APPLICATIONS OF TECHNOLOGY:
- Search, storage, and management of databases of biological parts and associated sequences
- Visualisation of biological part sequences
- Efficient sourcing and management of data
- Facilitates data sharing and exchange
ICE and Web of Registries
The Inventory of Composable Elements (ICE) is an open source web based registry platform for synthetic biological parts with support for microbial strains, plasmids, Arabidopsis seeds, and generic parts. The integration of a plasmid/vector editor enables the visualization and vector manipulation of any associated sequences. It can also be used by laboratories to track and search their constructs. It has an implementation of the Web of Registries concept that enables multiple standalone ICE instances to interconnect and form a distributed parts database.
Bioparts Search Portal
The Bioparts Search Portal is a web based application that enables users to search for publicly available biological parts using keywords or sequence fragments. For the initial version (1.0) of the application, Bioparts targets 10 sources of biological part data: the GenBank NIH genetic sequence database (https://www.ncbi.nlm.nih.gov/genbank/), the iGem parts registry (parts.igem.org), the Addgene plasmid repository (https://www.addgene.org/), and seven Inventories of Composable Elements (ACS Synbio, JGI, JBEI, JBEI Public, ABF, SynBerc, ABF Public). Bioparts has built-in automated web scrapers which extract data from sources that do not have a public or well-defined application programming interface (API). They extract as much public data as they can find and create a searchable index to speed up searches. Included in the indexed information is the source of the information. Additionally, the portal offers a REST API that enables third-party applications and tools to access the portal’s functionality programmatically.
FOR MORE INFORMATION:
The source code for ICE is available at https://github.com/JBEI/ice
The Bioparts Web Application is hosted at https://bioparts.org
- Hector Plahar, Lawrence Berkeley National Laboratory
- Steve Lane, Sandia National Laboratories
- William Morrel, Sandia National Laboratories
OPPORTUNITIES: Available/Open Source