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eXtensible Integrative Pipeline
Let's start XiP!

Contents

Application Startup

Version Release Date Release Notes Online Online(large) Offline
1.0 (stable) 20-04-2012 release notes launch launch download
2.0 (stable) 04-09-2012 release notes launch launch download
3.0 (stable) 18-04-2013 release notes launch launch download
latest 25-04-2017 release notes launch launch download

Manual     

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.


Online

Two types with different max-heap-size property of Java Virtual Machine are available:

  • Online : 1200MB.
  • Online (large) : 4096MB.

Offline

To start Offline version, please click on the link, download zip file, unpack it, and run bat or sh file (depends your OS).

Launcher

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.

Application Site

XiP https://xip.csml.org/
CIO 5.0 https://cionline.hgc.jp/cionlineserver/apps/usersman/main


Using the Application

Building own flow

Calculations


Using the Sub Functions

Samples

Training


Menu Bar

Window Views

Components Categories


Other Useful Information


Working With Plugins


Component Development


Use of HGC Environment


Development Notes


Publication

  • 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



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