How to start
The latest version of the tool, as well as the source code, can be downloaded from here: http://sealion.scripps.edu:8080/hudson/job/PACOM-no-examples/lastSuccessfulBuild/artifact/PACom/target/ However, this other link will provide you the latest version of the tool including a dataset as example, ready to be loaded by the user: http://sealion.scripps.edu:8080/hudson/job/PACOM_with_examples/lastSuccessfulBuild/artifact/PACom/target/
Download the zip file and decompress it in your local system.
It will generate the following files:
Important note: If you are updating PACOM to a newer version, decompress it to THE SAME folder, and OVERRIDE all files. It is recommended to extract the file using the option ?extract here?, which will create a folder called ?PACom?, which will be the same over new versions.
User data folders: Some data is locally stored by PACom. It will be located at the ?user_data? folder, and inside that folder, it will appear the following subfolders (some of them will be created after using the tool somehow):
? curated_exps: where curated experiments are saved (see ?Using curated experiments to save resources? section). ? manual_id_sets: where the manually created datasets are stored. (see ?Importing external data for comparison? section) ? miape_data: where all datasets will be saved in order to use it for the inspection analysis. ? miape_ms_metadata: where the Mass Spectrometry metadata templates are stored. ? projects: where the inpection projects are stored.
How to run it? For Windows systems, double click on the file ?START_win_XGb.bat? where X is the amount of RAM memory that you want to use for the program. For Linux or MAC OS, run the file ?START_mac_linux_XGb.sh?. Note: for experienced users, the .bat or .sh files can be edited in order to launch PACom with a custom amount of memory. Note??: some systems don?t allow to run the tool using the original .bat files. This is because wildcard ?? is not allowed for starting the Java Virtual Machine. In that case, edit the bat file and replace ?? symbol with the current version of the tool.
Using a windows machine, you may not be able to see the file extensions if your Windows system is not configured to show them. It is ok. Just use the START_win_* file you want. Other issue that may happen using a Windows machine is that the system doesn?t trust the program. You just should click on ?more info?: