Experimental Data

At the moment it is possible to include the following types of experimental data with your model tests.

  1. Growth data, for example, processed Biolog data, that lists whether growth was possible in different media.
  2. Gene essentiality data that lists for a single gene identifier whether it is essential, i.e., a knock-out is lethal, or not.

In order for memote to make proper use of your data, you should add them to the repository. If you use memote new to generate the repository structure, take a look at the files under data. It should look like this:

data
├── essentiality
├── experiments.yml
├── growth
└── media

Configuration

In order for anything to happen you have to edit the experiments.yml configuration file. The provided file contains a minimal setup but does not actually define any experiments.

version: "0.1"
medium:
  path: "media/"
essentiality:
  path: "essentiality/"
growth:
  path: "growth/"

The file simply states that files relating to media, essentiality, and growth experiments can be found at directories stated under path: relative to the location of the file.

Media

You can fill the configuration with life by adding medium definitions and experiments. So you could add:

medium:
  path: "media/"
  definitions:
    m9_minimal:

which by default would look for a medium file media/m9_minimal.csv. Definition keys need to be valid YAML keys. In addition to CSV, other data formats such as TSV, XLS or XLSX are also allowed. You can specify the filename which also allows you to use a different name, although that would probably be confusing.

medium:
  path: "media/"
  definitions:
    m9_minimal:
        filename: "minimal.xls"

Additionally, you can add a convenient label.

medium:
  path: "media/"
  definitions:
    m9_minimal:
        filename: "minimal.xls"
        label: "M9 minimal medium"

Format

A medium is defined by a tabular format with the following columns. A ‘comment’ column is allowed for your own convenience but no entry is required.

exchange uptake comment
EX_glc_e 10  

Each row must include the exchange reaction identifier and an uptake rate between 0 and 1000.

Growth

Growth data are included under the key experiments:. It works similarly to media but allows a few extra definitions.

growth:
  path: "growth/"
  experiments:
    my_growth:
      filename: "my_growth.csv"
      medium: m9_minimal
      objective: Biomass
      label: "Exhaustive carbon growth"

Again, each experiment should have a unique key. By default, memote will look for a relative CSV file of the same name. The specified medium refers to a medium key. The objective, for the moment, should refer to a reaction identifier such as that of the biomass reaction or ATP formation. Again, a more expressive label can be given.

Only the experiment key is really required as the default filename, medium, and objective may be used. However, growth data typically vary the carbon source which is not reflected by the default medium. This will become more clear when looking at the format.

Format

exchange uptake growth comment
EX_glc_e 10 yes  
EX_glc_e 0 no  

For the tabular growth data, each row represents one data point with a binary outcome. In order to take full advantage of this format it makes sense to define a minimal medium without any carbon source. That medium will be used as the basis and the exchange specified in each row of a growth experiment will be set in addition to the base medium. That means if you rely on the default medium you will likely end up with multiple carbon sources. The binary outcome in the ‘growth’ column will be compared to the model predictions. Any one of the following values is recognized: “true”, “True”, “TRUE”, “1”, “yes”, “Yes”, “YES” and “false”, “False”, “FALSE”, “0”, “no”, “No”, “NO”.

Essentiality

Essentiality experiments can be defined in the same way as growth experiments but the medium entry is interpreted differently.

essentiality:
  path: "essentiality/"
  experiments:
    knockouts:
      filename: "knockouts.xls"
      medium: glucose
      objective: Biomass
      label: "knock-out library"

Unlike for growth experiments, in the case of essentiality experiments the same medium is used in each individual gene deletion experiment. If you have knock-out experiments performed in different media, simply define the media and define one essentiality experiment for each medium.

Format

gene essential comment
b0025 yes  

An essentiality table should define unique gene identifiers as they are specified in the model. At the moment, only single gene deletion experiments are supported. The binary column ‘essential’ allows the same values as the ‘growth’ column above. Again, in silico deletion outcomes are compared to the provided ones.