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Re: Assistance with application task for "Quality assurance for biological and medical applications inside Debian"



Dear Andreas,

> On Mar 29, 2021, at 3:13 AM, Andreas Tille <andreas@fam-tille.de> wrote:
> thanks a lot for your interest in Debian Med and our GSoC project.
> Since our main communication channel is the mailing list and I can
> not see anything private in your e-mail I take the freedom to CC
> my answer to the public list.  (Hope this is OK for you.)

> There is no formal application for the Debian Med team.  You definitely
> should subscribe our mailing list[1] and if you want to contribute code
> you should create a login on salsa[2] and ask for membership in
> med-team.

Thank you for the prompt response and for forwarding my initial email to the 
correct spot! I seem to be subscribed to the mailing list, and hopefully this
message ends up in the right spot as well. I’ve also gone ahead with creating
an account on salsa and requesting membership within the med-team group.

> In many cases reading the docs or even publications associated with
> the software in question might give helpful hints ... or just asking here
> on the mailing list can be a sensible way to learn how to write a sensible
> test command.
> 
> But you can contribute in several ways to the Debian Med team in case
> you might realise that this kind of tasks is not feasible for you.

I do agree it does seem like a daunting task for someone with little to no
bioinformatics background such as myself. I’ll continue and see if I have
what it takes to properly contribute regarding this task with the tests,
however I am very open to any suggestions of other ways to 
contribute to the Debian Med team over the summer if there happens
to be any.

Thank you,
Shafeen

> On Mar 29, 2021, at 3:13 AM, Andreas Tille <andreas@fam-tille.de> wrote:
> 
> EXTERNAL EMAIL:
> 
> Dear Shafeen,
> 
> thanks a lot for your interest in Debian Med and our GSoC project.
> Since our main communication channel is the mailing list and I can
> not see anything private in your e-mail I take the freedom to CC
> my answer to the public list.  (Hope this is OK for you.)
> 
> On Mon, Mar 29, 2021 at 04:54:25AM +0000, Mohammed Rahman wrote:
>> Dear Mr. Andreas Tille,
>> 
>> I hope you are doing well. My name is Shafeen Rahman and I’m currently pursuing undergraduate studies at the University of Toronto in Canada. I am reaching out to you in regards to the Debian Med related project you are in charge of supervising for this year’s Google Summer of Code.
>> 
>> I’ve enjoyed using Debian whether as a development environment, for my personal computing usage, for server uses and my favourite experience, which was using Debian to configure an open hardware microprocessor with my friends to create an electric motor powered skateboard. From my positive experiences with Debian, alongside reading the Debian Med team’s goal to enable healthcare research with the power of free and open source software, I am incredibly excited at the prospect of contributing to the Debian Project and aiding the Debian Med team.
> 
> Debian helped to drive an electric motor powered skateboard - how cool
> is this! ;-)
> 
>> I bring intermediate university-level programming skills, having learned C and shell scripting at a reliable level recently and having known other languages like Java and Python for much longer. However, for any skills missing I’ve seemed to excel where I’ve needed to grasp concepts and apply them in time sensitive scenarios, such as in hackathons and a previous internship experience.
>> 
>> With that being said, I have attempted to follow through the recommended reading and have been able to the point where I have a Debian unstable environment working, with sbuild installed and seemingly ready to go. I’m looking at attempting to fix bug #970312 (src:intake: Please provide autopkgtest) which seems to ask the maintainer of the intake package to provide a test suite for the package. From one of the examples listed, snap-aligner, it seems that Mr. Pranav Ballaney creates a shell script that compares the output of snap-aligner to the reference output. My first idea seems to be to find the reference data for intake and write a shell script for it, although I seem to be lost for next steps here.
> 
> For this actual task it is not necessary but definitely helpful to have
> some background in bioinformatiks.  Being a physicist myself I'm lacking
> this background as well and so its also not that straightforward to me
> to write test.  Actual users of the programs are probably good in
> writing tests since they know how to use the program.  In many cases
> reading the docs or even publications associated with the software in
> question might give helpful hints ... or just asking here on the mailing
> list can be a sensible way to learn how to write a sensible test command.
> 
> But you can contribute in several ways to the Debian Med team in case
> you might realise that this kind of tasks is not feasible for you.
> 
>> I’d greatly appreciate any pointers or tips on going about fixing this, or next steps on the actual application for the Debian Med team (ie. is the application process simply fixing a bug or are there also further steps?).
> 
> There is no formal application for the Debian Med team.  You definitely
> should subscribe our mailing list[1] and if you want to contribute code
> you should create a login on salsa[2] and ask for membership in
> med-team.
> 
>> Thank you for your time,
> 
> Hope this helps so far.  Feel free to ask for more details.
> 
> Kind regards
> 
>    Andreas.
> 
>> Shafeen Rahman
>> (He/him)
> 
> [1] https://lists.debian.org/debian-med
> [2] https://salsa.debian.org
> 
> --
> http://fam-tille.de


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