Search your yeast number
Find quantitative, annotated data for mathematical modelling
Curated yeast data for mathematical modeling
YCMDB collects, annotates and categorizes published data on yeast physiology along with its experimental context to provide a quantitative resource for cellular modelling.
General information on yeast cell pysiology such as cell sizes, densities, composition, cell cycle phases >> Biophysical data
Information on the processes of translation and transcription such as mRNA and protein abundances, synthesis rates, translation initiation probabilities >> Genomic data
Information on metabolites such as concentrations, uptake and secretion rates >> Metabolic data
Publication
Lookup where the data was published and which other data and information are available from the study.
Strain
Find information on the used strain, its genotype and ancestry. Explore which other numbers are available from this strain.
Each data point is annotated with relevant experimental conditions.
(as far as available)Static Indexing
allows reprodicible documentation of you data sources. Each data point has a unique YCMDB-ID that can be used to reference calibration data unambiguouslyInformation displayed for medium:
YCMDB contains the following data points from this medium
Medium pH:
Composition of the medium:
Similarity to other media in YCMDB:
Dots represent individual media, select a closeby dot to see similar medium to the currently selected. Coloring is according to the concentration of a selected compound and can be changed on the right.Information displayed for strain:
Ploidity
Mating Type
Mutations
Link
YCMDB contains the following data points from this strain
Ancestry
The closest ancestor of the currently selected strain is highlighted in red in the ancestry tree below.Information displayed for publication:
Publication information
YCMDB contains the following data points from this publication:
Publication data overview
Search for publications that have data of the type you are looking for. Other available data points from the same publication will be displayed. they migth also be usefull for unit conversions.You are very welcome to submit your own relevant data to YCMDB!
Start with filling in all required meta-information in the fields below. The more we know about the experiment and the way the measurements were taken, the better they can be reused for modeling. All information has to be supplied before you will be able to submit your data. During the process you can always check your inputs with the button below. If you are unsure what to put in a specific field, feel free to contact us.
Then you can upload the actual data points. You can select from a list of data types (i.e. metabolite concentrations, cell sizes, etc.) to download a fillable template. Please adhere to the template's format closely.
You can download and save the entered information at any point (at the bottom of this page). If you want to continue working on your dataset you can upload the file again, also to reuse the meta information if you want to submit several data types for the same experiment.
1 General and/or publication information
Please enter contact information and an identifier (name) for you data set. The contact email will be used to contact you before your data can be added to YCMDB, so please make sure that we can reach you.2 Strain Information
You can either select a strain that is already in YCMDB (please carefully check the strain information to see if it is the strain you used). Or you can enter a new strain and provide all the required information on it (ploidity, mating type, mutations, any further information concerning ancestry or the genotype).3 Medium Information
4 Cultivation Information
Please enter details for the cultivation of the cells.5 Measurement method Information
Please enter details for the measurement method. Please provide reasonable units!6 Data points
Select a type of data that you want to add below, you can then download a csv template with all required columns to fit your data. Please fit your data in the downloaded template and try to fill in all columns. Finally you can upload the filled file in csv format:C Check and Submit your dataset
Once you have filled in all information above, you can check your dataset here. Once all checks are fine, you will be able to submit the dataset to YCMDB!R Down- and upload entered data or reset the form
You can download and save the entered information at any point (.RData format).
Download current data
Download current data
If you want to continue working on your dataset you can upload the file again, also to reuse the meta information if you want to submit several data types for the same experiment.
If you want to enter a new experiment, you can reset the entire form.
