Website documentation

This documentation covers how to use the website.

Content #

    media-components database structure The media view page strains and strain-specific modifications Find media by their components Find solutions using the solution finder Compare solutions Download content Link MediaDive

Media components #

A medium is basically composed of building blocks, which we call solutions. Each medium contains at least one solution, but 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 look for. The following is a brief explanation of the main 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. Tribe-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, in turn, unique for each media.
  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.

All other solutions

These are all other solutions that do not have a special role in MediaDive. They are not the main solution of a medium. They may also be associated with multiple media.

Accordingly, if we plot the structure of a medium, it looks like this:

  • Medium

    • Main solution

      • Solutions
        • | |

      • Ingredients

      • Steps

    • Meta data

Database structure #

The above structure results in the following database:

DB Scheme

The database consists of a whole set of tables, which are linked together with a complicated logic. Five tables stand out because they are highlighted in color. These five tables are the core tables of the database, which means that all other tables relate to them in some way. The connecting lines between each data point show links between primary keys (marked with and ) and foreign keys (marked with or ). The links are always shown in the color of the primary key table.

The media-overview page #

This page is the heart of MediaDive, as it brings together all the information we have about a medium.

At the top of the page, you'll find the toolbar. Here you can navigate to neighboring media, download the media as a PDF, or leave a comment.

On the left side you will find the media recipe. Here are listed all solutions of the recipe. Above you'll find two ways to customize the recipe to your liking. On one side you can select a microorganism. In some cases, a strain requires adjustments to the medium. When you select the strain, they will be added directly to the recipe accordingly. More on this here. On the other hand, you can adjust the total volume of the manufactured medium by a factor. All solutions are affected by this. If you only want to adjust the volume of the main solution, you can do it right there in the header.

On the right side you will find all the metadata for this recipe. This includes, among other things, the final pH value and the required equipment. Furthermore, you will also find other metadata, such as all strains that grow on the medium and the final composition of the medium.

Here you can also generate a QR code that allows you to seamlessly transfer the recipe to your smartphone and cook it directly in the lab. On the smartphone, you also have access to the Cooking Guide, a specially designed page. If you still prefer to print the recipe, a PDF export is available. Strain adjustments and volume changes are also applied in the process.


Strains and strain-specific modifications #

At MediaDive, not only media can be found, but also the associated microorganisms. On the strain overview page, this can be done by searching specifically for individual strains. Also on the media view page you can find the information how many strains grow on the selected media. You can find this in the infobox Related strains in the metadata. Clicking on this will take you to an overview page that lists all strains for the medium and provides more information.

Also in the metadata on the right side of the media view is media-centric phenotypic data from all strains growing on that medium. These data are from our sister database BacDive.

As mentioned earlier, there are some strains in MediaDive that require an adaptation of the medium to grow on. We call these strain modifications. Above the media recipe in the media view, there is a dropdown menu from which you can choose a strain. Clicking will show you the strain-specific media. If modifications are needed, they will be briefly described above the actual recipe. If ingredients should be added, omitted or replaced in the recipe, this is usually entered directly into the recipe. The gas phase and pH in the metadata can also be edited by a strain modification. A modification is indicated by red font and an asterisk. The changes will also be shown in the exported PDF.

Example of a root modification

Find media by their components #

The medium finder helps you find a medium based on its components. It gives you the following filter criteria:

  • The medium must contain the selected ingredient. There is an option to specify the minimum and maximum concentration in g/l and mmol/l.
  • The medium must not contain the selected ingredient.
  • The medium must have a certain final gas phase. There is the possibility to define the gas phase in %.
  • The medium must contain a chosen solution. There is an option to specify the minimum and maximum amount in ml.

The following example searches for all media containing 2 – 10 g/l glucose and any concentration of MgCl2:


Find solutions with the solution finder #

The Solution finder is a counterpart to the medium finder, which can be used to find solutions based on their components. Compared to the Medium finder, it has fewer functions, since only the presence of certain ingredients can be defined. Nevertheless, it is a useful tool if you want to make sure whether a certain solution is already present in the database.


Compare solutions #

Many solutions are referenced in more than one medium (e.g. track element solution SL-10). However, it is common for solutions to have the same name while their ingredients differ significantly. This tool is designed to help compare two solutions and show the differences at a glance.


Download content #

There are several ways to download content from MediaDive. Where you find the download buttons and which formats are supported depends on what you want to download.

Downloading a Medium recipe

The most common use case is that you are looking for a medium recipe because you want to culture a microorganism and need to prepare the medium in your lab. We have the solution for you! In the toolbar above each media recipe is a button labeled Download Here you have the option to download the recipe directly as a PDF or as a text document. If you choose to download a PDF, customized volume and strain-specific modifications can be displayed. You can save the PDF to your computer or print it directly from your browser.

Download a solution recipe

In some cases, you are only interested in one specific solution. Perhaps you want to test different trace element solutions? Either way, there are two ways to download a solution: You can either click on the download button in the solution header (on the Medium page), or download it directly from the solution search by following the steps below:

  1. Click on the ID of the solution you are interested in to open the details page.
  2. On the right you will find a download button.
  3. Select a format to download the solution.

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

Download a molecular media composition

If you are interested in modeling metabolic processes, for example, you are probably not interested in media recipes. Instead, you may be more interested in the final composition of the medium. In this case, you can look at the table on the right side of each medium called medium composition Here you will find all the compounds and their concentration (if any) in g/L and mmol/L. In addition, you can also download the entire table as a CSV or JSON file by using the buttons directly below the table.

Downloading data via the API:

We also have a URL-based API for downloading content. Learn more here.