-up gain achieved in exploiting the inherent parallelism in the problem and also elicits the advantages of using multi-core platforms towards designing more sophisticated methodologies for handling a fairly long sequence of RNA.
  
  
  CONCLUSIONS
  The speed-up performance reported here is promising, especially when sequence length is long. To the best of our literature survey, the work reported in this paper is probably the first-of-its-kind to utilize the IBM Cell Broadband Engine (a heterogeneous multi-core chip) to implement a DP. The results also encourage using multi-core platforms towards designing more sophisticated methodologies for handling a fairly long sequence of RNA to predict its secondary structure.
authors.affiliation: Institute for Infocomm Research, 1 Fusionopolis Way, #21-01, Connexis South Tower, Singapore 138632. krishnan@i2r.a-star.edu.sg
authors.forename: S P T
authors.initials: SP
authors.lastname: Krishnan
authors.forename: Sim Sze
authors.initials: SS
authors.lastname: Liang
authors.forename: Bharadwaj
authors.initials: B
authors.lastname: Veeravalli
mesh_terms: D003205:Computing Methodologies; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA