Proceedings of the second international workshop on Emerging computational methods for the life sciences

It is our great pleasure to welcome you to the 3rd International Emerging Computational Methods for the Life Sciences Workshop -- ECMLS'12. This year's workshop follows up our successful first meetings in this series at HPDC'11 and HPDC'10, which are well documented at ECMLS'11 and ECMLS'10. The basic motivation is as before with the dramatic importance of next generation sequencers in biology leading to a big data deluge and a corresponding increase in new algorithms and new computing systems growing more apparent. Computing systems are rapidly changing with multicore, GPUs, clusters, volunteer systems, clouds, and grids offering an array of opportunities. New programming paradigms such as MapReduce and Many Task Computing have joined the traditional repertoire of workflow and parallel computing for the highest performance systems. Meanwhile the Life Sciences are continuing to expand in data generated with continuing improvement in the instruments for high throughput analysis. This "fourth paradigm" (data driven science) is joined by complex systems or biocomplexity that can build phenomenological models of biological systems and processes. This workshop juxtaposes these trends seeking those computational methods that will enhance scientific discovery in the life sciences arena. The call for papers attracted 13 submissions from Europe and the United States. The program committee accepted 7 papers that cover a variety of topics, including biomedical grid workflows, biomedical simulation environment for Grid middleware and Cloud, a million compounds virtual screening using a Petascale supercomputer, molecular evolution computation using GPUs, an iterative parameter estimation for biological systems, accelerating protein database search using OpenCL, and hybrid MapReduce workflow. In addition, the program includes a panel on "The Challenges at the Interface of Life Sciences and Cyberinfrastructure and how should we tackle them?", keynote speeches by Chris Johnson on "Image-Based Biomedical Modeling, Simulation and Visualization" and Eugene Kolker on "Biomed Data at Work". We hope that these proceedings will serve as a valuable reference for novel "computational thinking" for (Systems) Biology, Bioinformatics, Biocomplexity and Cheminformatics, so that future activities and collaborations will be initiated, as well as fostering discussions about the utilization of HPDC systems in their respective research initiatives.