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Cell Integrative Pipeline
Let's start CelliP!


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 04-12-2018 release notes launch launch download


Video (How to start)

Video (Quick Guide)

CelliP 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.
CelliP 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.
CelliP already comes with several ready-to-use pipeline flows for the most common genomic and transcriptomic analysis and ∼300 computational components. In the latest CelliP 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 CelliP. Start button invokes stable Online version of CelliP.

If signature-related error is encountered in invoking CelliP, remove Java cache in the following way and restart CelliP, 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 CelliP 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.

Application Site

CIO 5.0

Using the Application

Building own flow


Using the Sub Functions



Menu Bar

Window Views

Components Categories

Other Useful Information

Working With Plugins

Component Development

Use of HGC Environment

Development Notes


  • 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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