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binbase compound browser
BinBase Compound Browser
The BinBase system ships with a small tool to query and compare bins. We call this tool the BinBase Compound browser and it is currently only available in the svn repository. We will release it as soon as possible.
how does it work
the access is fairly simple, just open the website of the tool.
http://<applicationserver>:8080/binbase-compound
this will bring you to the select database dialog or if only one database is configured it will automatically forward you to the search database dialog.
Once you selected your database this tool will open the query dialog. In this dialog you can enter a query of your choice. The format a query is like this
bin_id, bin_id, name,bin_id : name
If you enter id's it will search for exact id's, if you enter a name it will search for names and similar names.
For example execute the query for the bins
C08,C16,C30
as result we become now a list of bins for this query
If you click on one of these entry it will now show you the properties for this bin including a massspec with the most important masses.
this gives you now informations like
- mass spec of this bin
- retention index, quant mass, name and unique id
- in which group is this bin, groups are combined during the export to one bin and are usefull if a bin was generated twice for some weird reason. For example a massspec was to dirty in a a class and so generated a new bin
- a list of the 10 most similar bins, excluding bins in the same group
- information in which species this bin is found, if available
- a list of references to this bin like pubchem id's or kegg id's
If you now want to compare this bin to other bins, you can select the bins of interest in the right table and press the button "compare to..." This will display now all the selected bins with there properties and to each of these bins it also gives you the list of similar bins
I hope this gets you started with this tool.
