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I am presently developing a handbook/manual based on our published methods in a not-open access journal. The content of the manual is different (i.e., format and structure) from the published version and we made a modification, for example, we structured our manual to a "recipe style" so it's easy to use and follow by users. We cited the original paper and we borrowed and cited some of the figures (and some new ones). I am wondering would it be against the journal policy if I do this? Or any advice about how I will handle this. We also plan to publish the manual through an organisation.

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would it be against the journal policy if I do this?

It is not against journal policy for

a handbook/manual [to be] based on...published methods in a...journal.

Indeed, anyone is free to write a handbook/manual based upon published materials. (Such a handbook/manual should not plagiarise, of course, and the OP has noted that the handbook/manual differs in content, format, structure, and style. Furthermore, the OP notes that the original sources have been cited.) Regarding,

we borrowed and cited some of the figures

You need to check this is permissible, it has been answered elsewhere on this site.

There may be other concerns, but the question doesn't raise them.

TL;DR: Write your handbook/manual as-if you didn't write the original sources.

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That would depend

  • on the particular journal/publisher policy
  • the exact ways you intend to reuse the material (figures only? >x% of the paper? only in English?)
  • the nature of your new publication (commercial, study material, report, etc)
  • whether the author of the new publication was a co-author of the already published one

Some publishers explicitly allow the re-usage of the materials by authors in non-commercial teaching materials, some would require you to request permissions, which might be granted for a price or free of charge.

For example, a screenshot from IEEE "Request Permission" form, which shows you the variables that IEEE, in particular, considers determining the price:

enter image description here

The other publishers would have similar policies; however, might not have a convenient tool for quick licensing and price estimation, – so you would have to contact them directly.

If you decide to reuse the figures, you certainly have to request permissions from the publisher. You would also have to do so if you decide to borrow large chunks of text from the published papers.

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