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

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.

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).

A
B
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.