@article{Collier:2002wd, Author = {Collier, A. and Gallego, J. and Klinck, R. and Cole, P. and Harris, S. and Harrison, G. and Aboul-ela, F. and Varani, G. and Walker, S.}, Date-Added = {2008-12-17 21:25:32 +0100}, Date-Modified = {2008-12-17 21:39:39 +0100}, Journal = {Nature Structural Biology}, Number = {5}, Pages = {375--380}, Title = {{A Conserved RNA Structure Within the HCV IRES elF3-Binding Site}}, Volume = {9}, Year = {2002}} @misc{saga-req, Author = {Andre Merzky and Shantenu Jha}, Date-Added = {2008-02-24 20:36:03 -0600}, Date-Modified = {2008-02-24 20:36:03 -0600}, Howpublished = {Grid Forum Document GFD.71}, Note = {Global Grid Forum}, Title = {{A Requirements Analysis for a Simple API for Grid Applica tions}}, Year = 2006} @misc{saga-uc, Author = {Andre Merzky and Shantenu Jha}, Date-Added = {2008-02-24 20:35:56 -0600}, Date-Modified = {2008-02-24 20:35:56 -0600}, Howpublished = {Grid Forum Document GFD.70}, Note = {Global Grid Forum}, Title = {{A Collection of Use Cases for a Simple API for Grid Appli cations}}, Year = 2006} @inproceedings{mapreduce, Address = {Berkeley, CA, USA}, Author = {Jeffrey Dean and Sanjay Ghemawat}, Booktitle = {OSDI'04: Proceedings of the 6th conference on Symposium on Opearting Sys tems Design \& Implementation}, Date-Added = {2008-02-23 20:47:01 -0600}, Date-Modified = {2008-05-12 23:43:10 +0200}, Location = {San Francisco, CA}, Pages = {137--150}, Publisher = {USENIX Association}, Title = {{MapReduce: Simplified Data Processing on Large Clusters}}, Year = {2004}} @misc{allpairs, note = {All-Pairs: An Abstraction for Data Intensive Cloud Computing, Christopher Moretti, Jared Bulosan, Douglas Thain, and Patrick Flynn, IEEE International Parallel and Distributed Processing Symposium (IPDPS), April 2008.}} @article{sagastuff, Author = {Goodale, Tom and Jha, Shantenu and Kaiser, Harmut and Kielmann, Thilo and K leijer, Pascal and von Laszewski, Gregor and Lee, Craig and Merzky, Andre and Rajic, Hrabri a nd Shalf, John}, Date-Added = {2007-12-08 18:56:12 +0100}, Date-Modified = {2007-12-08 18:56:12 +0100}, Journal = {Computational Methods in Science and Technology}, Number = {1}, Pages = {7-20}, Title = {{SAGA: A Simple API for Grid Applications, High-Level Application Programmin g on the Grid}}, Url = {http://saga.cct.lsu.edu/publications/saga_paper-a_simple_api_for_grid_applicat ions_sc05.pdf}, Volume = {12}, Year = {2006}, Bdsk-Url-1 = {http://saga.cct.lsu.edu/publications/saga_paper-a_simple_api_for_grid_a pplications_sc05.pdf}} @misc{saga_gfd90, author={Tom Goodale and Shantenu Jha and Hartmut Kaiser and Thilo Kielmann and Pascal Kleijer and Andre Merzky and John Shalf and Christopher Smith}, title="{A Simple API for Grid Applications (SAGA)}", howpublished = {OGF Document Series 90, http://www.ogf.org/documents/GFD.90.pdf}} @inproceedings{saga_gin, Address = {Washington, DC, USA}, Author = {Shantenu Jha and Hartmut Kaiser and Andre Merzky and Ole Weidner}, Booktitle = {E-SCIENCE '07: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007)}, Date-Added = {2008-02-16 18:54:59 -0600}, Date-Modified = {2008-02-16 18:54:59 -0600}, Doi = {http://dx.doi.org/10.1109/E-SCIENCE.2007.39}, Isbn = {0-7695-3064-8}, Pages = {584--591}, Publisher = {IEEE Computer Society}, Title = {Grid Interoperability at the Application Level Using SAGA}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1109/E-SCIENCE.2007.39} } @article{10.1109/GPC.2009.17, author = {Andre Merzky and Katerina Stamou and Shantenu Jha}, title = {Application Level Interoperability between Clouds and Grids}, journal ={Grid and Pervasive Computing Conference, Workshops at the}, volume = {0}, isbn = {978-0-7695-3677-4}, year = {2009}, pages = {143-150}, doi = {http://doi.ieeecomputersociety.org/10.1109/GPC.2009.17}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, } @inproceedings{saga_escience07, Author = {Jha, Shantenu and Kaiser, Hartmut and El Khamra, Yaakoub and Weidner, Ole}, Booktitle = {Accepted for 3rd IEEE Conference on eScience2007 and Grid Computing, Ban galore, India.}, Date-Added = {2007-12-08 18:56:12 +0100}, Date-Modified = {2007-12-08 18:56:12 +0100}, Title = {Design and Implementation of Network Performance Aware Applications Using SA GA and Cactus}, Url = {http://saga.cct.lsu.edu/publications/saga_cactus_escience.pdf}, Year = {2007}, Bdsk-Url-1 = {http://saga.cct.lsu.edu/publications/saga_cactus_escience.pdf}} @misc{saga_tg08, note = {Developing Large-Scale Adaptive Scientific Applications with Hard to Predict Runtime Resource Requirements, {\it Proceedings of TeraGrid08}, available at http://tinyurl.com/5du32j}} @misc{saga_mapreduce, note={Exposing the Power of Google through SAGA, {\it Google Summer of Code} http://www.omii.ac.uk/wiki/MPGoogleSAGA}} @misc{bigjob_cloud_tutorial, note={BigJob Tutorials, \url{http://saga.cct.lsu.edu/projects/abstractions/bigjob-a-saga-based-pilot-job-implementation}}} @Article{SPdynamics, author = {Shirts, Michael R. and Pande, Vijay S.}, title = {{Mathematical Analysis of Coupled Parallel Simulations}}, journal = {Phys. Rev. Lett.}, volume = {86}, number = {22}, pages = {4983--4987}, numpages = {4}, year = {2001}, month = {May}, doi = {10.1103/PhysRevLett.86.4983}, publisher = {American Physical Society} } @article{pande_bj03, author = {Rhee, Young Min and Pande, Vijay S.}, title = {{Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation}}, journal = {Biophysical Journal}, volume = {84}, number = {2}, pages = {775-786}, year = {2003}, OPTURL = {http://www.biophysj.org/cgi/content/abstract/84/2/775}, OPTeprint = {http://www.biophysj.org/cgi/reprint/84/2/775.pdf} } @misc{dpa-paper, note = {S. Jha et al., {\em Programming Abstractions for Large-scale Distributed Application s}, Submitted to ACM Computing Surveys; draft at \url{http://www.cct.lsu.edu/~sjha/publications/dpa_surveypaper.pdf}}} @misc{remd-manager_url, note={https://svn.cct.lsu.edu/repos/saga-projects/applications/REMDgManager/src/main.py}} @misc{saga_url, note={{http://saga.cct.lsu.edu}}} @misc{glite, note={{http://glite.web.cern.ch/glite/}}} @inproceedings{escience07, author = {Shantenu Jha and Hartmut Kaiser and Yaakoub El Khamra and Ole Weidner}, title = {{Design and Implementation of Network Performance Aware Applications Using SAGA and Cactus}}, booktitle = {E-SCIENCE '07: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing}, year = {2007}, isbn = {0-7695-3064-8}, pages = {143--150}, doi = {http://dx.doi.org/10.1109/E-SCIENCE.2007.28}, OPTpublisher = {IEEE Computer Society}, OPTaddress = {Washington, DC, USA}, } @misc{cloud-grid-autonomics, note = {"An Autonomic Approach to Integrated HPC Grid and Cloud Usage", H. Kim, Y. el-Khamra, S. Jha and M. Parashar, accepted for IEEE eScience 2009, Oxford.}} @misc{dirac, note= {A. Tsaregorodtsev et al., DIRAC: A community Grid solution, J. Phys.: Conf. Ser. 119 (2008), p. 062048. }} @article{diane, title = "Distributed analysis environment for {HEP} and interdisciplinary applications", journal = "Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment", volume = "502", number = "2-3", pages = "426 - 429", year = "2003", issn = "0168-9002", doi = "DOI: 10.1016/S0168-9002(03)00459-5", OPTurl = "http://www.sciencedirect.com/science/article/B6TJM-480C1TX-V/2/4d0dbeda4627cf2e89ac9447360e7460", author = "J. T. Moscicki", } @inproceedings{enkf-gmac09, author = {El-Khamra, Yaakoub and Jha, Shantenu}, title = {Developing autonomic distributed scientific applications: a case study from history matching using ensemblekalman-filters}, booktitle = {GMAC '09: Proceedings of the 6th international conference industry session on Grids meets autonomic computing}, year = {2009}, isbn = {978-1-60558-578-9}, pages = {19--28}, location = {Barcelona, Spain}, doi = {http://doi.acm.org/10.1145/1555301.1555304}, publisher = {ACM}, address = {New York, NY, USA}, } @misc{LONI_web, note = {\url{http://www.loni.org}}} @misc{new-ec2, note = {\url{http://aws.typepad.com/aws/2009/10/two-new-ec2-instance-types-additional-memory.html}}} @misc{sagamontage09, note = {A. Merzky, K. Stamou, S. Jha and D. S. Katz, A Fresh Perspective on Developing and Executing DAG-Based Distributed Applications: A Case-Study of SAGA-based Montage, accepted for IEEE Conference on eScience 2009, Oxford. \url{http://www.cct.lsu.edu/~sjha/dpa_publications/saga_montage_G09.pdf}}} @misc{nanocmos, note = {\url{http://www.nanocmos.ac.uk/}}} @misc{saga-tools, note = {\url{http://saga.cct.lsu.edu/projects/tools-and-infrastructure}}} @inproceedings{comethpdc, author = {Zhen Li and Manish Parashar}, title = {A computational infrastructure for grid-based asynchronous parallel applications}, booktitle = {HPDC '07: Proceedings of the 16th international symposium on High performance distributed computing}, year = {2007}, isbn = {978-1-59593-673-8}, pages = {229--230}, location = {Monterey, California, USA}, doi = {http://doi.acm.org/10.1145/1272366.1272404}, OPTpublisher = {ACM}, OPTaddress = {New York, NY, USA}, } @misc{dpagrid2009, note = {Critical Perspectives on Large-Scale Distributed Applications and Production Grids, Proceedings of the 10th IEEE/ACM International Conference on Grid Computing (GRID09), 2009 \\ \url{http://www.cct.lsu.edu/~sjha/dpa_publications/dpa_grid2009.pdf} }} @conference{luckow2009adaptive, title={{Adaptive distributed replica--exchange simulations}}, author={Luckow, A. and Jha, S. and Kim, J. and Merzky, A. and Schnor, B.}, booktitle={Theme Issue of the Philosophical Transactions of the Royal Society A: Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructure Proceedings of the UK e-Science All Hands Meeting}, volume={367}, year={2009}, } @conference{repex_ptrs, title={{Adaptive Distributed Replica--Exchange Simulations}}, author={Luckow, A. and Jha, S. and Kim, J. and Merzky, A. and Schnor, B.}, booktitle={Theme Issue of the Philosophical Transactions of the Royal Society A}, volume={367}, year={2009}, }