ICE: Inventory of Composable Elements

ICE is a registry platform that provides robust data storage for DNA components, integrated tools for part characterization, as well as mechanisms for secure access and information sharing with other users and software tools.

ICE is open source and distributed under the Modified BSD license. You can try it out at https://public-registry.jbei.org by creating a free account

Major Features

• Support for storing biological parts in addition to plasmids, microbial strains and Arabidopsis seeds. Supported sequence formats are genbank, FASTA and SBOL
• Full text and BLAST search capabilities
• Advanced collection management
• Graphical application and other tool integration for sequence design, annotation and verification
• Real time DNA editing with live vector map display and sophisticated feature annotation
• Opt-in community collaboration capabilities that enable dataset publishing and sharing across multiple ICE instances
• Granular read and write permissions for entries or collections across users and groups
• Automatic Sequence Annotation

Installation

Production

To install in a production environment, please consult our manual for detailed setup and configuration instructions.

Development

To set up a development environment or local machine installation make sure you have the following dependencies installed

• Open JDK 16
• Maven 3
• Git

Command line installation steps (linux environment):

• Clone this repo

  git clone https://github.com/JBEI/ice.git ./ice
  cd ice

• Build ICE. This may take a few minutes to download additional dependencies

  mvn clean install -DskipTests=true

• Start the embedded undertow server

  java -cp "./target/ice-{version-number}-classes.jar:./target/ice-{version-number}/WEB-INF/lib/*" DevelopmentServer

  Where "ice-{version-number}" is the version of ICE that was cloned. e.g. "ice-5.10.3"

• Access the application at http://localhost:8080 and login using username and password "Administrator"

• Ctrl + C to stop the application

Links

• Documentation including user manual and API documentation

Related Projects

Open Vector Editor is used in ICE to display and edit sequences