Provide definitions as part of documentation

Hi there -

I have been trying to implement your virtual-flow system. I appreciate your efforts in setting this up and showing that it can work.

One of my barriers to implementing it for my system is a lack of definitions in the documentation.

Terms like ‘step’, ‘collection’, ‘queue’, ‘job’ all appear to be important to know how to set variables in the all.ctrl file, yet I haven’t been able to find the exact definition for these terms. I have spent the past several weeks guessing at what they may mean based on posted examples but haven’t made much progress.

Perhaps a page of very well described definitions and suggested guidelines for ranges on these variables would be helpful here. I realize that some of this available as comments throughout the file - but these are easy to miss and for some when I have inquired it seems that they have no consequence. It has been a little bit frustrating trying to understand what should be changed.

Many thanks for your contribution to open-source highthroughput screening and looking forward to more great work from the virtual-flow team.

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Inside the tutorial there is some explanation of these terms, altough i dont know, for instance, why they use step for a node

Hi Byron,

Thank you very much for the feedback, we appreciate it.

We recognize that some terms used in the documentation could be explained more clearly.

“Job” and “step” are terms which come from the batch system (e.g. SLURM), and were not created by us. There is a lot documentation about these terms provided by the SLURM developers, but by testing and using the SLURM cluster and can get also a better feeling by experience what exactly these terms mean. If you are new to computer clusters and supercomputers, it is normal that this process takes a bit of time.

What a collection is can be understood better for example by exploring the structure of ligand library, and the documentation: https://docs.virtual-flow.org/documentation/-LdE8RH9UN4HKpckqkX3/principles-and-theory/naming-conventions

Also Supplementary Figure 9 in the publication defines what a collection is:

Screenshot at 2020-08-22 15-06-40

Again, thank you for your feedback, which will be helpful when we continue to improve the documentation in the coming time.

Best,
Christoph

But,I cann’t open the link of collection: https://app.gitbook.com/@virtualflow/s/documentation/principles-and-theory/naming-conventions
image

@chunqiongli: Thank you for the hint, I have corrected the link in the above post ( https://docs.virtual-flow.org/documentation/-LdE8RH9UN4HKpckqkX3/principles-and-theory/naming-conventions )