Development Prerequisites

Understanding lab information management in a scientific context is one of the more powerful skills in genomics research today. The Clarity LIMS Rapid Scripting™ API is designed to use these skills, allowing a knowledgeable scientific programmer to adapt lab informatics with scripts and automation.

NOTE: Based on experience working with bioinformaticians and scientific programmers, assumptions about your background, setup, and skills have been made.

Before you begin

Before using the API Cookbook, set up a Non-production scripting sandbox servers.

If any of the topics covered on this page are a concern, contact the IlluminaSupport team for additional training or custom scripting services.

Terminology

Within the Cookbook, the term scripting refers to programs running independently of the client and server that direct the input and output of information. Use scripts and the API for file handling and text processing in the context of biological samples, containers, and instruments.

Skills and Training

• This API Cookbook assumes that you can program in modern computer languages, and are comfortable with scripting and bioinformatics.

• The topics are best understood by those users who can program small applications and are experienced with experimental processes in molecular biology.

• The topics assume that you have received administrator-level training or know how to configure the system. The topics also assume that a nonproduction server is set up to play with cookbook examples, develop real scripts, and test before deploying in production.

• Be comfortable with the following skills:

  • XML

  • System file handling

  • General-purpose scripting languages

  • Working on the command line

Non-production scripting sandbox servers

Illumina provides multiple server licenses for API users: a production server license and one or more non-production server licenses for developing and testing.

To allow developers to design, build, test, and upgrade efficiently, it is recommended to install at least two servers. Installing three is even better.

The non-production server licenses serve the following purposes:

• To provide a sandbox in which to experiment with the API and the system configuration.

• To provide a verification platform for upgrading scripts, software components, and overall system integration before deploying to production.

All the examples in the Cookbook are intended to be used with the nonproduction scripting sandbox server. See Useful Tools.

If you do not have the time or resources to use the API, but are interested in expanding your implementation, contact the Illumina Support team. There are various consulting, training, and scripting services available.