11
4.3. Future directions
In developing collaborations and ultimately a user base to conduct research, having a persistent infrastructure is required. By this we mean access to tools and software for researchers to experiment with. The National Centers for Research Resources provide that type of infrastructure for the community. In the case of NBCR, access to the tools and services discussed in this article can be found at the NBCR 9 website.
While the experiences and developments discussed above have been informed by our local activities, the concepts of cyberinfrastructure are not bound by national borders. Examples of large scale projects and smaller team projects have been commented on in prior CTWatch issues (e.g., February 2006). Furthermore, it is essential that we actively participate in the international arena, both to ensure the various CI efforts can interoperate (e.g., when we want to use unique resources in other countries) and to reduce reproduction of tools that already exist.
Another exciting development that will link biomedical research with the environment across various scales is the newly funded CAMERA project. CAMERA will provide a community resource that links genetic information from a metagenomics effort, the Global Ocean Survey, with environmental factors such location, temperature and chemistry of the sampled environment.
The critical role played by NBCR to bridge the multiscale modeling research community and cyberinfrastructure is an important one, and will require collaborative efforts from other projects to expedite the translational/medical potential of multiscale biomedical and cyberinfrastructure research.
Acknowledgment
The authors are all members of the National Biomedical Computation Resource, which is supported by the NIH National Centers for Research Resources award P41-RR08605. Major support for APBS is provided by NIH grant GM069702 to NAB.
The authors are all members of the National Biomedical Computation Resource, which is supported by the NIH National Centers for Research Resources award P41-RR08605. Major support for APBS is provided by NIH grant GM069702 to NAB.
References
1 McCulloch, A.D., Paternostro G. Cardiac systems biology. Ann N Y Acad Sci 1047: 283-295. 2005.
2 Hunter P.J., Borg, T.K. Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol 4: 237-243. 2003.
3 Hunter P., Nielsen P. A strategy for integrative computational physiology. Physiology (Bethesda) 20: 316-325. 2005.
4 Hunter P.J., Li W.W., McCulloch A.D., Noble D. Multi-scale Modeling Standards, Tools Databases for the Physiome Project. Computer: In Press. 2006.
5 Oden J.T., Belytschko T., Fish J., Hughes T.J., Johnson C., et al. Revolutionizing Engineering Science through Simulation. 2006
6 IMAG: Interagency Opportunities in Multi-Scale Modeling in Biomedical, Biological, and Behavioral Systems - www.nsf.gov/pubs/2004/nsf04607/nsf04607.htm . 2006.
7 PITAC: Computational Science: Ensuring America's Competitiveness. www.nitrd.gov/pitac/reports/index.html . 2005.
8 NRCNA: Catalyzing Inquiry at the Interface of Computing and Biology. www.doegenomestolife.org/pubs/NRCComputingandBiology/index.shtml . 2005.
9 NBCR: National Biomedical Computation Resource - nbcr.net/ . 2005.
10 NCRR: National Center for Research Resources - www.ncrr.nih.gov/ . 2006.
11 MCMBR: Multiscale Computational Modeling for Biomedical Research - nbcr.net/physiome/ . 2004.
12 McCulloch, A.D., Arzberger, P.W., Hunter, P. Computational Physiology: From Genome to Physiome. The Physiologist 49: 94-95. 2005.
13 DCBC: Data and Collaboratories in the Biomedical Community. - nbcr.net/Collaboratories/index.html . 2002.
14 Usyk, T.P., McCulloch, A.D. Relationship between regional shortening and asynchronous electrical activation in a three-dimensional model of ventricular electromechanics. J Cardiovasc Electrophysiol 14: S196-202. 2003.
15 Trayanova, N. In pursuit of the elusive culprit. Heart Rhythm 2: 729-730. 2005.
16 Xie, F., Qu, Z., Yang, J., Baher, A., Weiss, J.N., et al. A simulation study of the effects of cardiac anatomy in ventricular fibrillation. J Clin Invest 113: 686-693. 2004.
17 Kaiser, T.H., Brieger, L., Healy, S.N. MYMPI - MPI Programming in Python. International Conference on Parallel and Distributed Processing Techniques and Applications; Las Vegas. In Press. 2006.
18 Koh. X., Srinivasan, B., Ching, H.S., Levchenko, A. A 3D Monte Carlo Analysis of the Role of Dyadic Space Geometry in Spark Generation. Biophys J 90: 1999-2014. 2006.
19 Soeller, C., Cannell, M.B. Analysing cardiac excitation-contraction coupling with mathematical models of local control. Prog Biophys Mol Biol 85: 141-162. 2004.
20 Sanner, M.F., Stolz, M., Burkhard, P., Kong, X.-P., Min, G, et al., (Eds.). Visualizing Nature at Work from the Nano to the Macro Scale.John Wiley & sons, Ltd. p. 7-11. 2005.
21 Osterberg, F., Morris, G.M., Sanner, M.F., Olson, A.J., Goodsell, D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46: 34-40. 2002.
22 Goodsell, D.S., Morris, G.M., Olson, A.J. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9: 1-5. 1996.
23 Morris, G.M., Goodsell, D.S., Huey, R., Olson, A.J. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des 10: 293-304. 1996.
24 WCG: World Community Grid: FightAIDS@Home. www.worldcommunitygrid.org/projects_showcase/viewFaahFaq.do?shortName=... . 2005.
25 Lin, J.H., Perryman, A.L., Schames, J.R., McCammon, J.A. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68: 47-62. 2003.
26 Schames, J.R., Henchman, R.H., Siegel, J.S., Sotriffer, C.A., Ni, H., et al. Discovery of a novel binding trench in HIV integrase. J Med Chem 47: 1879-1881. 2004.
27 NIH: Clinical Trials Database - clinicaltrials.gov/ct/show/NCT00293254?order=1 . 2006.
28 FEtk: Finite Element Toolkit - www.fetk.org/ . 2005.
29 Holst, M.J. Adaptive Numerical Treatment of Elliptic Systems on Manifolds. Advances in Computational Mathematics 15: 139-191. 2001.
30 Baker, N.A., Sept, D., Joseph, S., Holst, M.J., McCammon, J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041. 2001.
31 iAPBS: iAPBS Interface - nbcr.net/forum/viewforum.php?f=17 . 2006.
32 Krishnan, S., Stearn, B., Bhatia, K., Baldridge, K., Li, W.W., et al. Opal: Simple Web Service Wrappers for Scientific Applications. International Conference for Web Services. In Press. 2006.
33 Zhang, D., Suen, J., Zhang, Y., Song, Y., Radic, Z., et al. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J 88: 1659-1665. 2005.
34 Atkins, D., Kroegemeier, K., Feldman, S., Garcia-Molina, H., Klein, M., et al. Revolutionizing Science and Engineering Through Cyberinfrastructure: Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrasturcuture. Arlington, VA: National Science Foundation. 2003.
35 Hey, T., Trefethen, A.E. Cyberinfrastructure for e-Science. Science 308: 817-821. 2005.
36 Graham, S.L., Sni,r, M., Patterson, C.A. Getting Up to Speed: The Future of Supercomputing: The National Academies Press. 2004.
37 Foster, I., Kesselman, C. (Eds.). The Grid 2: Blueprint for a New Computing Infrastructure. 2 ed. San Francisco: Morgan Kaufmann Publishers, Inc. 2004.
38 Bal, H., Casanova, H., Dongarra, J., Matsuoka, S. Application-Level Tools. In: Foster, I., Kesselman, C. (Eds.). The Grid 2. 2 ed. Amsterdam: Elsevier. 2004.
39 Yerushalmi, R., Scherz, A., Baldridge, K.K. Direct experimental evaluation of charge scheme performance by a molecular charge-meter. J Am Chem Soc 126: 5897-5905. 2004.
40 BIRN: Biomedical Informatics Research Network - www.nbirn.net/ . 2005.
41 CAMERA: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis - camera.calit2.net/ . 2006.
42 OptIPuter: A Powerful Distributed Cyberinfrastructure to Support Data-Intensive Scientific Research and Collaboration - www.optiputer.net/ . 2005.
43 JCSG: Joint Center for Structural Genomics - www.jcsg.org/ . 2005.
44 TeraGrid: TeraGrid - www.teragrid.org/ . 2004.
45 OSG: Open Science Grid - www.opensciencegrid.org/ . 2006.
46 PRAGMA: Pacific Rim Applications and Grid Middleware Assembly - www.pragma-grid.net/ . 2004.
47 OMII: Open Middleware Infrastructure Institute - www.omii.ac.uk/ . 2006.
48 Foster, I. Service-oriented science. Science 308: 814-817. 2005.
49 Abramson, D., Lynch, A., Takemaya, H., Tanimura, Y., Date, S., et al. Deploying Scientific Applications to the PRAGMA Grid testbed: Strategies and Lessons. Sixth IEEE International Symposium on Cluster Computing and the Grid, 2006 CCGrid 06; Singapore. 1: 241-248. 2006.
50 NBCR: NBCR Software and Tools Description and Download Site - nbcr.net/tools.php . 2006.
51 Li, W.W., Krishnan, S., Mueller, K., Ichikawa, K., Date, S., et al. Building cyberinfrastructure for bioinformatics using service oriented architecture. Sixth IEEE International Symposium on Cluster Computing and the Grid Workshops Singapore. 2: 39-46. 2006.
52 KEPLER: The Kepler project - kepler-project.org/ . 2006
53 Bhatia, K., Chandra, S., Mueller, K. GAMA: Grid Account Management Architecture. 1st IEEE International Conference on e- Science and Grid Computing; Melbourne, Australiapp. In Press. 2006.
54 Gridsphere: GridSphere - www.gridsphere.org/ . 2004.
55 Baldridge, K., Bhatia, K., Greenberg, J.P., Stearn, B., Mock, S., et al. GEMSTONE: Grid Enabled Molecular Science Through Online Networked Environments. Life Sciences Grid Workshop; Singapore. World Scientific Press. 2005.
56 Lin, A.W., Dai, L., Ung, K., Peltier, S., Ellisman, M.H. The Telescience Project: Applications to Middleware Interaction Components. The 18th IEEE International Symposium on Computer-Based Medical Systems; Dublin, Ireland:. 543-548. 2005.
57 MYMPI: My MPI - nbcr.net/forum/viewforum.php?f=16 . 2006.
58 FEtk: Finite Element Toolkit - www.fetk.org/ . 2006.
59 Baldridge, K.K., Bhatia, K., Greenberg, J.P., Stearn, B., Mock, S., et al. Grid-Enabled Molecular Science through Online Networked Environments. Life Sciences Grid Workshop; Singapore. World Scientific Press. 2005.
60 Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., et al. General atomic and molecular electronic structure system. Journal of Computational Chemistry 14: 1347-1363. 1993.
61 Dolinsky, T.J., Nielsen, J.E., McCammon, J.A., Baker, N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32: W665-667. 2004.
62 Bailey, T.L., Williams, N., Misleh, C., Li, W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369-373. 2006.
63 Li, W.W., Arzberger, P.W., Yeo, C.L., Ang, L., Tatebe, O., et al. Proteome Analysis using iGAP in Gfarm. The Second International Life Science Grid Workshop 2005; Grid Asia 2005, Singapore. World Scientific Press. 2005.
64 Wei, X., Li, W.W., Tatebe, O., Xu, G., Hu, L., et al. Integrating Local Job Scheduler - LSF with Gfarm. Lecture Notes in Computer Science 3758: 197. 2005.
65 ROCKS: Rocks Cluster Distribution - www.rocksclusters.org/ . 2005.
66 Litzkow, M., Livny, M., Mutka, M. Condor - a hunter of idle workstations. Proceedings of the 8th International Conference of Distributed Computing Systems; June 1988pp. 104-111. 1988.
67 Song, Y., Zhang, Y., Shen, T., Bajaj, C.L., McCammon, J.A., et al. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J 86: 2017-2029. 2004.
2 Hunter P.J., Borg, T.K. Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol 4: 237-243. 2003.
3 Hunter P., Nielsen P. A strategy for integrative computational physiology. Physiology (Bethesda) 20: 316-325. 2005.
4 Hunter P.J., Li W.W., McCulloch A.D., Noble D. Multi-scale Modeling Standards, Tools Databases for the Physiome Project. Computer: In Press. 2006.
5 Oden J.T., Belytschko T., Fish J., Hughes T.J., Johnson C., et al. Revolutionizing Engineering Science through Simulation. 2006
6 IMAG: Interagency Opportunities in Multi-Scale Modeling in Biomedical, Biological, and Behavioral Systems - www.nsf.gov/pubs/2004/nsf04607/nsf04607.htm . 2006.
7 PITAC: Computational Science: Ensuring America's Competitiveness. www.nitrd.gov/pitac/reports/index.html . 2005.
8 NRCNA: Catalyzing Inquiry at the Interface of Computing and Biology. www.doegenomestolife.org/pubs/NRCComputingandBiology/index.shtml . 2005.
9 NBCR: National Biomedical Computation Resource - nbcr.net/ . 2005.
10 NCRR: National Center for Research Resources - www.ncrr.nih.gov/ . 2006.
11 MCMBR: Multiscale Computational Modeling for Biomedical Research - nbcr.net/physiome/ . 2004.
12 McCulloch, A.D., Arzberger, P.W., Hunter, P. Computational Physiology: From Genome to Physiome. The Physiologist 49: 94-95. 2005.
13 DCBC: Data and Collaboratories in the Biomedical Community. - nbcr.net/Collaboratories/index.html . 2002.
14 Usyk, T.P., McCulloch, A.D. Relationship between regional shortening and asynchronous electrical activation in a three-dimensional model of ventricular electromechanics. J Cardiovasc Electrophysiol 14: S196-202. 2003.
15 Trayanova, N. In pursuit of the elusive culprit. Heart Rhythm 2: 729-730. 2005.
16 Xie, F., Qu, Z., Yang, J., Baher, A., Weiss, J.N., et al. A simulation study of the effects of cardiac anatomy in ventricular fibrillation. J Clin Invest 113: 686-693. 2004.
17 Kaiser, T.H., Brieger, L., Healy, S.N. MYMPI - MPI Programming in Python. International Conference on Parallel and Distributed Processing Techniques and Applications; Las Vegas. In Press. 2006.
18 Koh. X., Srinivasan, B., Ching, H.S., Levchenko, A. A 3D Monte Carlo Analysis of the Role of Dyadic Space Geometry in Spark Generation. Biophys J 90: 1999-2014. 2006.
19 Soeller, C., Cannell, M.B. Analysing cardiac excitation-contraction coupling with mathematical models of local control. Prog Biophys Mol Biol 85: 141-162. 2004.
20 Sanner, M.F., Stolz, M., Burkhard, P., Kong, X.-P., Min, G, et al., (Eds.). Visualizing Nature at Work from the Nano to the Macro Scale.John Wiley & sons, Ltd. p. 7-11. 2005.
21 Osterberg, F., Morris, G.M., Sanner, M.F., Olson, A.J., Goodsell, D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46: 34-40. 2002.
22 Goodsell, D.S., Morris, G.M., Olson, A.J. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9: 1-5. 1996.
23 Morris, G.M., Goodsell, D.S., Huey, R., Olson, A.J. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des 10: 293-304. 1996.
24 WCG: World Community Grid: FightAIDS@Home. www.worldcommunitygrid.org/projects_showcase/viewFaahFaq.do?shortName=... . 2005.
25 Lin, J.H., Perryman, A.L., Schames, J.R., McCammon, J.A. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68: 47-62. 2003.
26 Schames, J.R., Henchman, R.H., Siegel, J.S., Sotriffer, C.A., Ni, H., et al. Discovery of a novel binding trench in HIV integrase. J Med Chem 47: 1879-1881. 2004.
27 NIH: Clinical Trials Database - clinicaltrials.gov/ct/show/NCT00293254?order=1 . 2006.
28 FEtk: Finite Element Toolkit - www.fetk.org/ . 2005.
29 Holst, M.J. Adaptive Numerical Treatment of Elliptic Systems on Manifolds. Advances in Computational Mathematics 15: 139-191. 2001.
30 Baker, N.A., Sept, D., Joseph, S., Holst, M.J., McCammon, J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041. 2001.
31 iAPBS: iAPBS Interface - nbcr.net/forum/viewforum.php?f=17 . 2006.
32 Krishnan, S., Stearn, B., Bhatia, K., Baldridge, K., Li, W.W., et al. Opal: Simple Web Service Wrappers for Scientific Applications. International Conference for Web Services. In Press. 2006.
33 Zhang, D., Suen, J., Zhang, Y., Song, Y., Radic, Z., et al. Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J 88: 1659-1665. 2005.
34 Atkins, D., Kroegemeier, K., Feldman, S., Garcia-Molina, H., Klein, M., et al. Revolutionizing Science and Engineering Through Cyberinfrastructure: Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrasturcuture. Arlington, VA: National Science Foundation. 2003.
35 Hey, T., Trefethen, A.E. Cyberinfrastructure for e-Science. Science 308: 817-821. 2005.
36 Graham, S.L., Sni,r, M., Patterson, C.A. Getting Up to Speed: The Future of Supercomputing: The National Academies Press. 2004.
37 Foster, I., Kesselman, C. (Eds.). The Grid 2: Blueprint for a New Computing Infrastructure. 2 ed. San Francisco: Morgan Kaufmann Publishers, Inc. 2004.
38 Bal, H., Casanova, H., Dongarra, J., Matsuoka, S. Application-Level Tools. In: Foster, I., Kesselman, C. (Eds.). The Grid 2. 2 ed. Amsterdam: Elsevier. 2004.
39 Yerushalmi, R., Scherz, A., Baldridge, K.K. Direct experimental evaluation of charge scheme performance by a molecular charge-meter. J Am Chem Soc 126: 5897-5905. 2004.
40 BIRN: Biomedical Informatics Research Network - www.nbirn.net/ . 2005.
41 CAMERA: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis - camera.calit2.net/ . 2006.
42 OptIPuter: A Powerful Distributed Cyberinfrastructure to Support Data-Intensive Scientific Research and Collaboration - www.optiputer.net/ . 2005.
43 JCSG: Joint Center for Structural Genomics - www.jcsg.org/ . 2005.
44 TeraGrid: TeraGrid - www.teragrid.org/ . 2004.
45 OSG: Open Science Grid - www.opensciencegrid.org/ . 2006.
46 PRAGMA: Pacific Rim Applications and Grid Middleware Assembly - www.pragma-grid.net/ . 2004.
47 OMII: Open Middleware Infrastructure Institute - www.omii.ac.uk/ . 2006.
48 Foster, I. Service-oriented science. Science 308: 814-817. 2005.
49 Abramson, D., Lynch, A., Takemaya, H., Tanimura, Y., Date, S., et al. Deploying Scientific Applications to the PRAGMA Grid testbed: Strategies and Lessons. Sixth IEEE International Symposium on Cluster Computing and the Grid, 2006 CCGrid 06; Singapore. 1: 241-248. 2006.
50 NBCR: NBCR Software and Tools Description and Download Site - nbcr.net/tools.php . 2006.
51 Li, W.W., Krishnan, S., Mueller, K., Ichikawa, K., Date, S., et al. Building cyberinfrastructure for bioinformatics using service oriented architecture. Sixth IEEE International Symposium on Cluster Computing and the Grid Workshops Singapore. 2: 39-46. 2006.
52 KEPLER: The Kepler project - kepler-project.org/ . 2006
53 Bhatia, K., Chandra, S., Mueller, K. GAMA: Grid Account Management Architecture. 1st IEEE International Conference on e- Science and Grid Computing; Melbourne, Australiapp. In Press. 2006.
54 Gridsphere: GridSphere - www.gridsphere.org/ . 2004.
55 Baldridge, K., Bhatia, K., Greenberg, J.P., Stearn, B., Mock, S., et al. GEMSTONE: Grid Enabled Molecular Science Through Online Networked Environments. Life Sciences Grid Workshop; Singapore. World Scientific Press. 2005.
56 Lin, A.W., Dai, L., Ung, K., Peltier, S., Ellisman, M.H. The Telescience Project: Applications to Middleware Interaction Components. The 18th IEEE International Symposium on Computer-Based Medical Systems; Dublin, Ireland:. 543-548. 2005.
57 MYMPI: My MPI - nbcr.net/forum/viewforum.php?f=16 . 2006.
58 FEtk: Finite Element Toolkit - www.fetk.org/ . 2006.
59 Baldridge, K.K., Bhatia, K., Greenberg, J.P., Stearn, B., Mock, S., et al. Grid-Enabled Molecular Science through Online Networked Environments. Life Sciences Grid Workshop; Singapore. World Scientific Press. 2005.
60 Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., et al. General atomic and molecular electronic structure system. Journal of Computational Chemistry 14: 1347-1363. 1993.
61 Dolinsky, T.J., Nielsen, J.E., McCammon, J.A., Baker, N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32: W665-667. 2004.
62 Bailey, T.L., Williams, N., Misleh, C., Li, W.W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: W369-373. 2006.
63 Li, W.W., Arzberger, P.W., Yeo, C.L., Ang, L., Tatebe, O., et al. Proteome Analysis using iGAP in Gfarm. The Second International Life Science Grid Workshop 2005; Grid Asia 2005, Singapore. World Scientific Press. 2005.
64 Wei, X., Li, W.W., Tatebe, O., Xu, G., Hu, L., et al. Integrating Local Job Scheduler - LSF with Gfarm. Lecture Notes in Computer Science 3758: 197. 2005.
65 ROCKS: Rocks Cluster Distribution - www.rocksclusters.org/ . 2005.
66 Litzkow, M., Livny, M., Mutka, M. Condor - a hunter of idle workstations. Proceedings of the 8th International Conference of Distributed Computing Systems; June 1988pp. 104-111. 1988.
67 Song, Y., Zhang, Y., Shen, T., Bajaj, C.L., McCammon, J.A., et al. Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J 86: 2017-2029. 2004.
