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Talk with the BioC Core Team

Marcel Ramos
Senior Data Scientist and Machine Learning Engineer в CUNY Graduate School of Public Health and Health Policy
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BioC2020
30 июля 2020, Онлайн, USA
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Talk with the BioC Core Team

Marcel Ramos, MPH (Roswell Park Comprehensive Cancer Center) Biostatistician

Kayla Interdonato (Roswell Park Comprehensive Cancer Center)

Lori Shepherd (Roswell Park Comprehensive Cancer Center / Bioconductor) Senior Programmer

12:00 PM - 12:55 PM EDT on Thursday, 30 July

WORKSHOP

Join the BioC Core Team for an open discussion on BiocSet, annotation pipelines for release, package creation/review (also doing workshop Thur at 11 am right before), managing youtube/course material, Bioconductor infrastructure. Bring your questions!

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Marcel Ramos
Senior Data Scientist and Machine Learning Engineer в CUNY Graduate School of Public Health and Health Policy
Kayla Interdonato
Programmer/Analyst в Roswell Park Comprehensive Cancer Center
Lori Shepherd
Senior Programmer в Roswell Park Comprehensive Cancer Center

Strong research professional with a Master of Public Health focused in Biostatistics from the CUNY School of Public Health, Hunter College. Experienced #rstats #Bioconductor user and developer with a demonstrated history of curiosity. Loves to mold tough

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I originally started my education in the hard sciences (biology, chemistry) but decided I needed more computational skills to be competitive in the working industry. I switched degrees and got a Bachelor's in Bioinformatics with minors in computer science and computer theory. I had an internship at the Southern California Earthquake Center for applied computer science. I completed my undergraduate degree and immediately started working for the Biostatisics department at University of Buffalo and Roswell Park Comprehensive Cancer Center where I have worked for the last 12 years. During my time, I went back part time for my Master's in Bioinformatics, a joint degree from the university and cancer institute. I now work for the subdivision of the Biostatisics department, Bioconductor. I program in R and help manage project infrastructure using python and ruby. I also assist and present with numerous short courses, workshops, and conferences.

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I was wondering if it would be worthwhile for someone to just walk us through it with a couple of Builder ports. Maybe every did you want to maybe share your screen, or maybe that's not a convenient testing, see you at the moment. So you'll be tricky here in a weird place, was very poor internet. A lot of things going on around me. See how probably make a mess mess up this. But here we are on the on the homepage again and then in this developer box, on their various developers sources, including the field reports,

and then you can see. So all software packages are built each night in the release branch and then the development branch. I'm done. And that is a bills report that describes these things. So if you were to look in the, if you need a new changed, your package and wanted to see how it was doing, you make the change one day, the bills, run on a nightly basis. And. And you'll see up here that's at see. We've got We got the snapshot date. This is when the build us started on 729 at 1450, and sometimes off. And then the bills report

came out on 730 about 22 hours for 23 hours later. So every night to build rapport goes, if you made a commitment before this date and time then the effects of Bactrim it would be revealed here. I did not There's a good example, I think. I think got the sanitation DVI package was at a recent change and when Kayla made the change, I think, I think it's this commit when she made that change, she pumps diversion to 15013 manufactured in in several days. So it's included in this report and you can see we built the cross We built across.

Across the Linux windows and my hot. And there's been several stops and install a build on a check. And she looked at one of these guys think there's there's the command that was Ron is our Command check of that, annotation DBI and then this is the output of Arc Manchaca and it says, hey we did looked at all of these things and everything except for This. Seemed to go. Well, and actually, this this seems like a note that could be fixed and release 15014 and, and then that's great. But the end result is there are two notes but no warnings or

errors. So the build report says, okay, this package built I'm just going back to the field report and maybe Setting it down here. You'll notice that they're these little LED lights here and there are actually different flavors of LED lights. Blue means we built the package last night, it passed, but it's no different and not a different version from the one, from the night before. And the green means actually the version of the package changed, but it also passed the installed Bill check commands. And so, we need to push a new version of the

package to the public repository and red means. But there's a new version of the package and and but it failed to build and so we didn't, we didn't. That's all right. The names of the packaging failed to build but I think it actually means that. For instance, there isn't a new changes to the package but no version bump for actually not. Myself all confused about what those red allergies. So I think that went with the package face, 222 Brees know that there's no question about whether we need to, but if the package is coming today

for propagation in the sense that it passed reading check successfully, it might still be blocked from propagating pothos propagation will result in impossible dependencies. That means that is a package. Requiring exertion of another package. He's not going to make it to the jury that you can even do. The package was that it ICS actually as long as you're there really quick cuz there is a a poll question and I know there are a couple not supported on the

Civil side. And the progress was how about Windows support? Is there a strong commitment to keep windows as a first-class osm by to see how many packages currently exclusively work on Unix? And is there any policy and forcing a new package to support both OS? Right. So what's this? Settles down. Yeah. So and math is an example of a not supported. So yeah, I guess so. Maybe someone wants to walk us through what that means goes into bioconductor. We try as strongly as possible to get a package on all three platforms,

Mac, windows and Os there. I would say, very few packages, a handful of packages may be that only work on Unix because we feel like a lot of researchers, I think, at some point, we kind of threw out a number of probably almost half are probably working on a Windows platform and you'll isolate them from using your package, if you don't support it out with those. So we do encourage packages, submitted to bioconductor to work on all three, whenever you could actually get them working on all three, there

are exceptions. So we do make exceptions where they could only Work on one platform but it is, how do we went into a super Windows? That's a good question. I don't know, but maybe the board has some thoughts about these It's so much fun. I wouldn't want to give it up. Yeah, you're right. One of the surprising that a large fraction of the at least the visitors to the support side and the package. Most are two windows say like 50% of the downloads. So by not supporting windows, or producing a

package, that doesn't work on Windows, you're losing half your audience, maybe that changes with like, to talk or containers and so on, and maybe in the future, they'll be less. Best need to support multiple platforms, will just support like the pilot partner, doctor image. So I just to add one more thought to the description Martingale about how their bill system works and like where you can check things. There's a workshop from a couple years ago. 2017 I think. And I pasted the link in the

chat most of it is still relevant but it's essentially what Martin described in the very comprehensive way. Right now, if people wanted to go back and look at it via page down, I understand. Exactly. But I think it's way different from the manual because of course, the vignettes are often in HTML. I wasn't exactly sure maybe if someone wanted to clarify. But what was meant by I got the Man pages. That requires packages to be on like get Hub or some location, right? Which would be somewhat problematic for us if we have packages like

our Legacy packages that were SVN. I don't have some sort of public facing repository besides, what's in bioconductor right now, right? Or maybe I'm misunderstanding how they generated working. I will mention, we are at time so if anyone needed to pop off to us, you the start of the lightning talks while we reflect on this for a couple minutes and close out with it, but just so everyone's where time one can already generated a h d HDMI out from the Man pages. And so it's really a but if there's a convenient way to all of those pages for

instance with package. I guess that's a really good question. I thank you. We heard everyone to come back. We have another one tomorrow. Please think of some questions. We would love questions will come up with stuff if we need to but we would love more a commune Questions and get what you're dying. Ask us. See y'all tomorrow.

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