This program requires a Java runtime (java or jre) program, preferrably version 1.3 or later. It likely will work with version 1.2, but not version 1.1.
This java version requirement precludes its use on Macintosh OS 9 or earlier, as Apple Computer will not make available a Java version 1.2+ You can use this program on MacOS X, where it works well.
The easiest way to run this is with Java Web Start, if that is installed on your computer. This is a standard part of Macintosh OS X 10.1. Web Start software is available for MS Windows and Unix systems at http://java.sun.com/products/javawebstart/ To use Web Start for launching BioGridRunner, find the Web Start ".jnlp" script here
You will probably find source code (Java 1.2/1.3) for BioGridRunner included with the author's java source library at ftp://iubio.bio.indiana.edu/molbio/java/source/ as iubiojava-src.zip This is a work in progress, done on a fluctuating schedule, updates will be available as time permits.
java -cp lib/biogridrun.jar:lib/readseq.jar:lib/xerces.jar:lib/cog912all.jar iubio.grid.app(changing /: to \; for UNIX to MS DOS). If the program fails to run, check that you have the above .jar files.
This client program aims to make it easy to find information, and move it from there to here, or there to elsewhere. Each resource has a URL, such as we know of from web hyperlinks, but extending to non-web GRID Internet resources. These URLs are the "name" attached to an object, whether data, software, computer disk or other resource. In this grid-runner, you can find these in directories, and move them among places using Drag'n'Drop methods to pull a URL from here to there.
Another basic part of this program is the ability to run other programs, given a description of how those programs operate. In this case we focus on command-line programs for bioinformatics: such as Clustal W (sequence alignment), EMBOSS and GCG sequence analysis packages, and others. BioGridRunner uses descriptions of how these programs run - their input data, command-line program options, and outputs. Given this description (now in an XML format "BIX" command script), this program allows you to run such bio-apps with a form or dialog to select options easily, and select or drag'n'drop data for input into the program. You can select to run these programs on your own computer or ones you have GRID credentials to run programs on.
Security and authenticated data and resource use is a basic part of GRID methods included here. Directories of data may include collaborative projects where you and others share data in a secure, authenticated way.
The program uses Drag'n'Drop methods, and will improve these so you can move things by their URL between directories / computers and into program jobs. Note that these drag and drop methods work across this program and others on your computer. You can drag files from your computer windows (Finder, MS Explorer) into this app, or drag URLs out of this app into a web browser, or other.
The application window has a menu with File, Grid Options, Help and Windows.
The lightweight directory protocol (LDAP) is being tested here as a primary way for organizing federations of bioinformatic data and software. The test services at ldap://iubio.bio.indiana.edu/ include directories of gigabytes of bioinformatic data from the Bio-Mirror project; software cataloged at the IUBio Archive; genome data from the euGenes eukaryote genome service. These are and will change and be added to for testing of GRID-based data and software search and retrieval. One hope of this pilot test is to find methods whereby you can use this BioGridRunner to semi-automatically find current data of interest to you, and the software needed to analyze it, and move those data and software (with simple "Drag-n-Drop" visual methods) to the computer(s) you want to use them on. There is much behind the scenes programming and information engineering needed for this to work, but the LDAP, GRID and related tool sets make this all feasible now.
LDAP looks like an important method for automating methods of finding, searching and accessing current data in biology. LDAP provides means for searching among many computers, including globally linked ones, in ways that cannot be achieved with current Web or other means. It has been developed over the past decade for use with directories of people, computer resources, and other information, and has a range of methods for searching, joining disparate information sources, defining information objects and attributes, and offers security and wide spread software support.
The author even likes it :) I've used URL copy to move parts of this developing program to/from computers.