COMPUTER RESOURCE--MOLECULAR MECHANICS AND NEURO-ANATOMY

This computer resource facility is currently completing two major core projects which we believe will, during the next year, make a major contribution to the research community in general and our collaborative research in particular. FASTRUN, an attached processor computing device for which the original design was done at the facility, is now being constructed at the Brookhaven National Laboratory as a joint project. This processor, which is a long pipeline to compute the non-bonded pairwise forces, will be completed and delivered to Columbia within the next two months. Combined with a STAR-100 array processor, now running at the facility and a microvax as host, the system which MERCURY (Molecular Energy Refinement at Columbia University) is expected to have a computing speed somewhat greater than a CRAY-2 but only for molecular mechanics of large molecules; dynamics energy minimization, free energy of binding, etc. The system will be used in efforts to compute the conformations of molecules whose amino acid sequence is known and are homologous to structures which have been solved crystallographically. It will also be used to compute the ionic conductance through a protein which forms a small ion channel as the amino acid sequence of the protein is changed by site-directed mutagenesis. The second major project is the development of a computing system for a SUN 160/3 with image processing boards for automatic extraction of cell and fiber outlines from serial section micrographs. The system now works well enough so that it can reduce the time and tedium of manual nerve tracing by about a factor of ten. It will be available for neuroanatomical users in the near future, and will be used initially for reconstruction of the cerebellum in developing mice in connection with experiments which study gene expression by means of in situ hybridization. The programs will be improved substantially so that the system will run for long periods without any investigator intervention. The verification and decision making which must be done by the human observer, will be carried out in one interactive process after the automatic system has operated on previously stored images. As the hardware and the software for this system is developed, it will be available for use by many investigators both local and from other institutions. As new hardware becomes available in the second year of the proposed grant, we expect to convert the manual CARTOS system on the LOANER, so that it can carry out automatic nerve tracing and be available to outside users.