TeselaGen allows you to keep track of microbial strains and cell lines as they change and develop. However, we need to start somewhere, so let's see how to get data representing our strain database uploaded for the first time. Our example will be a database of fungal microbial strains. If you are originating your database from a well-curated external source that is great, and we can show you how to attach that database directly to your TeselaGen platform via our integration server. For our purposes here, we will simply start with a CSV upload. The upload that we focus on first will be the information listed under:
Materials > Microbial Strains > Upload > Strains
The three-dot button to the right of the upload region can be used to download a template that you can use to upload your strains. Note that you can double-click on these images to see them with better resolution.
Let's take a look at the structure of the strain upload template. Even though the only required fields are NAME and BIOSAFETY_LEVEL, there are several other fields that are interesting to have uploaded en masse so you get it done. Once the prerequisite data has been entered, an upload of a CSV with these columns is straightforward.
NAME | Required. This is the strain name. You will see it referred to in other CSV upload files as STRAIN_NAME. |
ALIAS | Optional. An alternative name for the strain. |
BIOSAFETY_LEVEL | Required. |
GENUS | Optional. To associate a strain with a genus and species, the genus and species must first be set in 'Settings > Genera and Speices'. |
SPECIES | Optional. To associate a strain with a genus and species, the genus and species must first be set in 'Settings > Genera and Speices'. |
GENOTYPE | Optional. This is a sub-type for a strain. |
DESCRIPTION | Optional. |
PLASMID_NAME | Optional. This is the plasmid name for a plasmid, whose file is specified in the 'GB_FILE' column. |
GENOME_NAME | Optional. To associate a genome, the genome must already be available in 'Settings > Genomes'. |
GB_FILE | Optional. To associate plasmid files, upload a zip file containing GenBank (.gb or .gbff) or Fasta files along with the CSV. Note: the 'GB_FILE column of the CSV must match the sequence file's name). |
SELECTION_METHOD | Optional. To associate a selection method, the selection method must already be set in 'Settings > Selection Methods'. |
ORGANISM_CLASS | Optional. To associate an organism "class", the name of the group must already be set in 'Settings > Target Organism Class'. |
GROWTH_CONDITION_NAME | Optional. |
GROWTH_CONDITION_DESCRIPTION | Optional. |
GROWTH_MEDIUM | Optional. To associate a growth medium, the name of the medium must already be set in 'Materials > Reagents > New Reagent'. |
TEMPERATURE | Optional. |
SHAKER_SPEED | Optional. |
SHAKER_THROW | Optional. |
LENGTH_UNIT_CODE | Optional. Required if shaker throw is specified. |
ext-strain- | This upload accepts extended properties for the strains. Add a property name to this header (ex. 'ext-strain-Date of Purchase') and values to the rows. To add additional strain properties just duplicate the column header. All extended properties are set in 'Settings > Extended Properties' before this upload. |
We now have all the reference information about our set of strains in the database. Next, we will want to add information about how the physical samples are stored. In the illustration below we have filled in the information in the block labeled 'References'.
In the next article, we will show how to get the information about the physical location of the strain database into the system.