Hi, thanks for IGB. I am using it a lot for data-analysis of RNAseq data relating to various conditions and organisms. Below some user-experience related to bookmarking. Sorry if it sounds all a bit harsh, but I just had a bad start of the day because of losing my most recent bookmarks (quite a lot of analysis to recover......).

Here it goes:

I found that with too many tracks to compare experiments in one window it is handy to use two instances of IGB side by side (different monitors/screens).

However, when bookmarking genomic locations in one window, the bookmarks in the other do not get updated. But worse, when closing the windows the most recent additions to the bookmarking are not kept; possibly because of the order in which the windows were closed (and the 'old' bookmarks did overwrite the 'new' ones). Restoring a saved session does not help in this case, as the bookmarks are not saved with the session (and only in ~/.igb/bookmarks.html). Also, bookmarks only get properly saved when the program is closed using 'quit'; closing the window the program is loaded in, results in a loss of bookmark-changes made (thus the signal for closing the java program in that window, igb, does not get forwarded to igb-quit).

The limited number of bookmarks.html backups (1) does not help to recover from this.

Further, the bookmarking is not linked to the loaded genome. Thus when looking at bacteria, I only need ecoli bookmarks; when at yeast, only the yeat bookmarks. In order to manage this, all bookmarks have to be specifically organised in separate folders for separate organisms. And then per separate annotation-version one uses them for, as that gets hard-coded with the bookmark when saving this - even when chosing 'position only'. That is not needed. Mostly annotations change but genomic sequences do not and the bookmarks should relate to the sequence. So, is it possible to remove that hard-link to the used annotation-file as one can screw up a session when clicking a bookmark and another annotation file gets suddenly loaded with it.

In order to reforming all bookmarks when a newer annotation file is used I had to edit the bookmarks to remove this hard-link. Also editing bookmarks is a pain. This can only properly be done by exporting them to a file, editing in an editor and reimporting them.... Much easier to handle all of this when bookmarks only link to genome and genomic position and nothing else.

Therefore, can you please, if possible incorporate some of:
1) sync bookmarks between windows (but maybe easier/better to do is the following
2) save bookmarks during a session/with a session; or
3) enhance no of bookmark-backups;
4) include a preference setting to add a user-defined-folder (other than ~/.igb) where bookmarks (and maybe other stuff) are copied/exported to automatically upon quiting/saving a session (which would create an extra back-up)
5) remove hard-link between bookmark and loaded gene-annotation-file (gtf) when saving bookmark as "position only"
6) link bookmarks to organism chosen/loaded in the program to keep bookmarks manageable (one could think of a bookmark-file as an option within the igb-quickload folder for each genome if one has that set-up locally; or sync this folder-structure locally in the ~/.igb)

Please, keep up the good work.

Best regards,

Rob

Reporter: Rob van Nues
E-mail: rob.van-nues@ed.ac.uk