Video (How to start)
Video (Quick Guide)
XiP is a flexible, editable and modular environment with a user-friendly interface that does not require previous advanced programming skills to run, construct and edit workflows.
XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed.
XiP already comes with several ready-to-use pipeline flows for the most common genomic and transcriptomic analysis and ∼300 computational components. In the latest XiP 3.0, several components run on K computer environment.
First, let's click on Quick Guide button and read the manual to know the brief overview of XiP. Start button invokes stable Online version of XiP.
If signature-related error is encountered in invoking XiP, remove Java cache in the following way and restart XiP, please.
For more advanced usage, click on Advanced Usage button.
The differences of Online, Offline and Launcher are explained below.
Java Web Start is required to run XiP Online and Launcher. Download the latest Java Runtime Environment (JRE), which includes Java Web Start and install it on your PC.
Two types with different max-heap-size property of Java Virtual Machine are available:
- Online : 1200MB.
- Online (large) : 4096MB.
To start Offline version, please click on the link, download zip file, unpack it, and run bat or sh file (depends your OS).
Online versions noted above is invoked with max heap size 1200MB, but larger heap size is required to process large data.
XiP Launcher enables you to assign max heap size of the invoked application.
Using the Application
Building own flow
- Available elements
- A simple example flow
- Procedure of fundamental data analysis
- Procedure of fundamental graph analysis
- Modes of calculation
- Managing of flow calculations order
- Pausing calculations (working with breakpoint)
Using the Sub Functions
- XDC Manager
- Clone application
- Working with console version
- Working with distributable package
- Working with other systems (Grid Engine, Galaxy, K)
- XiP Server
- K Server
Other Useful Information
- URI notation
- Flow control implementation with the use of script
- R server settings
- About EDF
- Reporting problems
Working With Plugins
Use of HGC Environment
- Handling of custom URI
- Custom URI for server
- Java Headless mode
- CSMLDB connection notes
- Manually updating of JWS how to
- Icon color definitions for components tree
- Ant tasks
- Java Script
- R Language
- Feedback seminar
- Application constants review
- Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S. XiP: a computational environment to create, extend and share workflows. Bioinformatics. 2013 Jan 1;29(1):137-9