Manuals & Tutorials

Manuals

•  Discovery Environment Manual 1.0: basic overview of the iPlant Discovery Environment, an introduction to its tools, and step by step instructions for using its features.
•  Atmosphere Manual : iPlant's cloud computing platform with detailed use instructions. 
• DNA Subway has several materials available:
  • DNA Subway Manual: DNA_Subway_Guide.pdf
  • DNA Subway Exercises and Handouts: Subway Worksheets.docx
  • DNA Barcoding Laboratory Manual: using-dna-barcodes.pdf
  • Barcoding 101: http://www.dnabarcoding101.org/
• Taxonomic Name Resolution Service (TNRS) Manual.

Tutorials (Written)

• RNAseq Using the iPlant Discovery Environment
• ChIPseq Using the iPlant Discovery Environment
• Foundation API Exercise One

Tutorials (Video)

These tutorials are also available on the appropriate tool webpages as well as the iPlant Collaborative YouTube site.

• iPlant Collaborative introduction
• Acquiring an iPlant Account
• DNA Subway introduction 
• My-Plant Overview
• Atmosphere overview and tutorial 
• Using the Discovery Environment for data management with the iPlant Data Store
• Using the DAVIS interface for data management with the iPlant Data Store
• Using iDrop for data management with the iPlant Data Store 

Other Documentation

• Getting Started with iPlant is a useful first-stop for most users and covers account creation, using the iPlant Data Store, resetting passwords, has a list of all end-user available iPlant resources, and includes our Frequently Asked Questions (FAQ).
• Storing Your Data with iPlant and Accessing that Data describes the use of the iPlant Data Store, including via multiple interfaces.
• Discovery Environment Tool Integration documentation provides a high level overview of the process of integrating a tool into the iPlant Discovery Environment.
• Foundational API v1.0 describes the application programming interface for the iPlant cyberinfrastructure.
• Semantic Web APIs describes the application programming interface for the semantic web.
• The My-Plant website has an informative page describing the site, its features and its use.  
• Reporting Issues with JIRA describes how to use our issue tracker.

Interactive User Help (Q/A)

• Our web forum is available for users who have specific questions about iPlant, enabling direct communication among iPlant staff, collaborators, and the wider community.  

Open Source Documentation

• Open Source Initiative outlines the plans and progress iPlant has made releasing program code with an open source license.
• http://www.iplantcollaborative.org/about/opensource lists released code with links to repositories (which each include developer-focused documentation created just for the open source community) and other details related to this project.