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github.com/JBEI/ice @6.0.0

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4,209 symbols 15,641 edges 650 files 862 documented · 20% ● updated 2y ago6.0.0 · 2024-02-22★ 4429 open issues

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README

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

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-5.6.0"

Access the application at http://localhost:8080 and login using username and password "Administrator"
Ctrl + C to stop the application

Related Projects

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

Extension points exported contracts — how you extend this code

IFormatter (Interface)

Interface for Formatters. @author Zinovii Dmytriv [6 implementers]

src/main/java/org/jbei/ice/entry/sequence/composers/formatters/IFormatter.java

DataModel (Interface)

@author Hector Plahar [80 implementers]

src/main/java/org/jbei/ice/storage/DataModel.java

IDataTransferModel (Interface)

Interface for data transfer objects @author Hector Plahar [77 implementers]

src/main/java/org/jbei/ice/storage/IDataTransferModel.java

IAuthentication (Interface)

Interface for different authentication types. @author Hector Plahar [6 implementers]

src/main/java/org/jbei/ice/account/authentication/IAuthentication.java

HeaderValue (Interface)

Value of header @author Hector Plahar [4 implementers]

src/main/java/org/jbei/ice/bulkupload/HeaderValue.java

Core symbols most depended-on inside this repo

get

called by 944

src/main/java/org/jbei/ice/storage/IRepository.java

getBuilder

called by 576

src/main/java/org/jbei/ice/storage/hibernate/HibernateRepository.java

add

called by 450

src/main/java/org/jbei/ice/entry/EntryHistory.java

error

called by 382

src/main/java/org/jbei/ice/logging/Logger.java

getId

called by 221

src/main/java/org/jbei/ice/storage/DataModel.java

getEmail

called by 211

src/main/java/org/jbei/ice/storage/model/AccountModel.java

respond

called by 196

src/main/java/org/jbei/ice/services/rest/RestResource.java

currentSession

called by 169

src/main/java/org/jbei/ice/storage/hibernate/HibernateRepository.java

Shape

Method 3,517

Class 632

Enum 48

Interface 8

Function 4

Languages

Java87%

TypeScript13%

Modules by API surface

src/main/java/org/jbei/ice/dto/entry/PartData.java57 symbols

src/main/java/org/jbei/ice/services/rest/PartResource.java48 symbols

src/main/java/org/jbei/ice/storage/hibernate/dao/EntryDAO.java37 symbols

src/main/java/org/jbei/ice/storage/DAOFactory.java37 symbols

src/main/java/org/jbei/ice/account/Account.java36 symbols

src/main/java/org/jbei/ice/storage/model/AccountModel.java35 symbols

src/main/java/org/jbei/ice/dto/access/AccessPermission.java35 symbols

src/main/java/org/jbei/ice/storage/model/Entry.java31 symbols

src/main/java/org/jbei/ice/dto/search/SearchQuery.java31 symbols

src/main/java/org/jbei/ice/storage/model/TraceSequenceAlignment.java27 symbols

src/main/java/org/jbei/ice/storage/model/Sequence.java27 symbols

src/main/java/org/jbei/ice/dto/DNAFeature.java26 symbols

For agents

$ claude mcp add ice \
  -- python -m otcore.mcp_server <graph>

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