@ man : evolutiomn

1. populating annot with backed up sample and reagent bricks.

1. populating annot with backed up study and investigation information.

1. populating annot with backed up experiment layouts

  and layout one acxis by set yourself.

  and layout one acjson by set yourself.

1. populating annot with backed up tracking information.

1. backup the work done.

## Controlled Vocabulary

---

### Enter An!

### Enter annot

1. `docker-machine ls` lists all the installed docker machines.

1. `docker-machine start an0` starts the an0 docker machine, if needed.

  first, when you completely fresh set up annot, reload the backups from all

  own ontologies before you run the cron_vocabulary.sh shell script. otherwise

  you will end up with own ontologies with no content!

1. run `nix/cron_vocabulary.sh` This shell script back up each and every

1. run `nix/cron_vocabulary.sh` This shell script backs up each and every

  vocabulary one by one. But, before it backs up a vocabulary, it tries as good

  as it gets to update the vocabulary to the latest version by first generate

  for an own ontology an origin ontology from the table content, then reloading

  the latest backup, then for a non-own ontology fetching and loading the latest

  origin version online. After it did so it will backup. if it not can download

  an origin version it will just step on with backing up and then with the

  next vocabulary.

  for an own ontology an origin ontology from the annot database table content,

  then reloading the latest backup, then for a non-own ontology fetching and

  loading the latest origin version online. After it did so it will backup.

  If it not can download an origin version it will just step on with backing up

  and then with the next vocabulary.

Now let’s find out with which ontologies and version annot's vocabularies

were populated.

  (primary antibody, secondary antibody, compound stain, compound, protein, proteinset and homo sapiens sample).

  Additionally you can download related bricks form the investigation, study,

  assay run and acaxis layer. From there the bricks are downloadable in the

  assay run and acaxis layer. From there the bricks are downloadable in

  annot's json and tsv standards and additionally in the

  [lincs data standard](http://www.lincsproject.org/LINCS/data/standards).

  The lincs data standard contains not all stored brick information.

  were you from now on can brick bricks by GUI.

    1. choose the brick types you like to brick by clicking the box in front of it.

    1. in the `Action` drop down list choose `Upload brick` and click 'Go'.

    1. in the `Action` drop down list choose `Upload brick` and click `Go`.

1. let's go back to `Home › Appsabrick`

1. click the `Uploaded endpoint reagent bricks` or `Uploaded perturbation reagent bricks` 

---

Annot provides you with a super flexible way to layout any biological experiment.

In a first step the three major axis from each biological experiment

- sample, perturbation, endpoint - are layouted on the acaxis layer.

In a first step the three major axis from each biological experiment - sample,

perturbation, endpoint - are layouted on the acaxis layer.

Then this axis are pulled together on the assay run layer.

For example, let's layout a lapatinib perturbation:

  If you can not find lapatinib in the list because the list is still empty,

  remember that you first have to brick the bricks that they become accessible

  for layouting. Do so. Then the brick should appear in the drop down list.

  In this example we will only layout an lapatinib perturbation. If you would

  In this example we will only layout a lapatinib perturbation. If you would

  have to layout a 384 well plate with dozens of different perturbations keep on

  selecting all the reagent bricks you need.

1. click `Save`

python3 on your computer and an additional python3 library called

[acpipe_acjson](https://pypi.org/project/acpipe-acjson/) to run this code.

1. How to install `python3` depends very much on the operating system you are running.

1. How to install `python3` depends very much on the operating system you are

  running. Just do it.

1. After you have installed python3, you can install acpipe_acjoson by running

  `pip3 install acpipe_acjson` from the command line.

  you see with a `#` hashtag in front is not interpreted by the computer.

  Programmers call such a line "commented out".

The *second part*(:

The *second part* loads the libraries needed to interpret the program beside

the python3 standard library. Those libraries are copy, json and acpipe_acjson.

  ```

  # python library

  import copy

  # check out: https://gitlab.com/biotransistor/acpipe_acjson

  import acpipe_acjson.acjson as ac

  ```

  Loads the libraries needed to interpret the program beside the python3

  standard library. Those are copy, json and acpipe_acjson.

The *third part* builds an acjson object. Acjson stands for *assay coordinate java script object notation*.

  Acjson is the format we will use to layout the entire experiment.

  based on the setname meaning full `s_runid`, `s_runtype` and `s_log`.

  However there are some `?` questions marks in the code. This is because

  annot had no idea which wellplate layout you will use for the experiment.

  You could for example have use a 384 wellplate (16x24) or a 96 wellplate (8x12) 

  You could for example use a 384 wellplate (16x24) or a 96 wellplate (8x12)

  or petri dish (1x1) or a tube (1x1). Actually because we will treat all

  our wells with the same lapatinib concentration we can in any case pretend

  we will use a petri dish layout. So, by `s_welllayout` please replace

  human readable output. However, the resulting file will as well take

  more disk space then a file without indent.

1. to upload the generated ac file

1. to upload the generated acjson file

    1. click the cyan `Set of Perturbation` link.

    1. then click the `ds-lapatinib1v1` link.

    1. then click the `Browse…` button.

      turn blue and get a tick.

    1. in the `Action` drop down list choose `Select selected set's acjson file against brick content`. 

      You should receive a message "Ds-Lapatnib1v1 # sucessfull checked.".

      Or a Warning or Error when something for annot not totally is as expected

      Or a "Warning" or "Error" when something for annot not totally is as expected

      with the uploaded acjson file.

When everything worked as expected, then it is now time to store the modified

    1. click on your `username`.

    1. You will see a list of all informative fields stored in an acjson. By

      clicking the boxes you can choose which one of those you like to

      have outputted, when you download a `tsv_long layout` file,

      have outputted when you download a `tsv_long layout` file,

      a `tsv_stacked datafarme`, or a `tsv_unstacked datafarme`.

    1. in the `Action` drop down list choose `Download select selected sets as tsv_long layout file`.

      This will generate a bunch of layout file with the reagent names and all content chosen in the AcjsonToTsv settings.

1. Downloading `dataframes`. Dataframes are tsv in a format easy to upload into

    [pandas](https://pandas.pydata.org/) or [R](https://cran.r-project.org/)

1. Downloading `dataframes`. Dataframes are tsv files in a format easy to upload

    into [pandas](https://pandas.pydata.org/) or [R](https://cran.r-project.org/)

    1. click on the cyan `Set of Perturbation` link

    1. click in the box in front of the `es-1layout2v3` row. This is a simple

    For a simple 384 well screen generating a dataframe is still done in

    ok time using the browser GUI. But for example the mema assays runs

    we uploaded during this tutorial will take far to long till they are

    we uploaded during this tutorial will take far too long till they are

    generated that you want to do this via browser GUI. An acjson file

    from such a mema 8 well spotted array screen has 5600 coordinates.

    To generate an unstacked dataframe from such an acjson will take about