How to use DiiPS software.

Introduction
How to use DiiPS

Introduction

DiiPS (Digital Information of iPS Cells) is a software developed to support researchers in selecting the most suitable disease-specific iPS cells (iPSCs) for their studies by comprehensively presenting their pluripotency through omics data, including micropatterned culture analysis. It can compile multiple experimental results that verify the differentiation potential of iPS cells and visualizes the differences in characteristics based on these experimental results. Additionally, it provides information on the originating diseases and the number of related publications, while also linking to the cell catalog of the RIKEN BioResource Research Center (BRC).

How to use DiiPS

The Top Page

(https://diips.brc.riken.jp/)

"Home" switches the screen to the top page.
"About" provides detailed information about this software.
"Menu" switches the screen to the user manual (this document) for this software.
The banner links to the RIKEN BRC Cell Material Development Laboratory or RIKEN BRC.
You can switch between English and Japanese using the language selector button in the upper-right corner of the screen.

Analysis List

The visualization of iPSC pluripotency in the DiiPS software is based on the results of various experiments. On the top page, under “Analysis List”, you can select any of the experiments used for evaluation and navigate to the Pluripotency Visualization Screen (Heatmap Screen).

Pluripotency Visualization Screen

The Pluripotency Visualization Screen (Heatmap Screen) consists of information on each iPS cell (table part: left) and heatmap part: right of omics analysis, allowing you to view the characteristics of each cell and differences in multipotency at a glance. Additionally, various filtering operations are available.

List part

Opening the Detail Screen

Click on the ID string in the Cell ID column to open the Detail of a Cell Screen. For detailed instructions, see the "Details of a Cell Screen" section below.

Accessing the BRC Cell Catalog

Click the blue arrowhead next to the Cell ID to open the BRC cell catalog in a new window and view detailed information.

Filtering by Column

Clicking the funnnel icon in each column opens a text input screen, allowing for filtering search.

Heat map part

In the heatmap part, cellular properties derived from omics analysis are summarized and displayed as “modules”. A module is a functional unit that groups together genes that co-vary in expression or are involved in the same biological function. (In the example below, cell characteristics are represented by six modules: Ectoderm, Emergent mesoderm, EPI, Nascent mesoderm, Amniotic, and Embryonic ectoderm.) The types and number of modules vary depending on the analysis. The horizontal dotted lines indicate the boundaries of cell clusters with similar characteristics.

The heatmap part is divided into the area displayed within the circle on the left and the full view on the right. The left section scrolls in sync with the list. The right-hand side always displays the full view. While the specific metrics represented by circle size (Metric 1) and color (Metric 2) vary depending on the analysis, they are indicated in the legend at the bottom along with their criteria. (In the example below, circle size: Metric 1 represents “Number of single cells,” and color: Metric 2 represents “Expression rate.”) Depending on the analysis, there may be only one metric; in that case, the circle size remains constant, and the legend displays only the color.

Filteling by color

In the heatmap, you can click the filter icon (funnel shape) for each module to use a slider to specify a color range. This allows you to filter the data to show only the cells with specific values.

Switching Between AND / OR Search Conditions

Use the AND / OR icon in the upper-right corner of the heatmap header to toggle between AND search and OR search when applying multiple filtering conditions.

Settings

Click the gear icon at the far right of the heatmap header to toggle column visibility and change the color scheme (color set).

Details of a Cell Screen

Clicking on the ID string in the Cell ID column opens the Detail Screen. This screen allows you to view detailed information about each cell.

Operations on the Details of a Cell Screen

Switching Cells with Arrow Keys

While the Detail Screen is open, you can switch between cells by pressing the Up or Down arrow keys on your keyboard.

Similarity Filtering

Adjusting the Similarity slider allows you to display only cells with similar differentiation characteristics on the heatmap. A lower Similarity value filters for cells with more similar differentiation properties. Press the Clear button to reset the filtering.

Link to RIKEN BRC Cell Catalog

There are two links to the RIKEN BRC Cell Bank.

Link on the heatmap screen

On the list on the left side of the heatmap screen, click the blue arrow next to the Cell ID to open the BRC Cell Catalog in a new window, where you can view detailed information about the selected cell. Information regarding cell availability is also provided.

Link in the Details of a Cell Screen

There is also a link to the RIKEN BRC Cell Bank at the very bottom of the details screen. Scroll to the bottom and click the Cell catalogue button. The details page for the relevant cell will open. Information regarding cell donation is also provided.

Manual