Re: [Biopython] Bioinformatics master's degree final project

Le 03/01/2022 à 11:39, Ferran Fàbregas
a écrit :

Have any tools been previously developed to do this using BioPython? Are there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or ClusterProfiler?

I’m also working on a BioPython GUI based on PySide6. I've seen some old projects related to BioPython GUI development but seem to be discontinued.

I would be very happy to use my time to contribute to the bioPython project, and I’m open to any suggestions or ideas.

Dear Ferran,

First of all,I wish an Happy New (covid-free) Year to all :-)

Considering these bioinformaticians additions (and/os systems
biology inclusion), most of the time

I do them in addition to parsing existing resources with biopython,
as separate projects.

I have tried to work on the aggregation of these resources, but
there are already some tools available,

see for instance the BioServices from Tom Cokelaer:

https://github.com/cokelaer/bioservices

I am not sure if you want to import some implementations into
biopython (and/or if the core developers want it),

but at least you have a pointer linking to it :-)

As for the GUI, which is a neat idea, I would recommend going to QT5
directly, so far this is the only GUI that seems to leave

enough to invest time on it. Just my 0.02 cents, though!

Wishing you all the best,

Stéphane

--
Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein Design In Silico
UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France
Tél : +33 251 125 636 / Fax : +33 251 125 632
http://www.ufip.univ-nantes.fr/ - http://www.steletch.org

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