[Bioc-devel] About the size limitation of the package

Hi You and Lori,

Are fitted models in scope for ExperimentHub? I thought it was more for
data. Maybe there should be a ModelHub for developers to include trained
models from papers in their packages?

@You: if that model has been fitted in R take a look at
https://github.com/tidymodels/butcher for some ways of reducing it?s size.

Thanks for these suggestions Stuart!  butcher certainly seems relevant.  I
tried it out on
the adabag output in You's package was able to effectuate some nice
reductions
tr1 = x$trees[[1]]
obj_size(tr1)
340,192 B
obj_size(axe_data(axe_call(axe_fitted(tr1))))
171,896 B

So this in conjunction with xz compression could make this a moot point
for @You Zhou.

As for the ModelHub, two thoughts.  First, I'd be more inclined at this
stage to partner with a
system like kipoi.org, with fitted models archived there and retrieved by
API as needed by bioc
packages.  I wonder if there are any good examples of this by now.

Second, although I don't feel we have capacity in core to introduce a new
Hub at just this point,
I think we'd be able to help a motivated community-based team to produce
one -- if kipoi suggestion isn't
viable -- utilizing some Azure resources that have been contributed by
Microsoft Genomics.  Interested
parties should write to the list.

I don't see a bioc slack channel devoted to AI/ML and maybe there would be
good traffic on one.
This "task area" could be added to biocchallenges, or could be a topic for
a developer forum meeting.
Thanks
Stuart
________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Kern,
Lori <Lori.Shepherd at RoswellPark.org>
Sent: Wednesday, 26 May 2021 10:01 PM
To: You Zhou <youzhoulearning at gmail.com>; bioc-devel at r-project.org <
bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] About the size limitation of the package

Please consider using Experiment Hub to host the large data file. More
information can be found here:

https://bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/CreateAHubPackage.html

Cheers,

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of You Zhou
<youzhoulearning at gmail.com>
Sent: Wednesday, May 26, 2021 5:09 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] About the size limitation of the package

Dear Bioc team,

I am compiling a package ?m6Aboost? and planning to submit it in the
Bioconductor. This package using a trained machine learning model to
identify the correct m6A signals from the miCLIP2 data set (more detail
about this machine learning model can be found in our paper
https://www.biorxiv.org/content/10.1101/2020.12.20.423675v1).

Now I meet a problem: the size of this machine learning model is 10 Mb,
which is bigger than 5 Mb. Since this model is crucial for the package, I
was wondering whether I can ignore the warning message about the size
limitation. Thank you : )

Best regards,
You Zhou

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[Bioc-devel] About the size limitation of the package

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