Abstract
Synthetic biology aims to introduce engineering principles into biology, for example, the construction of biological devices by assembling previously-characterized, functional parts. This approach demands new resources for cataloging and sharing biological components and designs, in order to accelerate the design-build-test-learn cycle. We evaluated two free, open source software platforms for managing synthetic biology data: Joint Bioenergy Institute-Inventory of Composable Elements (JBEI-ICE) and SynBioHub. We analyzed the systems from the perspective of experimental biology research groups in academia, which seek to incorporate the repositories into their synthetic biology workflow. Here, we define the minimal requirements for a repository in this context and develop three usage scenarios, where we then examine the two platforms: (i) supporting the synthetic biology design-build-test-learn cycle, (ii) batch deposit of existing designs into the repository and (iii) discovery and reuse of designs from the repository. Our evaluation of JBEI-ICE and SynBioHub provides an insight into the current state of synthetic biology resources, might encourage their wider adoption and should guide future development to better meet the needs of this user group.
Highlights
Synthetic biology as a discipline is bringing engineering practices into biology
Our evaluation of JBEI-ICE and SynBioHub provides an insight into the current state of synthetic biology resources, might encourage their wider adoption and should guide future development to better meet the needs of this user group
Both systems cover most of these minimal requirements and their user interface (UI) is presented in Figures 1 and 2
Summary
Practices being adopted include: standardization of components and conditions; abstraction of components and devices and decoupling of systems design and fabrication [1,2,3,4,5] The emergence of this approach in bioengineering has been paired with the development of registries of biological parts and devices. The community is aiming for automation of biological design, similar to the automation that has been achieved in other industries, e.g. in microelectronic designs. This requires adequate processes of abstraction and standardization, from single DNA elements to whole gene and whole circuit designs. CAD-like, assisted design and manufacturing requires access to such representations and creates a need for repositories for parts and designs [6, 7]
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