Table-based FIMS

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An example configuration of a table-based FIMS database

The Biocode plugin has several choices for connecting to table-based FIMS databases (those that store their data in a tabular format).

The key requirement for any table-based FIMS database is that it has one column/field representing tissues, and that the values in this column are quique for every record in the database (i.e. that there is a unique tissue identifier assigned to every record).

The following table-based FIMS connections are available:

  • MySQL FIMS - This is most useful for groups of users who have an existing FIMS system backed by a MySQL database, but do not want to set up a TAPIR server. Geneious will read the data directly from the database.
  • Google Fusion Tables FIMS - This is most useful for groups of users who want to access their FIMS data remotely, and do not already have a compatible way of storing it.
  • EXCEL FIMS - This is most useful for single users, or people who cannot set up a TAPIR server. The EXCEL FIMS will read tissue data in from an excel sheet.

To connect to a table-based FIMS, you must describe the structure of your table, by telling the plugin a little about what the columns in your table mean.

You will see a series of dropdown boxes in the FIMS connection dialog (see figure).

  • Choose your tissue id column from the first dropdown. If you have a specimen id column, you may choose it as well. If you do not, enter the tissue id in this dropdown as well.
  • If your table has plate and well information, check the The FIMS database contains plate information checkbox, and choose the columns that correspond to plate and well in the dropdowns. The plate name can be in any format, while the well number must conform to either A1 or A01 etc.
  • You must specify at least one taxonomy field in your FIMS. If you have named your taxonomy columns using the standard names, you can click Autodetect to fill this part of the form in for you. Otherwise click the + and - buttons to add and remove fields.