DeviceEditor visual biological CAD canvas

Abstract

Background: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly.

Results: We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs.

Conclusions: DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.

Figure 1

DeviceEditor design canvas. Screenshot of the browser-based DeviceEditor user interface [24]: (top left) buttons for activating the j5 controls dialog box and setting DeviceEditor properties, (left panel) palette of standardized SBOLv part icons, (center) drag-and-drop design canvas with part icons and a collection object (white oval with vertical lines demarking bins), and (right panel) information detail for the selected part or collection.

Figure 2

Mapping a DeviceEditor part icon to an annotated DNA sequence. A new part icon on the design canvas (top left) is created by clicking on the desired SBOLv icon (here "Origin of Replication") in the left panel of the user interface (Figure 1). At this point, a DNA sequence has yet to be mapped to the part icon. In a separate browser-tab or software application, the desired portion of a DNA sequence (here the pBbS8c-rfp backbone [27] spanning from XhoI to EcoRI) is selected and copied (top right) to the clipboard. Third-party software (here VectorEditor) may embed meta-data (including jbei-seq format [28] sequence data) into the clipboard along with the plain-text DNA sequence selection (see Methods). Returning to DeviceEditor, the copied DNA sequence is pasted (mapped) from the clipboard onto the part icon. Clipboard meta-data provides DeviceEditor with the selected start and stop base pairs (here 1934 to 1215) within the circular source sequence, along with the source's name (here pBbS8c-rfp), entire sequence, and feature annotations (displayed in the "Source Data" field; bottom left). If the third-party software (e.g. ApE [29]) does not embed this meta-data, the sequence annotations are not transferred to DeviceEditor, and the user must specify the source name and the selected start and stop base-pairs within the copied sequence. The user may alternatively map a Genbank-format sequence file to the part icon, which preserves the source name and feature annotations. The name for the part icon (here "pBbS8c_EcoRI_XhoI_vector_backbone") is specified, along with whether the part is associated with the reverse complement of the selected sequence. The "Done" button is clicked, the part icon has now been named, and the desired annotated DNA sequence has been mapped to the part icon (bottom right).

Figure 3

Example biological designs rendered on the DeviceEditor canvas. (A) pNJH00010 [12] consists of seven components: the pBbS8c-rfp backbone spanning from XhoI to EcoRI (blue highlight, bottom left), the RBS sequence from pBbS8c-rfp (purple highlight, bottom left), gfp_uv from its 5' end to its XhoI site (blue highlight, bottom right), a silent mutation in gfp_uv's XhoI site (star), gfp_uv between its XhoI and BamHI sites (purple highlight, bottom right), a silent mutation in gfp_uv's BamHI site (star), and gfp_uv_sig.pep from its BamHI site to its 3' end (blue highlight, bottom right). These components are arranged from left to right in their 5' to 3' order in pNJH00010 (top). The corresponding SBOLv icon is presented immediately above each component. (B) To reconstitute the design in (A), each of the component sequences is mapped to a part icon (as in Figure 2), and arranged from left to right in 5' to 3' order as in (A) in a 7-bin collection object (white oval with vertical blue lines demarking bins), with each part icon in its own bin. This DeviceEditor design has been saved in Additional file 1. (C) The combinatorial design for plasmids pRDR000001-pRDR000008 [12] consists of nine components, including the pNJH00010 backbone, two N-terminal signal peptides (sig1 and sig2), two Gly/Ser linkers (long and short), the gfp_uv mutant from pNJH00010, two 5' ssrA tags (standard and enhanced), and a 3' ssrA tag. These components are arranged from left to right from 5' to 3', with interchangeable components arranged from top to bottom. (D) Each of the component sequences in (C) is mapped to a part icon, and these part icons are then arranged from left to right as in (C) in a 6-bin collection object, with interchangeable part icons in the same bin. Each bin, now demarcated with purple lines indicating a combinatorial design, is then named according to the category of parts it contains (bottom) This DeviceEditor design has been saved in Additional file 2.

Figure 4

Adding Eugene design specification rules. (A) Graphical user interface for creating and modifying rules. A part icon (here "short", bottom left) on the design canvas is clicked, followed by the "Add Rule" button in the right panel of the user interface (bottom right). The name for the rule (here "rule3") is specified, and one of three Eugene operators (NOTMORETHAN, WITH or NOTWITH) is selected (here "WITH"). For the NOTMORETHAN operator, the maximum number of times the part may be present in a single construct is specified. For the WITH or NOTWITH operators, the other part icon on the design canvas (Operand 2, here "sig1") that should or should not be present in a single construct, respectively, with the selected part icon (Operand 1, here "short") is chosen. The list of Eugene rules associated with the selected part icon is shown in the right panel of the user interface (right). Part icons with associated Eugene rules are visually identified on the design canvas by an orange circle indicator light at bottom right, and part icons with specified forced assembly strategies are distinguished with a blue (bin consensus-matching assembly strategy) or a red (bin consensus-breaking assembly strategy) rectangle indicator at top left. (B) Importing Eugene rules from a file. From the "File" pull-down menu of the user interface (Figure 1, top left), "Import Eugene Rules" is clicked and a Eugene rules file (e.g. Additional file 3) is selected. The Eugene Rules Import dialog displays imported rules in green, rules identical to current rules in black, imported rules with names conflicting with current rules displayed in red (alternative names are auto-generated for the imported rules to resolve conflicts), and ignored rules (e.g. comment lines or rules with invalid operators or operands not present in the current design) in light grey. Importing a set of Eugene rules facilitates the batch creation of multiple rules for complex designs (Figure 5).

Figure 5

Hypothetical combinatorial DeviceEditor designs. (A) Metabolic pathway library: 29 bins and 19 unique part icons (several repeated through the design). Clicking on a repeated part icon, here "RBS_pET29_5'" (top left), highlights all replicates with thick blue outlines. (B) Gene over-expression library (rotated 90° counter-clockwise): 8 bins and 156 part icons (none repeated). Note that there are only 38 barcodes (sixth bin) that correspond one-to-one with the 38 vector backbones (first bin). This design allows for a single short sequencing read spanning the end of gene 2 (fourth bin) through the barcode and the beginning of gene 3 (eighth bin) to uniquely identify a plasmid combination. As a result, there is not a unique barcode required for each of the 38³ = 54,872 possible plasmid combinations. Zoom in with PDF display software to improve legibility.

Figure 6

Running j5 from within DeviceEditor. The j5 button at the top left of the user interface (Figure 1) is clicked to open the j5 controls dialog box (top left). The j5 design parameters [12] may be customized or returned to their default values by clicking the "from parameters" link at the top right of the "Run j5 on Server" tab (top left), which opens the j5 Parameters dialog box (top right). Otherwise, the user's latest set of design parameters (stored on the j5 server) will be employed. Similarly, the user's latest lists of plasmids, oligos, and direct syntheses will be used (shown here), unless empty or alternate lists are specified. For single construct designs (Figure 3B), the assembly method may be either "SLIC/Gibson/CPEC" or "Golden-gate". For combinatorial designs (Figure 3D), the assembly method may be either "Combinatorial SLIC/Gibson/CPEC" or "Combinatorial Golden-gate" (shown here). After the "Run j5" button is clicked, DeviceEditor submits the design contained within the collection to the j5 server (see Methods) and provides links to the resulting assembled sequences. Clicking on one of these links (here "pj5_00003.gb") will open the corresponding sequence in VectorEditor (bottom left) so that it may be easily verified (here, the N-terminal signal peptide, Gly/Ser linker, gfp_uv, and ssrA tag (Figure 3C, D) are confirmed to be in-frame). The "Condense Assembly Files" and "Downstream Automation" tabs in the j5 controls dialog box (bottom right) provide access to j5 downstream automation design.

Figure 7

Auto-generation of a DeviceEditor design from CSV and zipped sequence files. Third-party software can transfer component design and (combinatorial) arrangement information to DeviceEditor via spreadsheet (CSV) and zipped sequence files (i.e. a set of j5 files, see Methods). From the "File" pull-down menu of the user interface (Figure 1, top left), "Load Design → j5 Files" will open the j5 File Import dialog box (top left). After the requisite files are selected, a minimal design is auto-generated on the DeviceEditor design canvas (top right). As evident in the screenshot taken immediately after loading the design, there is no SBOLv icon information and some of the labels may be overlapping. The precise spatial arrangements of the part icons, SBOLv icon selection, and the collection object dimensions may then be customized as desired (bottom).

Figure 8

Integrated Synthetic Biology design-implement-assay cycle. The DeviceEditor BioCAD canvas (top right) assists the specification, selection and arrangement of biological component parts, and interfaces with upstream parts repositories (e.g. JBEI-ICE) and downstream DNA assembly automation (e.g. j5).