Biomedical Engineering Reference
In-Depth Information
desired column in the “Column Name” column of the Collection
Info table. To append a column to the design canvas or remove the
fi nal column, click on the “Add Column” or “Remove Column”
buttons, respectively, in the Collection Info panel. To insert a col-
umn before a particular column, or remove a particular column,
click to activate the desired column in the table in the Collection
Info panel, and then click on the “Add Column” or “Remove
Column” buttons, respectively. Each part that is contained within
a removed column is displaced to the Part Holding Area (bottom
left of the interface), unless another linked-paste (
see
Subheading
3.8
) instance of the part is present elsewhere in the
design canvas. To name a part in the design canvas, click on the
desired part (column/row), enter the desired part name in the Part
Info panel at the top right of the interface, and then click the
“Save” button next to the “Part Name” fi eld. New rows are auto-
matically added to the design canvas when bottom-most row of
any column is selected.
To create a prototype design in DeviceEditor, then, it is neces-
sary to add a column for each of the design's DNA fragments;
select an SBOL Visual icon, unique name, and directionality for
each column; and name the parts to be contained within each col-
umn. The circular design shown in Fig.
2
contains six columns, all
in the forward direction, each with an SBOL Visual icon (“Origin
of Replication,” “CDS,” “CDS,” “CDS,” “Protein Stability
Element,” “Protein Stability Element,” respectively), each with a
unique name (“vector_backbone,” “nterm_sig_pep,” “gly_ser_
linker,” “GFPuv,” “ssrA_tag_5prime,” and “ssrA_tag_3prime,”
respectively), and each containing named parts (“pS8c-vector_
backbone”; “BMC_nterm_sig_pep” and “ccmN_nterm_sig_pep”;
“long_gly_ser_linker” and “short_gly_ser_linker”; “GFPuv”;
“ssrA_tag_5prime” and “ssrA_tag_enhanced_5prime”; and “ssrA_
tag_3prime,” respectively).
3.5 Mapping
Annotated DNA
Sequence Information
from VectorEditor to
Parts in DeviceEditor
After creating a prototype design in DeviceEditor, the next step is
to map (i.e., associate) annotated DNA sequences to the named
parts in each column. There are two main methods for mapping an
annotated DNA sequence to a part, namely the preferred method
of mapping from VectorEditor via the system clipboard (i.e., copy/
paste), and mapping directly from a GenBank sequence fi le (
see
Note 3
). While the method presented below begins with import-
ing a DNA sequence fi le into the j5 web-server stand-alone version
of VectorEditor, the same methodology largely applies to begin-
ning with opening a JBEI-ICE repository DNA sequence with the
integrated version of VectorEditor [
19
,
48
].
To map an annotated DNA sequence from VectorEditor to a
part in DeviceEditor, open a new browser tab. From the main page
of the j5 web-server (Fig.
1
) [
31
], click on the VectorEditor icon.
At the top left of the VectorEditor interface (Fig.
3
), click on the
