[Bioc-devel] Participating in the development of Bioconductor

Vincent Carey @tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Wed May 3 18:23:21 CEST 2023

Hi Franck, thanks for writing.  I think it would be great to hear from
users about performance
concerns.  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


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.

Best regards
Vince Carey

On Wed, May 3, 2023 at 12:12 PM Franck RICHARD <franck.richard using winstars.net>

> 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]]
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