 One of the benefits, or maybe I should say detractions, of using version control on a project is that you can see the exact moment that you start a project. You may recall that about a year ago, in July, I started a project seeking to look at the sensitivity, specificity, the overall performance of Amplicon sequence variants. That project kind of evolved and I kind of took on a comparison between Amplicon sequence variants and different definitions of operational taxonomic units. Well, looking at my Git log, I see that that project was started at 11.43 and 11 seconds in the AM on Friday, July 3rd. Here we are, just over a year later, as I'm talking to you, it is July 12th, and I've got some exciting news to report back to you. We got the paper accepted into M-Sphere. I received the email on June 30th from Trina McMahon, who is an awesome professor, and I'm not just saying that because she accepted our paper, but she is just a phenomenal scientist at the University of Wisconsin. She's a real bright spot in peer review and just really grateful that she's helping out at M-Sphere. Anyway, she commented back, dear Pat, thanks for taking the time to carefully respond to the reviews. I think the article is in great shape. Thank you, Trina, for helping to shepherd this through the process and I'm sorry it took me so long to make the revisions that you requested like, I don't know, a few months ago. Anyway, it's through the process and so what I want to spend a little bit of time talking to you about today is that this decision letter is not the end of the story, right? The paper is not published. It is accepted as of June 30th, right? So I feel safe in updating my resume to tell people that I have yet another paper that's been published and, you know, I can do a happy dance and celebrate, but there's still a couple things that I still needed to do to get the paper published and that's what we're going to talk about in today's episode of Code Club. So the next thing that happened to me last Saturday was I got an email almost to the hour from the one year mark, so 5.50 a.m. on July 3rd, 2021, saying your paper's been accepted, we're ready to publish it in the issue 6.4 of M-Sphere, pay up, right? So they wanted me to pay for the page charges, the article publication costs, the APCs, I think I got that acronym right, and so if you publish things, open access, there's one fee, and if you pay at other journals under kind of a closed model of publishing, there's perhaps a different price. So M-Sphere is a completely open access, gold open access journal, and so I went ahead and paid those page charges. Don't worry, I'm not paying those out of my pocket. I have funds that I request through grants and through discretionary funds that I have at the University of Michigan that pay the costs of this manuscript. Because I had some supplemental materials and because this was a shorter form paper, the total bill turned out to be about $1,600. If it was a full length manuscript, it probably would have been about $2,500 or $3,000. Other journals like The Nature Publishing Group, I think, are quite a bit more expensive. So if you think that's a lot, could check out some of these other publishers. I think ASM has some very affordable rates for open access. And if you're at an institution that's underfunded or that you personally are underfunded, always reach out to the journal and say, hey, could you help us out here with some of the expenses? So I paid that and that kind of helps the manuscript move through the rest of the publication pipeline. Next, on July 9th, I received an email from Noel Lin. Noel is awesome. I've met him many times before at ASM headquarters and he does a lot of production work with M-Sphere and other journals at ASM. So it's always great to get an email from Noel. And so this is telling me the proofs for your upcoming M-Sphere article are now available. And so click here to access the proof file. So that link takes me to this website where I can click to download the article proof. And I will also use this site to then resubmit my proofs with any corrections or comments that need to be made. So again, I can click on this. And for the first time, I see my manuscript as it's actually going to be published here on the right side, going from my, you know, very vanilla, if you will, PDF on the left to the right, and seeing what it's going to look like as a published manuscript at M-Sphere. And so that's really exciting. And you know, not every journal gives you proofs. I know that a lot of the PLOS journals like PLOS ONE, for instance, doesn't give you proofs, or at least my experience was that they don't give you proofs. But the proofs are the opportunity for you as the author to see what your manuscript is going to look like when it's published. And so again, the reason they give you proofs is that so you can see them and make any corrections. If, I don't know, it was 20 years ago that I got married, but you know, the photographer that took pictures for our wedding gave us proofs, right? So these were kind of not the polished figures, the final figures, the final pictures. But we could, my wife and I could kind of go through those proofs and figure out which ones we wanted blown up, or if we wanted any alterations done, mainly to me to make me look a little bit more handsome. But you know, the proofs are kind of your last chance to fix anything in the manuscript. And so again, when I get these, I always love just kind of scrolling through the manuscript to see what it looks like, see my figures, and just be grateful. Be grateful that the manuscript was published, that we got through this process, and that we're like almost to the end of the process. So what I want you to pay attention to with the proofs are a few things. So the most important thing that you should pay attention to is the author queries. Now not every journal gives you author queries in the same way. ASM puts their author queries at the end of the proofs. And these are questions that the copy editors have for you. So ASM hires copy editors that work for ASM. They are phenomenal. They are phenomenal. I have had papers accepted at other journals, so say like plus one, and you can go look this paper up where the manuscript was submitted and it was published, not as I submitted it, but actually with errors incorporated, right. So I have this software called mother, M-O-T-H-U-R plus one managed to change that U-R to E-R in a number of places and then would not let me correct it, right. So because they didn't have a proof step, I wasn't able to correct that. So the great thing about publishing at ASM is that they do a great job of going through and creating the proofs of doing copy editing to make your text look even better than it already was. And at the end, they always have a series of questions, right. So they want to make sure that the author's names are spelled correctly, and that the given names and surnames are identified properly by these colors, the given name in this kind of purple color and the surname in this darker purple color. I'm not very good with colors, if you if you didn't notice. And that an ORCID ID was provided for at least one author. Make sure that that was right. A-Q-A-B-B-R, please check any additional introductions or abbreviations and correct them as necessary. And then want to make sure that these are my funding, right. So let me scroll back up to the top here. This first author query, so A-Q for author query is the author. And so the number one thing that you need to check here is that the name is spelled right, right. So yes, that is spelled correctly. The number two thing that's important is to check with your co-authors and make sure that you have a middle initial if that author needs the middle initial, right. So I go as Patrick D. Schloss, not Pat Schloss, not Pat D. Schloss, not Patrick Schloss, but Patrick D. Schloss. My dad is Patrick J. Schloss. My son, who's not an academic and probably never will be, is a Patrick N. Schloss. And so for all of the papers I've ever published, I have done my best to be Patrick D. Schloss. That way, if you do a search for Patrick D. Schloss, you get my stuff and not my dad. There's another Patrick Schloss, believe it or not, in Germany, who's a neuroscientist. And sometimes we get each other's emails, you know, when someone starts asking me to review papers on neurobiology, I know they've got the wrong Patrick Schloss. Anyway, to me it's important to have to be Patrick D. Schloss. Other people don't care so much about having that middle initial or, you know, having a formal first name. So you do you, but definitely check with your co-authors because you don't want to issue a correction because you got the name wrong and you want to get everyone's names right, right. That's just a basic kindness that you can do to all of your co-authors, okay. Also check your affiliation, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA. That's me. So I'm going to come back down to these author queries. They then have A, Q, A, B, C, and D, in my case. And so these are queries that are listed in the margin of the manuscript that they want you to double check or that they want you to respond to. Sometimes we have had author queries where perhaps a reference in the bibliography wasn't complete and they've done their best to figure out what it was, but they want me to confirm what it was, right. Or perhaps I put in a hyperlink to a web page and that link is dead, right. So they want me to find the right link, right. So what do they ask? So ASM policy requires that new nucleotide protein microwave data be available to the public upon online posting of the article. So verify the all links to records and whatever are available, right. So I didn't have any new sequence data, all the sequence data I got from the was from the RRNDB. So I'm not going to worry about that. A, Q, B. So I said, as a way to adopt the threshold suggested by genome sequencing to microbial community analysis. So is that correct as meant, or should adopt B adapt. So let's come back to the top and we're going to look for A, Q, B, right. So I'm not seeing A, Q, B in this sentence, but further up on this page, we do have adopt up here, right. And this is the sentence they're referencing, right. So Amplicon sequence variants have been proposed as a way to adopt the threshold suggested by genome sequencing to microbial community analysis using 16s RNA gene sequences. Should that be adopt or adapt? I think it should be adopt, right, because we're taking the thresholds, you know, that 0.985 or whatever I said up higher here, right, you know, that were too coarse or too fine, that we want to adopt those. So take those and use those. Don't think I want adapt. So let me come back down here then. And so I'm going to say it should be adopt. And so I do stuff here in preview, you can work with these proofs in, you know, Adobe or whatever you use. So I'll go ahead and click on the pen here. And then there's a text box here that I can grab. And I'm going to pull this down and I'll say adopt is correct. And then I will make that read by clicking on the letters read. And so adopt is correct. And then I will make another note up here for author query a that I'll say no new sequence data were generated for this manuscript. Okay, so that should be good. Next, spelling of intra quartile and not inter quartile as meant here and below. So this is one that I get confused by myself. So I'm going to go ahead and do a Google search for intra quartile and see what it should be. And so I'm seeing that showing results for inter quartile is seems to be the correct one. So if we go to the purveyor of all wisdom Wikipedia, they like inter quartile range. And so if you think about it, that is between the quartiles not within the quartiles. So I think it should be inter quartile. So I'll grab this text box. And I'll say inter quartile is correct. And so let's go ahead and search for intra quartile throughout. And so there's seems to be two cases here on page two and page five. So I can do is highlight intra quartile. And then on this note, I can say this should be inter quartile. Right. And so that way, then they will see that. And maybe I'll put that right next to the intra quartile. And then let's go to the other one here, right. And here we can also add another note. And say this should be inter quartile. And let me put that next to intra quartile. AQD, this makes it impossible to fit a distance threshold to define an OTU definition. So the note for author query D was a little bit sparse. My sense is that I've got define in here twice. And I think what I would do maybe is to just simplify the sentence overall to say to remove to define an OTU definition. So this makes it impossible to fit a distance threshold that matches a set of species names. So I think what I'll say is, let's remove this part, let's remove the to define an OTU definition. So again, I can come back down here, I can plop in another text box. And I can say, remove to define an OTU definition. So go ahead and move that up just to be closer to the query. And I think that removal of that phrase will make the sentence a little bit more compact and clear in what's going on. So that addresses the four queries that the copy editors and those that created the proofs had about the manuscript. I'm going to do my due diligence. And I'm going to read back through the manuscript now and look for any problems in the text. So something to keep in mind is that this is not the time to add text or to remove text, right? Unless there are big problems. So you're not going to add a paragraph, you're not going to add a sentence. Perhaps there's a word that's duplicated twice. Again, ASMs copy editors are pretty awesome, they would detect things like that. So little things like that, we're going to look at and try to find those types of problems. I don't expect to find any. I usually have to force myself to read back through the manuscript, because at this point, I've probably read the manuscript 100 times. And I'm sick of looking at it. And I know it's so well that my eyes just kind of glaze over things. But it's really important at this point to look back over the manuscript, double check all the words, make sure the figures look right, make sure you've got the right figures, right? Sometimes people get the figures out of order, right? So you want to make sure they look right, you want to make sure they're not cropped accidentally, you want to make sure the resolution looks good. Something else I'll often do is I'll put the manuscript as submitted right next to the proofs, and read them in parallel as I go through the proofs, and see, you know, were there any changes the copy editor made as they were reviewing the manuscript, I'm going to go ahead and do that now, and I'll report back. Once I've done that, you know, I'll report back what I found. So I read all the way back through the manuscript, it looks really nice. I'm happy with the way it's turned out. A couple things that I double checked as I was going through was that there was a link that I had in here to my GitHub page or repository for this project. And so double clicking on that brings us to the page. So I wanted to make sure that was live, I thought it was, but I just wanted to double check. Also, let's go to the YouTube link and make sure that works. This is the playlist on the Riffimonus channel that has all of the episodes associated with this paper. This episode will be at the end of this as well, or maybe it'll be up here at the top, who knows. Wanted to give you an example of how the copy editors subtly change things. Again, they are not making big changes to the text. They're trying to kind of get my text to align with their style guides. And again, looking for, you know, wording that is clumsy as we saw in their queries. So as an example, right here on these two lines, it says C references 19 and 20. What I had was EG comma, and then in parentheses 1920, and all that was in a set of parentheses. So that they made it EG C references 19 and 20, probably is more aligned with their style guide and taking my text and trying to kind of massage it, if you will, to fit their style guide, not a big change to the text, nothing that I would really worry about. A couple other things that I would do in here is I'm going to do a search for out. Because I know sometimes OTU gets changed to out. And like the couple cases here, so without that works. And it's getting out from YouTube. So I don't see any problems there. Something that I always do now is mother MOTH ER, that doesn't show up. But sure enough, you are definitely does show up there in a couple spots. So again, these are a couple things that I check as I review the proofs of my manuscript. Now, every publisher is going to have a different way of handling their proofs. And this is ASM system. I mean, why, why would you go anywhere else? No, but every system is going to be a little bit different. They might want you to do more markup of the actual text. I find that kind of highlighting the text and putting in a note here is generally good enough. Also, this is not meant to be a adversarial relationship, right? The copy editors and the people that make the proofs, they're trying to make the paper look good, right? And so if you have questions by all means, email them, follow up with them. And if they have questions and they're, you know, they're worth their their work, they will certainly follow up with you. I've had cases before where we've had figures kind of all out of whack or references out of order. We've had we've had problems, right? Something screwed up when we submitted. And we've had to make big changes. They've then given us another round of proofs and said, How does this look right? And I think that's certainly something that you could request as the author be to say, Hey, you know, there were a number of changes here. Could we see the next round of proofs just just so we can sign off on it that we're happy with the way things look. So I will go ahead and save this. And now I'm ready to resubmit the proofs. So again, looking at the proof response files and comments, that was where we got the proofs, changes needed, annotated file attached. And so I'm going to do a choose file. And then I will put in the PDF name of the proofs. And I'll say looks great. Thanks for your work to make the paper look better. Great. And so now that's the file. And I'll go ahead and submit the proof response. Generally, they will give you one or maybe two business days to respond to the proofs. Again, they are on a deadline where they have an issue that they want to put this paper in. And so they need to hit a deadline themselves, right? So again, they're trying to help us to make our science look as good as it possibly can. We need to go out of our way and help them by getting these proofs back to them in a timely manner. Sometimes it does happen where, you know, you get the proofs and it's a holiday, you know, or you're on vacation or who knows, but you can only do what you can do. But again, this is like the final step before your paper is published. Now, once this is published up on the M Sphere website, at some point, our paper will show up here in latest articles, and we will be excited to be fully published and to have it available for anyone to see. M Sphere is great in terms of helping to get the word out about your paper. Mike Imperiale, who's the editor in chief, has a Twitter handle and he tweets out, I think, all the papers. And I think when we submitted there, I probably use the title as the tweet. I think that's a pretty effective title, right? If you can tweet the title, if you're tight, if you can, yeah, if you can tweet your title, that's probably a pretty effective title. Again, that would almost be the final thing to do is to tweet it to, you know, advertise your paper because, you know, the next stage after it's been published is kind of the marketing of your paper. And as we've said all along, your data don't speak for yourself, your paper won't speak for yourself. You've got to now kind of push and promote the paper. And it's great that M Sphere does a lot of work to help authors in kind of promoting their science. And I think again, that's the beauty of a society publisher like ASM. Anyway, I think this is the end of the story for now. I'm not sure that I'll do another episode on this paper. I really hope you've enjoyed following along and can celebrate with me that we've gotten this paper accepted and published. I've really appreciated all the feedback people have given me over the last year, as we've gone about, you know, doing the analysis, thinking about what the paper might look like, putting it together, submitting, responding to reviews, and now, of course, getting it published. I've always had great experiences with M Sphere and all of ASM journals. I have a bit of a conflict of interest because I'm the chair of the ASM journals committee. But to be honest with you, I would not be the chair of the ASM journals committee if I did not think ASM had a great product. This is not something I have to do. It's something that I really strongly believe in that publishing in a society publisher like ASM is the way to go. The value they add, we saw today in these proofs and that they really look good. And the copy editors do a really thorough job of making sure that the manuscript looks as good as it possibly can. So with that, thank you so much and stay tuned for more exciting episodes from Code Club where you'll learn all sorts of things about doing reproducible research in microbiology and biology in general.