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Keiichiro Ono edited this page Mar 14, 2017 · 35 revisions

DeepCell Web v1.0

Introduction

DeepCell Web provides simple user interface to browse ontology DAG and access to the DeepCell neural network service for translating gene deletion.

Overview

There are two main features in this application:

  • Ontology DAG (tree) browser
  • Gene deletion translator

Ontology DAG Browser

The main view is designed for browsing GO/CLIXO ontology as a tree. The tree visualization is interactive, and you can use the following actions to zoom/pan the view:

  • Zoom-in/out - Mouse wheel
  • Pan - Left-click and drag

To show the details about the term, just click it to open the property panel.

Term Search

If you are interested in specific terms or biological functions, you can use the term locator to find the terms of your interest. Just type in the keywords/term name to find them.

Gene Deletion Translator

  1. Search genes - you can use keywords or exact gene ID for searching genes you want to use for the translation.
  2. Select genes - To select genes you want to send to the DeepCell server, just click the check box on the left of the gene name.
  3. Click RUN - This send the pair of genes to the DeepCell server and run the simulation. Usually, it takes few seconds to finish.

Limitations

For this version, you can choose up to two genes for the simulation.

Result Viewer

After few seconds, the app displays the result of the translation as an interactive network view.

Basic Network (DAG) View

Size of the term represents importance of the term in the result.

Once you click the term, the internal neurons used in the ANN will be displayed.

Neural Network View

If you choose Show Neurons option, it expands the nodes to show the internal neurons.

Developer's Guide

(TBD)

Deploy your own DeepCell Server

(TBD)

License

MIT

Questions?

Please send your kono ucsd edu

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