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

[You Zhou]

Hi Vincent,

Ah that sounds really cool. I will also try it out.

Kind regards,
You Zhou

发件人: Vincent Carey <stvjc using channing.harvard.edu>
日期: 2021年5月27日 星期四 00:53
收件人: Stuart Lee <lee.s using wehi.edu.au>
抄送: "Kern, Lori" <Lori.Shepherd using roswellpark.org>, You Zhou <youzhoulearning using gmail.com>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
主题: Re: [Bioc-devel] About the size limitation of the package



On Wed, May 26, 2021 at 5:55 PM Stuart Lee <lee.s using wehi.edu.au<mailto:lee.s using wehi.edu.au>> wrote:
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<http://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 using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Kern, Lori <Lori.Shepherd using RoswellPark.org>
Sent: Wednesday, 26 May 2021 10:01 PM
To: You Zhou <youzhoulearning using gmail.com<mailto:youzhoulearning using gmail.com>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using 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 using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of You Zhou <youzhoulearning using gmail.com<mailto:youzhoulearning using gmail.com>>
Sent: Wednesday, May 26, 2021 5:09 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using 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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