Hi Vincent, Ah that sounds really cool. I will also try it out.
Kind regards, You Zhou 发件人: Vincent Carey <st...@channing.harvard.edu> 日期: 2021年5月27日 星期四 00:53 收件人: Stuart Lee <le...@wehi.edu.au> 抄送: "Kern, Lori" <lori.sheph...@roswellpark.org>, You Zhou <youzhoulearn...@gmail.com>, "bioc-devel@r-project.org" <bioc-devel@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 <le...@wehi.edu.au<mailto:le...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of Kern, Lori <lori.sheph...@roswellpark.org> Sent: Wednesday, 26 May 2021 10:01 PM To: You Zhou <youzhoulearn...@gmail.com<mailto:youzhoulearn...@gmail.com>>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org>> on behalf of You Zhou <youzhoulearn...@gmail.com<mailto:youzhoulearn...@gmail.com>> Sent: Wednesday, May 26, 2021 5:09 AM To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> <bioc-devel@r-project.org<mailto:bioc-devel@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 [[alternative HTML version deleted]] This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. 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