[Bioc-devel] Participating in the development of Bioconductor

[Neumann, Steffen]

Hi,

On Wed, 2023-05-03 at 12:23 -0400, Vincent Carey wrote:
> Hi Franck, thanks for writing.  I think it would be great to hear
> from users about performance concerns.

Super-crazy idea, would it make sense to enable some R profiling
on the build system, and report what takes the most time ?

We already do so for the tests (total time per test iirc),
and it probably won't make sense in the daily builds,
but maybe similar to (or including) the longtests builds
around the weekends ?

I never did propoer profiling, so I am way out of my comfort zone
here...

Yours,
Steffen


> We would like to do more profiling and instrumentation of key
> worksteps to help
> increase throughput and ensure available compute resources are used.
> In
> the cuda/gpu
> space we don't have anything touching
>
> https://github.com/NVIDIA-Genomics-Research/rapids-single-cell-examples
>
> as far as I know and it would be interesting if you would have a look
> at
> this and see whether
> the is a clear path to some development integrating these approaches.
>
> You might want to join our community slack for more interaction.
> slack.bioconductor.org
>
> Best regards
> Vince Carey
>
> On Wed, May 3, 2023 at 12:12 PM Franck RICHARD
> <franck.richard using winstars.net>
> wrote:
>
> > Hello community!
> >
> > I am the author of several software programs including this
> > astronomy
> > program:
> > https://winstars.net/en
> >  I recently had the opportunity to
> > participate in the activities of a neuroscience laboratory in
> > Madrid. I
> > learned how to use Bioconductor and I would like to participate in
> > the
> > development of new features (if possible). The researchers in the
> > lab
> > complain about the slowness of these tools when used on simple PCs.
> > So I
> > wonder if it would not be interesting to integrate Cuda in some
> > indexing
> > packages, I think of Bowtie2 or Salmon for example... (there is a
> > version of bowtie2 that works with cuda, but it seems old). But the
> > task
> > would be very complex I guess. There are simpler things to do, like
> > creating a wrapper for Salmon or something like that. What do you
> > think
> > would be useful to do at this moment for Bioconductor users?
> >
> > With my thanks,
> >
> > Franck
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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