This project is directed toward establishing, improving, and maintaining linkages and interfaces to and on the Analytical Biostatistics Section (ABS) website, a compendium of molecular biology service modules that allows users to submit data via the internet and have the results sent back to them over HTTP as the analysis is completed. The ABS website also harbours a series of programs that analyze ligand experiments, dose-response curves, and time series data and are downloadable as executable routines for both PC and Macintosh versions. The linkage and interface software have been developed and implemented by student interns from a local high school, by summer students, and by STEP employees using PC and Macintosh platforms. A major effort in FY99 has been to transfer the website from the aging ABSALPHA server to the new ABSHP1 server, to upgrade modules and programs along the way and to restructure the website by moving separate service modules into subdirectories. To facilitate development and testing, the new server was split into a development port where the source for the cgi scripts are kept and a public port which does not contain the source. This process is more than 90% complete. MSCL is moving towards Linux as an additional operating system for its desktops. One reason is: Windows NT can require frequent rebooting for minor alterations such as adding applications or changing devices. This can be major time-waster and impede progress. One advantage of the Linux GUI over Windows is a highly configurable feature called WM (WindowsManagers), which handles how windows are resized, moved, hidden, animated, etc.; a graphical front-end to the Linux kernel, called X, handles connections between the WMs and the applications. Since there were a few applications that were better implemented in NT, the PC was set up to be dual-boot, i.e. at boot-time either NT or Linux could be selected. A new product, VMWARE, creates a virtual computer inside a PC that can boot NT, Linux, or Windows as a sub operating system (sub-OS). VMWARE sets up a layer of indirection that acts exactly like a computer would, using resources requested from the host OS, to run and encapsulate a sub-OS. VMWARE can be run as a window or full screen, and supports cut-&-paste between the sub-OS and other windows running in X (Linux GUI). In this way Linux and Windows can be used complementary to each other. The power and flexibility of the system is thereby expanded, allowing one, for example, to slowly make the adjustment to a new OS. Running an OS in VMWARE does incur a slight performance penalty, however this slight performance penalty is not significant for applications such as office applications or browsers. For applications needing extensive resources and time such as 3D rendering and animation, one can simply reboot the computer into pure Windows mode. - protein structure analysis ligand dose response curve fitting
| Holbrook, P G; Geetha, V; Beaven, M A et al. (1999) Recognizing the pleckstrin homology domain fold in mammalian phospholipase D using hidden Markov models. FEBS Lett 448:269-72 |
| Di Francesco, V; Munson, P J; Garnier, J (1999) FORESST: fold recognition from secondary structure predictions of proteins. Bioinformatics 15:131-40 |
| Geetha, V; Di Francesco, V; Garnier, J et al. (1999) Comparing protein sequence-based and predicted secondary structure-based methods for identification of remote homologs. Protein Eng 12:527-34 |
