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Documentation


How this documentation works

Before we dive into this documentation, let me have a word. This documentation is interactive and responsive. This means the following: I included a lot of example pages that change their layout with the screen size (just as the original pages will do) and that include some additional explanations. Basically, all the stuff that is highlighted in green gives you some further explanation once you hover over it.

If you still have questions after reading this documentation, feel free to ask me.


Table of contents #

    Media components Database structure The medium overview page Medium similarity Find media based on components Find solutions with the solution finder Stock solutions The solution comparison tool Download content Link to BacMedia

Media components #

A medium generally consists of various building blocks, which we call solutions. Each medium contains at least one solution, but it can also contain over ten solutions. A solution, in turn, may contain ingredients as well as other solutions. In addition, solutions often contain instructions on how to prepare them and what to pay attention to.

The following is a brief explanation of the most important types of solutions.


Main solution

Each medium contains a main solution. It is the starting point for preparing a medium, always comes first in the recipe, and serves three important functions:

  1. The main solution contains all the steps, ingredients and solutions needed for the medium itself. For example, if a medium contains many solutions, they are gathered here and indicated in what quantities they are used. This is to simplify the preparation of the medium.
  2. Strain-specific adjustments are mainly made here. If a strain requires additional ingredients, they will be added to the recipe at this point. This is important because some other solutions are used for multiple media, but the customization is only for one specific strain. The main solution is unique for each medium.
  3. From the main solution, in turn, you can reach all other solutions. This is important for the calculation of the media composition, which is done automatically.

Reference solutions

Reference solutions are used in many media. For this reason, they have a special role within BacMedia. These are often trace element solutions or vitamin solutions.

  1. Reference solutions get their own ID to be found quickly. This ID starts with an RS.
  2. Reference solutions can be used in the medium finder to find media.

Normal solutions

These are all other solutions that have no special role in BacMedia. They are not the main solution of a medium, but are still needed only for that one medium. These solutions can also be redundant, since this is not automatically resolved. They are sometimes numbered with letters, e.g. Solution A.

.

  • Medium

    • Main solution
      • /
        Solutions
        • | | |

      • Ingredients

      • Steps

    • Meta data

Database structure #

The above structure resulted in the following database schema:

DB Scheme

The medium overview page #

This page is the center piece of BacMedia. It displays basically every information we have for the selected medium, e.g. all corresponding solutions, the recipes, and instructions.

A toolbox on top helps you navigate through media, see all BacDive strains that grow on this medium, adjust the final volume of the medium by a fold-change, or download the medium recipe as PDF. On the left-hand side, the medium recipe is listed. You find the name of the medium and some additional information, e.g. the final pH. Some general remarks are shown below, if there are any. Then follows a list of all solutions needed to prepare this medium. This list starts with the main solution. From here on out, all other solutions and ingredients are listed, meaning if you want to prepare a medium, this is the right place to start. On the right-hand side, additional information is given, e.g. the final medium composition, cultivation metadata and the gas composition.

If you have questions regarding the media or the interface, feel free to contact me.

Example

42. MEDIUM NAME


Defined medium pH 7

Solution A #

1000

Medium similarity #

BacMedia suggests media that are similar to the one you are currently looking at. We used cosine similarity ( Wikipedia) to estimate how similar the media from our database are. Thereby, not only ingredients but also their molecular concentrations in the final medium are considered. The color of the arrow indicates how similar the media are:

  • over 90 %
  • between 90 and 70 %
  • between 70 and 50 %

Find media based on components #

This tool helps you to find a medium based on its ingredients. You can also define concentration ranges for each compound. Only media that fulfill all your requirements are shown.

Example

In the following example, we are searching for all media containing 2 – 10 g/L glucose and any concentration of MgCl2:

Medium finder

Compound Min. conc. Max. conc. Unit
Glucose 2 10
MgCl2
+ Add compound Search

Search result

Searched compounds: Glucose MgCl2
Your search received 7 results.

100: Another medium

Compound Amount [g/L] Concentration [mM]
Glucose 1.5 8.3
MgCl2 0.33 3.463
Go to medium
...

Find solutions with the solution finder #

This tool helps you to find a solution based on its ingredients. You find the button to toggle the Solution finder on the Solutions page in the toolbar on the top:

All solutions

Solution finder
Order by
...

When you click on this button, a modal opens. You can enter one to many different compound names that should appear in the solution. When you start typing, you get suggestions from all compounds we have in the database.

The result is a list of solutions filtered by your selection. On top you can find a list of ingredients that you used for filtering.

Example

Stock solutions #

We refer to all solutions that are referenced in multiple media as stock solutions. An example is the solution SL22: Wolin's vitamin solution, which is used in over 300 media. The X number that precedes the solution is intended to help uniquely identify these solutions. Stock solutions are generally associated with the following icon:


The solution comparison tool #

Many solutions are referenced in more than one medium (e.g. Trace element solution SL-10). However, it often happens that solutions have the same name while their ingredients differ significantly. This tool should help, comparing two solutions with each other and depicting the differences at one glance.

Why is it useful to reference solutions instead of defining them over and over again?
Good question. On one hand, data redundancy is always not good since curation requires more work. For example, if one common trace element solution changes, it has to be changed in many media recipes. To avoid this, the solutions are cross-referenced. On the other hand, shared data allow more analysis possibilities. And if you create a new medium, you don't have to copy-paste established solutions in the document.

Example

Compare Solutions


Strain-mods #

Example

Compare Solutions


Download content #

There are multiple ways to download content from BacMedia. Where you find the download buttons and which formats are supported depends on the item you like to download.

Download a medium recipe

The most common use case is that you are searching for a media recipe because you want to cultivate a microorganism and need to prepare the medium in your lab. We got you covered! In the button toolbar on top of each medium recipe is a button named Download. This button will generate a PDF document from our database. You can save it on your computer or print it directly from the browser.

Download a solution recipe

In some cases you are only interested in one special solution. Maybe you want to test different trace element solutions? Whatever it is, there are two ways to download a solution: you can either click on the download button in the header of the solution (on the medium page), or download them directly from the solution search via the following steps:

  1. Click on the solution you are interested in to open the info box.
  2. On the right you find a button with a symbol.
  3. Choose a format to download the solution.

Solutions can be downloaded as PDF file (recommended for printing), CSV files (for MS Excel), or JSON files (for data scientists and other experienced users).

Download a molecular medium composition

If you are e.g. interested in metabolic modeling, you are likely not interested in media recipes. Instead, you might be more curious about the final medium compositions. In this case, you can check out the table on the right-hand side of each medium, named Molecular composition. You find all compounds and their weight (g/L) and molecular (mmol/L) composition here. And on top of that, you can also download the whole table as CSV or JSON file by using the buttons right beneath the table.

Download data using the API:

We also have a URL-based API for downloading content. The link is as the following:

    https://bacmedia.dsmz.de/download/<type>/<id>/<format>
   

containing the following elements:

  • type: defines what kind of item will be downloaded. Possible values are composition, solution, or medium.
  • id: the database ID of the item that should be downloaded. Normally an integer value, except for medium IDs that can contain letters, e.g. 1194a.
  • format: defines the format of the returned. Possible values depend on the type, e.g. pdf, json, or csv.

Examples: