[ Comments passed along by Rodrigo Galindo-Murillo ]

• I would drop the text animations (text dropping down when appearing)
• There are multiple "tweaks" about the visual design that can be
  improved and are not necessarily critical, for example, removing the
  ISSN number from the welcome header, this information is correctly
  displayed in the About; the header image is way to large, it wastes
  useful space, The RSS feed should be divided in categories (blog,
  articles, news) so the user can choose.
• I am not sure if this is possible, but something to consider, the
  text should adjust to the size of the window, in 4 different devices,
  the text sticks to ~640 px, which wastes so much space in the side
  bars. Again, this is a question of learning how the content management
  system is working and adjust accordingly
• Footer; Include navigation links, useful when reading long tests and
  avoids scrolling up.
• Switch the drop window of text when clicking the Abstract link for
  articles. Redirect to the article's landing page instead.
• Instead of a single image, potentially have a carousel of images for the index site, each image showing an abstract of the different categories of the journal. This could
  alternatively also show recent articles in the future.
• Include feeds from social media (at least links).

Please change "Heather Mayes" to "Heather B. Mayes". Thank you!

Reading through "for authors", I am wondering what we want this to provide?
a) Instructions for authors?
b) Information for authors?
c) Both?

Right now it seems like a combination of all of the above, plus notes to ourselves. I THINK we should be going for "information for authors" with links to additional instructions they might need, and break off notes about how we do things to elsewhere.

I think we should break off the following as separate documents:

• Document preparation instructions: We can just have a one or two sentence summary of what needs to happen with a link to a detailed set of instructions that can be posted in the Editorial category
• It will be important for the document preparation instructions to note that accessibility to students is also important; this is the only part of the "review process" thing which will be especially important for authors to be aware of.
• Review process: Authors don't have to know how it works; instead we should have submission instructions, I think. These can be more brief. We can have a separate document describing the review process and how versions are reviewed.
• Getting credit for contributions/addition of authors: This is important, but it'll get overlooked here. We want it a separate document so it can receive careful treatment and be linked to from a variety of places, including from the versioning section of the revisions discussion.
• Policy on prior publication perhaps should also be moved?

One issue to be aware of with the website is that the text is fairly large, so relatively small amounts of content there can seem like a ton of text to read. So I'd try to keep it very concise. I think the essentials to keep here are:

• Quick intro as at present
• Before submission: Presubmission letter; use our LaTeX template and GitHub (link to document preparation instructions); note about accessibility to students
• Brief summary of submission instructions; link out to info on review process and info on how versions are reviewed
• Quick summary of goal of community contributions; link out to info on what warrants authorship
• Link to additional policies: Prior publication, licensing, ...

Process described here: https://clarivate.com/essays/journal-selection-process/ The form is here: http://mjl.clarivate.com/journal-submission/form/?

May be reasonable to apply for Emerging Sources Citation Index first, though there are a lot of predatory journals there.

I haven't gone though things in detail here yet.

New planned website is: https://journals.colorado.edu/index.php/livecoms

• Is there a way to customize what metadata appears on the article web page? (A: Not really, but it seems we can do everything we want to for now.
• Can we have the code repository appear on the article web page (A: can be added as a galley)
• Is there a way we can import author information from ORCID - seems like some permissions/account is needed? (A: No, it doesn't work that we, our way is fine).
• Registering isn't working currently? Answer: until website is unhidden, users need to be added manually.
• Is there a way to indicate "Blog Posts" as such (For example, putting the name of the article type at the top of the article section).

A policy is needed to handle this.

Right now references are by author, date, rather than by number. What would people prefer? I feel like in chemistry, its usually (superscript number), so that might be what people are more familiar with.

link to https://github.com/mobleylab/benchmarksets not working in .tex and .pdf

@davidlmobley @dmzuckerman @dwsideriusNIST

I will take charge of updating the editorial to use the mosts recent template version (I will work from the review template - maybe I should create an editorial template?)

What else should be changed besides the template? Things I noticed:

• How should we give the version for editorials since our version numbering mostly talks about reviewed version and whole number versions appearing. Is this article v2.0? Do we worry about versioning for editorials (seems maybe not, since they won't necessarily be maintained, nor are they peer reviewed?) But on the other hand, we are making tweaks to this document.

• We should add the lessons learned category @dmzuckerman, you want to add something on this?

• Any other publishing efforts we should talk about since then?

Otherwise, I think it holds up well for taking 18 months from then to get to publication.

Now that we have submissions coming in, we need to make sure the review form reflects what we want to have reviewers say.

You can see the current form if you log in to editor accounts (I think? Maybe only I can see, let me know) and look at
https://app.scholasticahq.com/journals/livecoms/settings?journal_settings_section=reviewer_form

Questions we can't change:

Overall Rating
Reviewer will rank from 1-5 stars.

For this manuscript I recommend...
Reviewer will choose between Accept, Revise and resubmit, and Reject

Comments to editor
Reviewer will be provided a blank text area to fill in.

We can add/change yes/no questions, and open response questions. All added questions will be required. The current default questions are (only editor sees the answers unless indicated otherwise).

• "The paper makes a significant contribution to scholarship" (yes/no)
• "The paper adequately engages with the relevant scholarly literature" (yes/no)
• "The paper is professionally written, easy to read, and free from grammatical errors" (yes/no)
• "The literature review was thorough given the objectives and content of the article" (yes/no)
• "Comments to the author" (open response, can be seen by author)
• "Is the content of this article appropriate for this journal (open response)

I will update this issue with different questions I propose asking during the morning. Please add any suggestions.

[Communicated from Rodrigo Galindo-Murillo]

This is: have a logo, a color palette and a series of design rules.
the audience will feel more identified with the journal, and hence,
the main objective of it. Think of the JCTC logo, or the overall
image of the Royal Society for all their journals. You immediately
know what is it about when you get a glimpse of their covers. This is
not urgent but would enhance the journal's seriousness. Another
example that I think is also a success is the strong visual image of
all the "Frontiers In" journals.

Just some things and possible improvements I noticed between viewing an article on PLOS and on our site.

Pros

1. The PDF viewer / integration with Firefox looks great.
   • I really like the way that is set up on our site.
   • Very pleasing to view compared to the html interactive view that defaults for PLOS
2. The longer we can prevent advertisements the better, looks very jarring when viewing PLOS.

Cons

1. The top of the page when viewing an article on LiveCOMS seems out of place. I feel like our logo should be bolder/bordered so the user can recognize that it is a link to the landing page.
2. When scrolling through an article on plos, the title and authors travels with the scroll.
   • See this PLOS example
   • Compared to our current view

Improvements

1. Change the logo when viewing an article to look more like a link/not blending into the background
2. Have the title, authors, link back to the landing page, and a download pdf button follow the user at as they scroll through an article.
   • Add an option to remove the dynamic bar if the user would like (small x in the top right)

I am unsure how difficult/possible this is to implement with our journal.

We should put the section editor contact info on the journal website somewhere now that we have it (putting this here partly so I don't lose the addresses):

[email protected]
[email protected]
[email protected]
[email protected]
[email protected]

Presumably also this should go somewhere on livecomsjournal.github.io as well.

The https certificate of livecomsjournal.org is not valid:

www.livecomsjournal.org uses an invalid security certificate. 

The certificate is only valid for the following names: *.scholasticahq.com, scholasticahq.com 

Error code: SSL_ERROR_BAD_CERT_DOMAIN

Related: livecomsjournal/livecomsjournal.github.io#53

There some discussion for the need for licenses that allow the data to in preprints to be scraped and processed. Need to think about licensing a bit more to make sure that we make it properly general. The current plan to have CC-BY 4.0 sounds good for now, will have to keep thinking about it.

As noted livecomsjournal/livecomsjournal.github.io#63, the editorial board is not correct. (And the formatting is still not good).

I tried to address this in a PR recently but presumably @mrshirts still needs to propagate my new content or something; checking master now.

[ Communicated from Rodrigo Galindo-Murillo ]

• The landing page for each article should be redefined. Even though
  the PDF is displayed, there are multiple items that we can show to
  enhance usability and experience.

At least two people have their papers ready for submission, so we need to make sure the process is set up.

I did a beta test of the submission process to get ready for submissions (at https://app.scholasticahq.com/journals/livecoms/manuscripts/new). I will submit an issue later today with specific changes to the text later today, but might get pulled away to tend kids / do yardwork before I finish, so you can provide preliminary comments to the issues.

As far as I can tell (I have a question in with the Scholastica team, but it might not get answered over the weekend), you can't really customize the submission forms themselves; if we want to provide extra guidance, it needs to be on the http://www.livecomsjournal.org/for-authors page, which is linked back from the submission page. We should provide specific guidance for this on the for-authors page. I suggest that instructions about the SUBMISSION FORM should be on the journal web page, where it can be easily references, but detailed instructions about he content of the paper can be on the

Things submissions asks for (all required unless noted)

• Import from arXiv yes/no (we want no for now).
• Title
• Abstract
• Keywords
• Primary Manuscript File
• Supporting files (optional)
  *Author details (First name, last name, email, Institution, Department ORCID iD - only last and first name are requried)
• Add additional authors. (There is no way to indicate equal contributions: we should probably do it though required acknowledgements sections).
• Review information: open form text field for suggested reviewers, and reviewers to avoid, with instructions to list names and institutions. (optional)

Guidance that we should add:

• A request to upload as a supporting file a picture (at least 300 x 200) that will appear on the articles front page (letting them know that it will appear whenever the article is shared). We suggest something evocative of the research, but containing less scientific detail than a table of contents page at, say, and ACS journal. POSTING the article requires a picture, so we might as well ask for it at submission.

• Word limit on the abstract (300 words?) Should it include the address of the github site?

• Guidance for keywords. Not really sure what to tell them. The only keywords we really need is what topic it is, but that should be clear from the presubmission letter. Keywords are required, so we could have them submit the article section (we provide the list for the right phrasing), and five others of their choice?

• Naming convention for supporting files and which files to include I imagine in general there wouldn't be any supporting information text (should probably all be in the main file?), but they might want to provide supporting information input files. Those should probably be in a archive. Right now, the files can only be *.aac, *.avi, *.csv, *.doc, *.docx, *.flac, *.gif, *.html , *.jpeg, *.jpg, *.key, *.m4a, *.md, *.mov, *.mp3, *.mp4, *.mpeg, *.mpg, *.odt, *.pdf, *.png, *.pps, *.ppt, *.tex, *.tif, *.tiff, *.txt, *.xls, *.xml, *.zip. So we can give instructions for making a .zip of input files with a README, etc. I would imagine movies are fine as well. Any other instructions you can think of for supporting information?

• Obviously, primary file would only be .pdf.

Information is here: https://doaj.org/publishers#applying, application form here: https://doaj.org/application/new#digital_archiving_policy-container

Looks like we will need to have at least one issue published. 5 articles per year is minimum, so we should be OK.

Specific points we may need to improve on (I think the rest are already satisfied)

All the necessary journal business information pages (by 'business information pages', we mean the journal's aims and scope, the editorial board, the instructions for authors, the description of the quality control system, the Open Access statement, the plagiarism policy, and the licensing terms) must be hosted on this same site and not be held centrally on another web site, or must be prominently linked to from the journal's homepage. This is a basic requirement for entry into DOAJ

I think we are OK on this with the secondary GitHub site, since it is prominently linked from the journal's homepage.

We strongly recommend that your content is preserved in a dedicated, digital archiving and preservation service, sometimes referred to as Long Term Preservation and Archiving (LTPA). You can find a list some of these services here.

Not a requirement but something we should look into.

Having detailed and comprehensive guidelines for authors (Instructions for Authors) is a good way of helping potential contributors. A link to these guidelines must be clearly presented on the journal's homepage. This is a basic requirement for entry into DOAJ.
We recommend that author guidelines include the following information:
A detailed style guide;
A description of the quality control processes;
Information about copyright (please note the importance of informing authors about whether the journal will be the copyright holder after publication of an article or if the copyright remains with the author(s). We strongly believe that authors should be informed about your copyright/licensing conditions before they submit their work);
the plagiarism policy;
description of how to submit an article;
a contact email address.

I think we have all of this, but will need to check, for example, and explicit plagiarism policy

Open Access statement: The journal's Open Access policy must be clearly stated on the journal's web site (not the publisher's own site). It should also be linked to from the home page. The full text of the articles of the journal should be freely available without embargo.These are basic requirements for entry into DOAJ.

DOAJ will accept a short open access statement—even as short as ‘This journal is open access.’—but ONLY in combination with a Creative Commons licensing statement, or equivalent licensing statement, on the same page and, preferably, in the same paragraph. If the licensing statement is not on the same page as the open access statement then the extended open access statement complying with BOAI definition will be required.

Not sure we have an explicit one, we will need to make sure this matches. Just a matter of getting the language right.

Licensing your material with a CC license: An optimum way of showing exactly how a journal is Open Access is by licensing the content with a Creative Commons (CC) license. DOAJ considers the application of a CC license, or its equivalent, as best practice. Such licensing is very beneficial for authors since it shows, for example, if there are any limits in creating derivative works. Read more about applying licenses and copyright on our Copyright and Licensing Help page.

Basically, we do this, but may need to make it more explicit. A little complicated since we don't actually have any copyright, we just ask that the articles are licensed to us. Will have to look into this. Looks like they do consider the case of authors retaining rights but I'll need to look into it further.

It is recommended that publishers make use of one of the several plagiarism detection services that are available. Plagiarism is a big problem and plagiarised articles on a web site are often an indicator of a poor quality journal, or a journal that uses no quality control system. You should publish a plagiarism statement on your site, as well as the name of the piece of software that you use to detect plagiarism.

We will need to look into this - at least an explicit statement.

They currently say it is taking up to 6 months to make a decision on an application or update request.

WE should check with Scholastica about how to upload journal metadata.

When applying for a journal to be included in DOAJ, one of the questions asks whether or not you have machine-readable licensing information embedded in your article metadata. There are guidelines on the Creative Commons web site that tell you more about this. The information must be embedded in the HTML, the XML or the PDFs. Sometimes, it will be embedded in individual article components too, such as an MP3, an image or a video. The emphasis for DOAJ is not HOW the license is embedded but that there IS a machine-readable version of it. Here are a couple of examples:

We should also check about how to add the machine-readable licensing information.

If you have ideas for how to improve the webpage, please make them as comments in this issue thread.

Note that if you have specific changes to text on the website, it should be filed as an issue to the respective Markdown page in this repository.

details here: https://www.ncbi.nlm.nih.gov/pmc/pub/addjournal/

One scope question "The journal must publish generally within the biomedical and life sciences,". I think we probably apply, since many articles will be about biophysical simulations.

Also note:

A journal must provide PMC with the full text of articles in an XML (eXtensible Markup Language) format that conforms to an acceptable journal article DTD (Document Type Definition) and meets the PMC Minimum Data Criteria. PMC does not accept articles in HTML format.

Something like this could be possible (https://en.wikipedia.org/wiki/LaTeXML), but will require investigation.

Usually they expect 2 years, but: "NLM may consider an application from a publishing organization that has been publishing scholarly content for less than two years if there is evidence that the management and individuals responsible for editorial quality and operations have adequate experience in comparable positions at other organizations."

Is unclear that we qualify, since it's not clear we have the adequate experience in operations :)

There's quite a lot of work here, since a full submission requires ~50 articles worth to be uploaded for verification.

• Send URL to Library of Congress when first issue is published, in accordance with the requirements for the temporary ISSN

Anyone want to take a shot?

• Likely, much of the detailed instruction will remain at https://livecomsjournal.github.io/, since we can edit it more easily. It could be useful to match that aesthetic in the main OJS-hosted main website.
• It would be useful to have a way to label the type of "announcement" as such. Existing announcements are given the category of "Blog Posts", but that doesn't appear next to the announcement. For example, putting the name of the article type at the front of the article. (MRS: very hard to do this with just CSS).
• Better header at the top of the web page. Images found on https://www.livecomsjournal.org/ can be used (except the individual articles ones). (MRS: I made this work bit better with CSS, now ALMOST full screen. I don't think the border can be eliminated with just CSS.).
• Make the PKP image in the footer, smaller, inline with the text (MRS: Done!).
• Change dates of release on blog posts on first issue/second issue/etc. (MRS: Required a database change, but done!).
• Larger, perhaps cleaner font (see https://livecomsjournal.github.io/ for a cleaner aesthetic). (MRS: I've made some changes, bumping up sizes of fonts a bit and reducing the amount of whitespace between lines sometimes?).
• Remove article number from the issue display (currently, they are on the far right of the article window) (MRS: probably can't be done with just CSS)
• Can the images be made larger in the article views? (like on https://journals.colorado.edu/index.php/livecoms/article/view/1113). Right now, they are small on the upper right, below the title. Perhaps bigger, centered at the top of the article, right below the title? (MRS: this could probably be done with some CSS work).
• In the main issue view (https://journals.colorado.edu/index.php/livecoms/issue/view/105), could some sort of cropping be done so that the images are more uniform in size, or different in size? (MRS: looks like could be done with some CSS work, but messy. Not clear the right choice)
• Spacing on https://journals.colorado.edu/index.php/livecoms/announcement looks really bad. (MRS: I made a few tweaks of whitespace/font size that should help a bit)
• Can we set it so browsing is by issues as well as categories? (MRS: this is now implemented, see how it looks!)
• Add an embedded twitter feed (MRS: Working now!)
• Can we get rid of the color around the cover image (MRS: no, not for now, not without some CSS work on the template. We could maybe blend it in a bit more with an image program beforehand).
• Is the title a bit blurry? (MRS: I could possibly redo it as a PNG, not sure if that would change things, probably is OK?).

Now that livecomsjournal/livecomsjournal.github.io#86 is merged we should link to the bylaws from the website.

which has instructions/checklists (that is, more of a "how do I actually do this?" guide with less about "how will the review process work?" than the "For authors" section. Some of current "for authors" section should be moved here.

The contact email address in the About section links to @mrshirts email address. However, on our github page, we have an email address for livecoms ([email protected]).

Should this be updated, or is that email address serving some other purpose?

If so, I can quickly change that and make a pull request.

There's been some discussion, if we are going to compare performance, that we have a community organized set of simulations for benchmarks. This would probably actually be a paper developed by authors, but the journal editorial board might need to be involved to help it along.

Comment from twitter: The submission fee is not listed on livecomsjournal.org and should be. :)

(Not sure the issue belongs here.)

Currently, we have:

https://livecomsjournal.github.io/policies/reviewer_information/

Which gives some reviewer information, but from the perspective of the editors. I'd like to turn this page into an actual reviewer instruction page. The biggest change will be to remove the sample letters, and maybe move them to journal_information repository (this one). Note that the letter templates themselves are saved in Scholastica where they can automatically be inserted via email, and the copies here will serve as a place where we can discuss the templates

I'm not sure we need to include the exact letters that we will use for invitation/declining/etc., as long as the information is communicated. I don't think we are being less transparent not including the exact phrasing, and it looks a bit weird.

The "about the journal" page needs links to, er, expanded info about the journal -- probably the "Why LiveCoMS" document as well as the "paper-writing as code development" document, and a brief explanation of the fact that most of the info is at livecomsjournal.github.io.