I love the program. I have a few suggestions for future development.

For empty bins, would it be possible to display not just the number but also the description?

For presentation purposes, it would be nice to display next to the symbols all the values and descriptions (for not so populated pathways), not as a pop up, but in the picture itself.

Another handy feature would be to know how big one particular bin is, without going through the mapping file.

Since I am uploading my own mapping file and it changes quite often, the database backup increases a lot. I would love the possibility to choose wether to save all the databases or not.

Thanks!

Dear andrea,

thank you for your input!
> For empty bins, would it be possible to display not just the number but also the description?
will go into the next release
> For presentation purposes, it would be nice to display next to the symbols all the values and descriptions (for not so populated pathways), not as a pop up, but in the picture itself.
do you mean by mouse over?
> Another handy feature would be to know how big one particular bin is, without going through the mapping file.
we could include that in the mapping browser on the bin folders, as that is the only place where all genes(identifiers, reportes) are present.
> Since I am uploading my own mapping file and it changes quite often, the database backup increases a lot. I would love the possibility to choose wether to save all the databases or not.
We know that problems with the database can occur. You can just delete the database. The database will be rebuild from the mapping files. The reason for using the mapping database is saving computer memory during program execution as all the additional information can be stored within the database and does not need to be held in memory. I also now that in the first versions, using the database, we had not included proper deletion of old mapping data. In the current version this should removed properly and space should reallocated.
But the new versions will not remove spae left over from the previous one.

Axel

> > For presentation purposes, it would be nice to display next to the symbols all the values and descriptions (for not so populated pathways), not as a pop up, but in the picture itself.
>do you mean by mouse over?

No, I meant to have an option that adds in the display a box with values and descriptions so that it could be moved around and saved with the image.


> > Another handy feature would be to know how big one particular bin is, without going through the mapping file.
>we could include that in the mapping browser on the bin folders, as that is the only place where all genes(identifiers, reportes) are present.

This could be as above, another box where it says that it is displaying values for i.e. 4 genes out of 10 in that bin. Thus you will know how much coverage you get in one experiment.


> We know that problems with the database can occur. You can just delete the database. The database will be rebuild from the mapping files. The reason for using the mapping database is saving computer memory during program execution as all the additional information can be stored within the database and does not need to be held in memory. I also now that in the first versions, using the database, we had not included proper deletion of old mapping data. In the current version this should removed properly and space should reallocated.
But the new versions will not remove spae left over from the previous one.

I'm not sure I understood it all. I'm using the latest version of the program (1.8.0). Because of adding and deleting mapping files, db.backup got to >50Mb and db.data to >256Mb, slowing down considerably my computer. So I deleted the files and let the program rebuild them. It is just an inconvenience and more of a problem for less computer literate users.

Andrea

Regarding the display of values and descriptions next to the symbols I have looked into possible implementations and we will have to discuss if and when we might introduce that. I listed it on our agenda.