Media & Subsets
refineGEMs has an in-build database for different media, media compounds and Subsets to facilitate model curation and allow for a range of different simulations.
Hint
The media and substances in the database are manually curated. If you find any discrepancies or want something added, feel free to reach out to the maintainers and developers (GitHub page or open a discussion here).
Content of the Database
Below, the currently available media and subsets are listed. For additional information refer to the documentation pages of these media. For more details on the substances and database links, please install the database and inspect it on your computer.
- Available media
- Basal Medium as described in Swaney et al. 2023 (BMS23)
- Artificial Sweat (artSw)
- Blood medium (Blood)
- Casamino Acids medium (CasA)
- Corynebacterium glutamicum optimized growth medium (CGXII)
- Defined Gut Microbiota Medium (dGMM)
- Lysogeny broth (LB)
- M9 minimal medium (M9)
- Multi-Purpose Artificial Urine (MP-AU)
- Roswell Park Memorial Institute 1640 Medium (RPMI)
- Synthetic Nasal Medium Version 3 (SNM3)
- Available subsets
Hint
For more information on how to access the database, please refer to Usage.
Working with the Data
For understanding the database and the data it contains, it is vital to understand the meaning of an in silico medium and how to transform a medium e.g. from the labratory (in vivo medium) into an in silico medium. Our standardised aproach is described in From laboratory to in silico medium.
You can find a detailed explanation of the database architecture under In silico media & subsets database.
Additionally, the last point refers to more information about accessing the database. TODO Worauf bezieht sich das hier genau?