[Biopython] Bioinformatics master's degree final project

[Ferran Fàbregas]

Hi Peter,

Well, now I'm in the first stages of the research, because I need to make
an initial proposal in one month approx, so I don't have yet a clear idea
of what to do.

I'm personally interested in pathway enrichment and I'm going to take a
look at BioServices / GOenrich python packages and see their features, but
If you think that adding pathway enrichment functionalities to Biopython
can be interesting, I can go deep into it.

Talking about the GUI, I understand that  with Galaxy, maybe there's no
need for a biopython GUI, but I think that can be interesting for
educational purposes or more basic / on the fly needs. Galaxy can be
overwhelming for quick jobs.

One feature I was thinking about (maybe it's a little bit crazy) is that
the GUI generates a Biopython script of your sequence of actions, so you
can start using the GUI, download the script and then continue coding by
yourself. This feature may not be very useful to professionals, but can be
very helpful for students or newcomers.

F


On Mon, Jan 3, 2022 at 7:07 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:

> Hello Ferran,
>
> Personally I never saw the need for a Biopython GUI, and have used
> Galaxy instead for a web-based interface for many of my own scripts.
>
> Something for pathway enrichment could make sense for Biopython
> though, do you have a clearly defined idea in mind?
>
> Kind regards,
>
> Peter
>
> On Mon, Jan 3, 2022 at 3:06 PM Ferran Fàbregas <ferri.fc at gmail.com> wrote:
> >
> > Thanks for your replies, it seems that the community prefers to use
> different bioinformatics related modules for different functionalities
> instead of one big, more complex module :)
> >
> > A couple of questions about that:
> >
> > Do you think that it makes sense adding some enrichment functions to
> biopython?
> >
> > Do you think that it can be useful to create a modular Python GUI that
> integrates biopython functionalities plus Bioservices / GoEnrich / etc...
> ? Or maybe it is not useful at all because you can already use some servers
> like the Galaxy project website (https://galaxyproject.org/)?
> >
> > What do you think about that?
> >
> > Thanks in advance,
> >
> > F
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220103/146e61b5/attachment.htm>