I am going to start work on the Materials and Methods for a paper I contributed to a lot in the bioinformatics processing part. I have seen some papers nowadays tend to first present the processing steps that they followed as a flow chart, to show the reader what happened generally before going into details in the written M&M section.

Are there any specific guidelines for creating this flowchart? Do you have any tips or advice from personal experience?

(I am aware that this may be off-topic. I have a meta question about it here)

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    $\begingroup$ Still waiting for the PLOS Computational biology "10 simple rules..." on this one ;) $\endgroup$ Dec 12 '19 at 17:02
  • $\begingroup$ I don't know... Is a flow chart actually better than a concise description possibly divided into sections with headers and bullet points? The flow chart you linked doesn't strike me as particularly clear or informative given it takes a full page with a big figure and a wall of text. (I'm not being critical I'm genuinely asking...) $\endgroup$
    – dariober
    Dec 14 '19 at 16:22

If you're using a workflow management system for pipelining like snakemake or ruffus, you can actually build a flowchart based on the rules/functions in your code:

Snakemake example with the --dag flag:

enter image description here

Ruffus example using pipeline_printout_graph:

enter image description here

You'll probably still need edit the image aftwards in software like inkscape or illustrator though.

  • 1
    $\begingroup$ I think it's better and easier to understand to make a more concise flowchart than this, and to just publish the code along with the paper. The first flowchart seems to list every single input on which the analysis was run. The second one is far too complex to read. $\endgroup$
    – Pallie
    Dec 13 '19 at 8:05
  • $\begingroup$ @Pallie agreed, the flowcharts can get quite complicated fast, or contain elements that you don't really need to show. You can edit them as suggested, but it would be nice to be able to display just certain parts of the pipeline in the flow chart as an option. $\endgroup$
    – Whitehot
    Dec 13 '19 at 9:15
  • $\begingroup$ Flow charts in vogue, when they are not ... reviewers are very quick to point this out $\endgroup$
    – M__
    Dec 13 '19 at 15:18

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