Training sessions

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Seminar on September 08, 2010

Media:ST-feno-002-101-1-2hr.zip

Media:20100908lecture.zip

This seminar explains how to analyze gene networks in CSML format file by adding visual attributes.

  1. Load the CSML file containing the estimated gene network.
  2. The color of each edge of the network can be set up by modifying the attribute “EdgeType” of the “edge”.
  3. By adding information about "in degree", "out degree" and, "node degree", it is possible to set up the nodes’ size proportional to them. The obtained network can be displayed by using the CIO5 software.


Seminar on September 09, 2010

Media:20100909lecture.zip

This seminar explains how to analyze gene networks estimated by a general mathematical model by adding visual attributes to the estimated network.

  1. Display the estimated network by loading both the Edge and Attribute files (both in Excel format).
  2. Set both the color and shape of the nodes.
  3. Set the color, shape, and width of the edges.
  4. Add the properties of Node and Edge obtained from the Attribute file.


Seminar on September 10, 2010

[Part1]

Media:pipeline_demo_20100910.zip

This seminar explains how to copy the specified biologicalProperty to the Name attribute of each Node in the CSML model. Furthermore, by setting the copied Name attribute as a key, several biologicalProperty of each Node can be added.
Due to the characteristics described above, it is possible, for example, to add several attributes such as gene expression level to a network where gene name is registered in the Node.
Explains both how to convert from a Matrix data to a DataFrame and also from Matrix data to a Sub Matrix data.

[Part2]

Media:pipeline_demo_20100910_2.zip

This seminar explains how to upload two Edge files (networks) and use the layout information of one of the networks to the other network.


Seminar on CelliP on October 15, 2010

Sample flow

  • Pipeline Application Overview
    • Dialog Menu Button
    • Install Components
    • Run Console
    • Export Distributable Package
  • Description of the sample flow CSML
    • Sample1
  • Description of the EDF
    • EDF start-up manual ver.1.0
  • R networks using a description of sample flow estimation
    • Sample3
    • Sample4
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