Supplementary Figure 1: Anatomy of a dynamic Galaxy External Display Application.

(A.I) A dynamic GEDA is initially defined in the same fashion as the static type (see main Fig. 1). (A.II) A set of “dynamic_links” are defined according to the entries contained within a Galaxy Data Table (see panels B and C), with the link “id” and displayed “name” coming from the “value” and “name” fields, respectively. (A.III) This URL is generated using the Python string format operator (%) using the value of “url” from the Data Table, along with a dictionary containing an encoded URL to the “intermine_file” dataset content. (A.IV) The URL containing the InterMine dataset content is defined as containing a “DATASET_HASH” value that is unique to the Galaxy instance. This can be helpful to differentiate between multiple datasets within external resources that may only utilize or display the base filename of uploaded content; Galaxy dataset names can also be used (Supplementary Figs. 2 and 3). (B) A flat file (colloquially referred to as a “.loc” or “location” file) is tab-delimited and can be modified outside of the Galaxy codebase to configure this display application. There is a single entry shown (B.I) which contains 3 columns: (B.II) a unique id for the entry, (B.III) the display name for the entry, and (B.IV) a variable named “url” that contains the URL template used in (A). (C) The Data Tables configuration (C.I) can contain any number of defined “table”s (C.II) which declare a “name” for the table, as well as to ignore lines in the file that begin with a comment character (#) and to not allow duplicate entries. The (C.III) columns for the three fields in the table are defined as “value”, “name”, and “url”. The (C.IV) source of the data table content is loaded from the specified flat file (B). Reference: Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, et al. InterMine: extensive web services for modern biology. Nucleic Acids Res 2014;42:W468–72. https://doi.org/10.1093/nar/gku301.