HiCOMB 2013, May 20, 2013

Advance Program

8:25-8:30am Welcome and Introductory Remarks
Jaroslaw Zola, David Bader, Srinivas Aluru
Session I: Sequence and Structure
8:30-9am Biological Sequence Comparison in Hybrid Platforms with Dynamic Workload Adjustment
Fernando Mendonca, Alba Cristina Magalhaes Alves de Melo
9-9:30am Accelerating All-to-all Protein Structures Comparison with TMalign Using a NoC Many-cores Processor Architecture
Anuj Sharma, Antonis Papanikolaou, Elias S. Manolakos
9:30-10am Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce
Daniel Yehdego, Boyu Zhang, Vikram Kodimala, Kyle Johnson, Michela Taufer, Ming-Ying Leung
10-10:30am Coffee Break
Session II: Phylogenetics and Metagenomics
10:30-11am A generic Vectorization Scheme and a GPU kernel for the Phylogenetic Likelihood Library
Fernando Izquierdo-Carrasco, Alexandros Stamatakis, Simon Berger, Nikolaos Alachiotis, Tomas Flouri, Solon Pissis
11-11:30am Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library
Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis
11:30-12am A Map-Reduce Framework for Clustering Metagenomes
Zeehasham Rasheed,Huzefa Rangwala
12-1:30pm Lunch Break
Keynote and Invited Talks
1:30-2:30pm Keynote Talk: Parallel Multiscale Simulations of Brain Aneurysms
George Karniadakis, Brown University
2:30-3pm HPC Software Libraries for Next-Gen Sequencing Analytics
Srinivas Aluru
3-3:30pm GPU-accelerated Protein Family Identification for Metagenomics
Changjun Wu, Ananth Kalyanaraman
3:30-4pm Coffee Break
Session III: Molecular and Systems Biology
4-4:30pm Polarization Energy on a Cluster of Multicores
Jesmin Jahan Tithi, Rezaul A. Chowdhury
4:30-5pm GPU-based Steady-State Solution of the Chemical Master Equation
Marco Maggioni, Tanya Berger-Wolf, Jie Liang