Prepare Metadata

Table of Contents


AMiGA can process one or multiple data files in a single command. These data files describe the optical density (or any other unit of measurement) in wells of one or more plates at different time points. AMiGA can analyze your data and report its results in text files where each row is a well and columns correspond to different summary metrics or growth parameters.

If you want to take advantage of several unique features of AMiGA, you should also pass meta-data or information about your plates or the specific wells in those plates. This can be done automatically by AMiGA if it recognizes that your data corresponds to a specific Biolog PM plate.


The main types of mapping files auto-generated by AMiGA

In the case of no meta-data available for a plate, the minimal internal mapping file generated by AMiGA will look like this:

  Plate_ID
A1 ER1_PM2-1
A2 ER1_PM2-1
… …
H11 ER1_PM2-1
H12 ER1_PM2-1


If it however recognizes the plate as a specific Biolog PM (based on its data file name), the internal mapping file generated by AMiGA will look like this:

  Plate_ID Isolate PM Replicate Substrate Group Control
A1 ER1_PM2-1 ER1 2 1 Negative Control 1 1
A2 ER1_PM2-1 ER1 2 1 Chondroitin Sulfate C 1 0
… ER1_PM2-1 ER1 2 1 … 1 0
H11 ER1_PM2-1 ER1 2 1 2,3-Butanedione 1 0
H12 ER1_PM2-1 ER1 2 1 2-Hyrdoxy 2-Butanone 1 0


The main types of user-generated mapping files

If you have a mapping file that describes the wells in each of your plates, you can easily pass these descriptions to AMiGA by saving them in the mapping folder. This is recommended for data files that do not correspond to a standard plate of 96-wells. Here is an example for a hypothetical mapping for growth in only 8 wells of data\CD_treA.txt and saved as the mapping\CD_treA.txt file. AMiGA will only match mapping and data files if they share the exact file names. You also must make sure that the index (first) column (i.e. well IDs) matches exactly the index column in the corresponding data files. Please save mapping files as tab-separated text files.

  Plate_ID Isolate Substrate Ribotype Comments Group Control
A1 CD_treA CD89_wt Negative Control RT027 Wild-type 1 1
A2 CD_treA CD89_wt Negative Control RT027 Wild-type 1 1
A3 CD_treA CD89_wt D-Trehalose RT027 Wild-type 1 0
A4 CD_treA CD89_wt D-Trehalose RT027 Wild-type 1 0
B1 CD_treA CD89_ko Negative Control RT027 treA knock-out 2 1
B2 CD_treA CD89_ko Negative Control RT027 treA knock-out 2 1
B3 CD_treA CD89_ko D-Trehalose RT027 treA knock-out 2 0
B4 CD_treA CD89_ko D-Trehalose RT027 treA knock-out 2 0


Note on Group and Control columns:

In growth assays, researchers will often have multiple wells that correspond to negative controls. These control wells may correspond to blank media or growth of a negative control (e.g. wild-type vs mutant). AMiGA users can indicate which wells correspond to controls using the Control column in the mapping file. If there are different groups of samples with unique group-specific controls, AMiGA users can further discriminate these group with the Group column. In the above example, the Fold Change for rows A3 and A4 will be based on the average of the maximum OD values for A1 and A2, while the Fold Change for rows B3 and B4 will be based on the average of the maximum OD values for B1 and B2.


Note on column headers:

Users must avoid passing meta-data with specific column headers unless they are used as indicated above. In particular, Plate_ID,PM,Rep,Isolate,Substrate,Group, and Control are used by AMiGA as desribed above. Subset and Flag are used by AMiGA for selecting samples for analysis. If users pass meta-data in these columns for other purposes from what is indicatd here, AMiGA would likely be conflicted and analysis would fail.


How to use a meta.txt file?

Short answer: In a “mapping” file, each row describes a specific well. However, in a “meta.txt” file, each row describes a specific plate. When AMiGA reads the below example table of meta.txt, it will internally create eight distinct “mapping” files, one for each row of information in meta.txt.

Long answer: If you have a table that describes multiple plates in your data folder, you can thus easily pass its information to AMiGA as the mapping\meta.txt file. For each plate, AMiGA will generate a plate-specific mapping file based on the content of this mapping\meta.txt file. If a specific plate listed in mapping\meta.txt is a Biolog PM, make sure to include a PM column with values between and including 1 and 7 and accordingly AMiGA will auto-generate a Substrate column in the plate-specific mapping files. mapping\meta.txt must include a Plate_ID column that matches the name of the data file (without the file extension). Using the mapping\meta.txt file, AMiGA will automatically generate individual mapping files for each plate unless an individual mapping file has already been provided by the user in mapping folder. Please save mapping\meta.txt as a tab-separated text file.


Plate_ID Species Strain PM Isolate Replicate
ER1_PM1-1 E randomii USA 1995 1 ER1 1
ER1-PM2-1 E randomii USA 1995 2 ER1 1
ER2_PM1-1 E randomii USA 1995 1 ER2 1
ER2_PM2-1 E randomii USA 1995 2 ER2 1
ER3_PM1-1 E randomii MEX 2019 1 ER3 1
ER3_PM2-1 E randomii MEX 2019 2 ER3 1
ER4_PM1-1 E randomii MEX 2019 1 ER4 1
ER4_PM2-1 E randomii MEX 2019 2 ER4 1


This approach can be very useful if you are processing Biolog plates where you want to describe the isolates in more details. As shown above, we include information about the species and strain designations for all isolates. We can accordingly use these meta-data labels for hypothesis testing.


Mixed use of mapping and meta.txt

You can pass mapping information using a mixture of the above options. You can have individual plate-specific mapping files in addition to a mapping\meta.txt file. However, a user-generated plate-specific mapping file will always supersede and over-ride the plate-specific info in meta.txt.