Mapping Tool
A tool to assist name mapping if different nomenclatures are used by different models (e.g. metabolic networks).
Download
- DownloadVersion 1.3 (14-Sep-2007) (ZIP, 14.3 MB)vertical_align_bottom, with KEGG compounds / enzymes and sample files
- DownloadVersion 1.3 (14-Sep-2007) (ZIP, 2.6 MB)vertical_align_bottom, no KEGG data, no sample files
License
Redistribution and use in source and binary forms, with or without
modification, are permitted provided agreeing to the Simplified BSD Style License.
- DownloadLicense (TXT, 2 KB)vertical_align_bottom
- Read about Simplified BSD Style License at external pagehttp://www.opensource.orgcall_made
Installation
- Java version 1.5 (SDK or JRE 5.0) or newer must be installed on your computer, see external pagehttp://java.sun.comcall_made
- Unzip the downloaded file, a mapping directory will be extracted
- To run, use the start.sh or start.bat scripts, or directly run
java -jar mapping.jar
With 512 MB memory:
java -Xmx512m -jar mapping.jar
FAQ
How do I load KEGG data?
Select the folder containing the compund and enzyme files. In the standard installation with data, this is the folder mapping/data/kegg
Where can I download the newest kegg data files?
Here: external pageftp://ftp.genome.jp/pub/kegg/ligand/call_made
How do I access the OMA-browser database?
Use the URL external pagehttp://omabrowser.orgcall_made
Note that only some rows are fetched when clicking Reload, thus the only match strategy of use is DatabaseQuery. The first attribute(s) are usually the ones to take as match attributes.
→ Read more about OMA browser external pageherecall_made.
I get an out of memory exception. What can I do?
If java has not enough memory reserved, you get an exception like this in the command window where you started the application: java.lang.OutOfMemoryError. Add the -Xmx<n> parameter to the java command to start the application. Examples can be found in the install section.
How do I perform a search (find) operation on the table?
A rudimentary find operation is available by pressing Ctrl-f and regular expressions can be used with the find methods on the context menu (right click on table).
How do I unsort a table?
Shift-click on the table header.