August 2006
Trends and Tools in Bioinformatics and Computational Biology
Wilfred W. Li, University of California, San Diego (UCSD), San Diego Supercomputer Center (SDSC)
Nathan Baker, Washington University in Saint Louis
Kim Baldridge, UCSD, SDSC
J. Andrew McCammon, UCSD
Mark H. Ellisman, UCSD, Center for Research In Biological Systems (CRBS)
Amarnath Gupta, UCSD, SDSC
Michael Holst, UCSD
Andrew D. McCulloch, UCSD
Anushka Michailova, UCSD
Phil Papadopoulos, UCSD, SDSC
Art Olson, The Scripps Research Institute (TSRI)
Michel Sanner, TSRI
Peter W. Arzberger, California Institute for Telecommunications and Information Technology (Calit2), CRBS, UCSD

3.4. MYMPI

The development of MYMPI57 is an effort of NBCR, driven by the requirement of Continuity, to improve interprocess communications between Python and FORTRAN.17 It is a Python module used with a normal Python interpreter. MyMPI is an implementation following the standard specifications of MPI, supporting more than 30 of the commonly used MPI calls. The syntax of the calls matches the syntax of C and FORTRAN calls closely to support mixed Python with the other languages. MYMPI will also allow access from Python to other application packages such as the Finite Element Toolkit (FEtk).58

3.5. Gemstone, My Worksphere as Portals to Grid Services

Gemstone59 is developed with major support from the NSF National Middleware Initiative, in close collaboration with NBCR, especially in the interaction with strongly typed and Opal based web services (Figure 8 A). For example, Gemstone provides an interface to GAMESS60 and APBS strongly typed web services,30 both developed by NBCR. It also supports the GARNET visualization web service from the NMI (NSF Middleware Initiative) project. Opal based web service for PDB2PQR,61 a utility package for APBS calculations, is also accessible from Gemstone as web service based workflows. Gemstone utilizes the open source Mozilla engine and uses XML User Interface Markup Language (XUL) to describe the user interface. My WorkSphere is a prototype GridSphere based portal environment, which leverages portlets that are JSR168 standard compliant. As an example, we have deployed MEME62 as a portlet using Opal, as part of a generalized Cyberinfrastructure for bioinformatics applications,51 with Gfarm63 and CSF464 as the other key middleware components.

3.6. Rocks and Rock’n Roll

In an effort to make cyberinfrastructure more readily available to scientists and engineers, it is necessary to not only develop different middleware to support legacy applications, but also to make the different software packages easy to deploy into existing infrastructure. Rocks cluster environment toolkit65 (Figure 8B) has proven to be invaluable for NBCR to build the basic infrastructure, deploy our software stack, and make our infrastructure replicable by others. NBCR has contributed critically to the development of the Condor roll66 (a roll is a mechanism, similar to the Red Hat RPM, though fully automated, for building reproducible cluster and grid environments). Other rolls available from NBCR include the APBS, MEME, GAMA, AutoDock, and PMV. Additional rolls for SMOL67 and FEtk will be available soon (Figure 8 B).

Figure 8A
Figure 8B
Figure 8. A) Gemstone offers a light weight mode of access to distributed resources using Opal based web services or strongly typed web services. B) Rocks cluster environment software has provided a replicable infrastructure for easy deployment and production use.

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Reference this article
Li, W. W., Baker, N., Baldridge, K., McCammon, J. A., Ellisman, M. H., Gupta, A., Holst, M., McCulloch, A. D., Michailova, A., Papadopoulos, P., Olson, A., Sanner, M., Arzberger P. W. "National Biomedical Computation Resource (NBCR): Developing End-to-End Cyberinfrastructure for Multiscale Modeling in Biomedical Research," CTWatch Quarterly, Volume 2, Number 3, August 2006. http://www.ctwatch.org/quarterly/articles/2006/08/national-biomedical-computation-resource/

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