Morphology Database (DB) utility.
The case for databases of biological data is not in question. How such databases can best be made remains unclear. The Catacomb MorphiologyCB component implements one of the possibilities for cell morphology cdata: distributed web-based data storage, optionally with centralised indexes. The principal advantage of this approach is that the originators of the data maintains complete control over its availability, distribution and presentation. The disadvantages of having data distributed in a variety of formats can be overcome with appropriate search and indexing tools.
The MorphologyDB component takes a local directory containing morphology data in a format Catacomb understands [Neurolucida ascii files or SWC files], warns the user for any missing information [particularly keywords for indexing] and produces a mini website with images of the cells, links to the raw data, keywords and indexes. The user should upload this onto their own webserver, or, for those who do not have their own it can be transferred directly compneuro.org. Optionally, the address of the host site can be submitted to compneuro.org and neuroml.org where indexing robots will update their lists of available morphology data.
Structures can be documented by first opening them in the morphology editor and selecting the edit header option. This step is essential for producing a useful database.
Usage Instructions
To create a database, first fill out or select the necessary fields in the MorphologyDB component, then click build site at the bottom. The configuration can be saved with the save component option from the file menu. You can rebuild the same site as often as you like.
If you select check documentation [which is strongly reccomended] then any morphology files with incomplete headers will be opened in the morphology editor for the header to be updated.
The fields to be filled int are:
sourceDirectory - the directory containing the files to be processed.
targetDirectory - the directory where the site is to be created. It may be the same as the source directory, or could be a directory on the webserver. If the directory does not exist it will be created.
checkDocumentation verifies that all the header fields are present.
checkStructure verifies that each file contains a single fully connected cell structure, with no floating branches.
failAction selectes what to do with files that fail one of hte checks - leave them out of the web site, put them in as they are, or wait while the user edits them.
submission selects how the site is to be publicised. The options are to do nothing as when the site is for internal use only, to submit a link on compneuro.org and neurml.org showing where the site will be installed, or to submit the while site to compneuro.org. In the latter case, the password field must be filled in too. Once the site is installed, it can only be updated or deleted with the right password.
Once all the fields are OK, click build site tyo crate the site and submit links. If you have selected the check options then the morphology editor will be started for any cells that fail the checks.