Resource for the Visualization of Biological Complexity (RVBC)
SPIRE: The SPIDER Reconstruction Engine (2001-2005)
Single-Particle Reconstruction, one of the main techniques developed and actively supported at the RVBC, entails a large number of SPIDER operations on thousands of files containing particle images. A reconstruction project is organized as a sequence of calls to batch files, accessible through a web page. As the reconstruction procedure has grown in complexity, the task of tailoring the batch files to a particular experimental data set has become quite cumbersome.
SPIRE, the SPIder Reconstruction Engine, has been developed in the third Core area, to provide a simplified way to organize the processing flow, without sacrificing the flexibility of SPIDER.
SPIRE is controlled by a graphical user interface to processing with SPIDER batch files, and contains a database for keeping track of reconstruction projects. It provides a simple interface that ties buttons to batch files and displays their outputs. SPIRE detects if a copy of Jweb is running, and if so, uses it to display SPIDER images.
In addition to Jweb, other platform-independent graphical user tools have been developed for e.g., plotting document file data in Gnuplot, and analyzing micrograph power spectra. These have been developed for SPIRE but they also run as independent programs. In fact, any external program can be tied to a button on the SPIRE display, via a SPIRE configuration file, which enables the user to execute that program. Outputs of the program must be compatible with the usual SPIDER binary and text formats, for SPIDER commands to be used on those outputs farther down the processing stream. If the external programs also send some additional information to the standard output (i.e., print out on the screen), then SPIRE can add its outputs to the project database.
SPIRE has been used to teach students how to run SPIDER at various cryo-EM workshops. SPIRE-1.4 was made available in October 2005. The next release will be distributed sometime in 2006.
