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ballaxy_Help
Note to Editors: Note, this page belongs to the ballaxy server, do not remove!
ballaxy offers tools and workflows aiming at tasks in the field of computer aided drug design that are computationally very demanding and typically generate large numbers of structures in a defined and parameterized sequence of steps. ballaxy offers a well defined interface for complex software to a large number of users, e.g. a research group and collaborators. It is based on the popular Galaxy system.
We offer ballaxy via https://ballaxy.bioinf.uni-sb.de
Click on the User menu of the top menu bar.
Our collection of tutorials is listed here.
A tool is a single task program and can be found on the left hand side bar. We currently offer four types of tools: "BALL/BOA Constructor", "BALL/NMR", "GetData", and "!Graph/Display Data".
A workflow is a predefined sequence of tools. The BOAConstructor workflow , e.g., allows any valid input file, converts it via the MolecularFileConverter into mol2 format, applies the BOAConstructor tool to compute a bond order assignment which is returned in mol2 file format, and finally computes an SD file for that bond order assignment using the "Structure Diagram of a molecule" tool.
For more information on workflows and tools, please see the documentation of the galaxy workflow system which was customized to build ballaxy (http://wiki.g2.bx.psu.edu/FrontPage).
The published workflows can be accessed via the menu Shared Data -> Published Workflows in the top level menu. Detailed instructions are given here.
The framework offers a full history of input and output data. If you use a login, your history is stored on the server (at least as long as there is hardware space available). Otherwise the history will be deleted after leaving the webpage.
A file (molecular or other) can be uploaded via the "Upload File" tool which you can find in the "Get Data" tool box on the left hand side. A file can be either copied and pasted into the URL/Text box in ballaxy's "Get Data => Upload File" tool, or uploaded. It is then entered into the users framework history (seen on the right hand side).
Select your file of choice in the history by clicking on its name. Then a disc icon appears, click on that icon to start the download.
Please contact the BALL developer team via our user list or developer list.
Please find information on how to access our source code here.
Please find instructions on how to set up your own ballaxy instance here.
Information on what and how to cite ballaxy can be found here.