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@ annot : release 5.0.2 - compatible with acpipe_acjson fileformat library 0.1.17

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README.md

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## Version Log



+ **v0.5.02 - autumn alpha release 2019-10-31:** publication.

+ **v0.5.01 - autumn alpha release 2018-11-01:** publication submission.

+ **v0.5 - spring alpha release 2018-03-21:** acpipe acjson based reimplementation. more solid more flexible.

+ **v0.4 - midsummer alpha release 2017-06-21:** this is anNot.

man/man_reference.md

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This workflow representation gives an overview, how from a user point of view

experiments with annot are annotated.



![An! workflow](img/annot5_workflow_20190716_07.png "An! workflow")

![An! workflow](img/annot5_workflow_20190716_06.png "An! workflow")





Assay reagents and samples are first annotated via the annot web interface or via Excel spreadsheet that can be uploaded into annot. 

This annotation step enforces the use of controlled vocabulary and official gene, protein, compound and cell line identifiers. 

This annotation step enforces the use of controlled vocabulary and official gene, protein, compound and cell line identifiers (red arrows). 

Annotated reagents and samples are next combined into endpoint, perturbation, and sample sets. 

In this step, additional experimental details can be specified, for example reagent concentrations, cell seeding density, or cell passage number (red arrows).

In this step, additional experimental details can be specified, for example reagent concentrations, cell seeding density, or cell passage number (orange arrows).



For assays that involve robot pipetting, array spotting, or cyclic staining, super sets can be generated (light green arrows). 

Finally, for each assay run, endpoint, perturbation, sample and super sets are merged to a run specific assay layout (dark green arrows).



Assays and supersets that are regularly processes by the lab can be directly tracked in annot. 

There the exact data, protocol and the person who did the lab work can be specified. 

Lastly, assays can be grouped into studies and studies into investigations (blue arrows).

There the exact data, protocol and the person who did the lab work can be specified (blue arrows). 

Lastly, assays can be grouped into studies and studies into investigations (purple arrows).





## Docker and how the **annot** folder is structured