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Projects --> Visual Brain Application

Visual Brain Application

Organizer: Shaheen Lakhan

Producer: David Kelleher

Database Developer:  Seth Aaronson

Description:  The Visual Brain Application project will provide a visualization of brain disorders, neuroanatomy, and neurotransmitters. As a free and open-access application, the project will incorporate advanced Flash technologies with a summary of each neurological or mental health disorder, neurotransmitter, and neuropeptides involved. The project will use advanced MEDLINE and PubMed database integration for full search capabilities, including options for Clinical Search Queries (therapy, diagnosis, etiology, and prognosis articles) and Systematic Reviews essential for locating clinically sound studies and systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, and guidelines, respectfully. Summary information for brain disorders and affected brain regions and neurotransmitters will provide copious links to the NCBI Entrez System, including Online Mendelian Inheritance in Man, a catalog of human genes and genetic disorders

Audience: students, professionals, and educators who are studying, practicing, or teaching basic sciences (neuroscience, neurobiology, biochemistry), medical sciences (psychiatry, neurology, nursing), and/or psychology (neuro, clinical, abnormal, health).

  1. Objectives

  2. Project Overview

  3. Project Details

  4. Design

  5. Technology

  6. Production Schedule

  7. Updates

1. Objectives

This project will provide a visualization of brain disorder knowledge with links to relevant research articles.

For the researchers:

  • Create a web form that scientists can use to enter details about brain disorders
  • Use graphics and animation to show changes in the brain that occur with the disorders
  • Provide a space to summarize and link to current research.

For the developers:

  • Create documents and files that can be used for articles, books, or courses on application development
  • Develop graphics, animation, and code that can be reused in commercial projects
  • Produce a portfolio piece that can be submitted to design contests and shown to prospective clients

2. Project Overview

For the neuroscience web site home page, there will be a small Flash animation of just the brain portion of this project. It will explain and link to the full project. This 'splash' animation can be embedded in a small box on the home page. Since the full project will require enough screen space to fill an entire browser window, that should be a separate Flash movie linked from the home page.

The neuroscience project will include a brain disorder dropdown menu, illustrations of the brain and neurons, and a summary box where scientists can enter research details. Visualizations of changes in the brain that occur for each disorder will also be shown.

The admin area for the scientists will have a brain disorder form where scientists can add and delete disorders, and a detail form including fields for brain part size, activity level, neurotransmitters, summary, and links.

3. Project Details

The project window will include the following components

  • Project title, which incorporates the Neuroscience Initiative logo
  • Brain disorder drop down selection menu, including a 'normal' option and the disorders
  • Illustration of the brain where the size and activity level of each part can be changed
  • Comment area, where clicking the parts of the brain prints size and activity level changes
  • Illustration of presynaptic and postsynaptic neurons, to show normal activity and when they fail
  • Comment area, listing the neurotransmitter that is suspected for the selected disorder / brain part
  • Summary box, including research and web links for the selected disorder and selected brain part

The brain disorders, and details for each disorder, will be stored in a database on the neuroscience website.

The disorder drop down menu will retrieve the available disorders from the database. When a disorder is selected, the illustration of the brain, illustration of neurons, comments, and summary box will be updated.

The illustration of the brain will include the following parts:

  • Frontal Lobe
  • Parietal Lobe
  • Occipital Lobes
  • Temporal Lobes
  • Brain Stem
  • Cerebellum

A second illustration can show the parts of the limbic system:

  • Hypothalamus
  • Thalamus
  • Amygdala
  • Hippocampus

The illustration of the brain will also include a trace outline of a normal sized brain. When a disorder is selected, parts of the brain can increase and decrease in size according to the information entered into the database. The trace outline of a normal brain will remain so the difference can be seen visually. The comment area next to the brain will state which parts changed size and by how much.

The activity level of each brain part will also be shown. This could be visualized using colors, patterns of dots, or motion. A test will be completed during the design phase to identify which technique would be most successful for showing the activity level of the brain. The comment area will state how the activity level changed for the selected disorder.

Each part of the brain will be clickable. When a disorder is first selected, the summary box will show general information about the disorder. When a part of the brain is selected, the summary box will change to show information specific to that part of the brain. A button next to the brain illustration will allow users to switch back to the general information. Clicking on a brain part will also change the comment areas that expain how the size, activity level, and neurotransmitters are changed in that part of the brain.

The illustration of presynaptic and postsynaptic neurons will show dots moving from one to the other.

The number of dots and percentage that successfully make it to the postsynaptic neuron can be controlled. The comment area will state which neurotransmitters are involved what goes wrong for each part of the brain.

The list of neurotransmitters available in the database will be:

  • glutamic acid
  • GABA
  • aspartic acid
  • glycine
  • vasopressin
  • somatostatin
  • neurotensin
  • norepinephrine
  • dopamine
  • seratonin
  • acetylcholine

The administration section of the web will include these forms:

There will be a web page to add and disable brain disorders

There will be a detail page for each disorder, including the following fields:

  • Overview of research for the disorder
  • Links to research
  • There will also be subforms on the disorder page for each part of the brain, including the following:
  • Overview of research for the disorder, specific to a part of the brain
  • Links to research, specific to a part of the brain
  • Brain part size increase or decrease (specify percentage)
  • Activity level increase or decrease (specify percentage)
  • The name of the neurotransmitter involved in the disorder at the selected part of the brain
  • The amount of the neurotransmitter (specify percentage increase or decrease)
  • The failure rate of the neurotransmitter (specify percentage that fail)

A web form could also be created to let researchers add other neurotransmitters.

4. Design

The logo and style of the existing neuroscience initiative will be used as a guide for developing the interface and graphics in this project.

The illustrations will be created in a scalable vector format, so the project could be deployed for different screen sizes, on the web, and as a standalone application or CD-ROM.

The web version could be a 600x400 pixel box, in a popup window or embedded on a web page.

5. Technology

The server portion of this project will be written in PHP and connect to a MySQL database.

The project will be developed in Flash MX 2004 and one of the remoting techniques will be used to connect to the database.

6. Production Schedule

After the proposal is revised and accepted, work will begin on a design document. Development will first start on the scripts and database, and a Flash prototype will be created to test the visualization techniques.

The final stage will be to complete the graphics and scripts for the project using Flash MX 2004.

7.  Updates

07/09/04 Two new mockups

Visual Brain Application Mockup 1

Visual Brain Application Mockup 2

Feedback: There should also be a section on this application that lists articles from the PubMed server ( For instance, if one searches for "Parkinson's disease" and "Frontal lobes" both of these phrases will be searched on PubMed and the listing automatically places in this field/cell. Then, there should also be a field and search box for general searches that will reveal entries from PubMed.

We foresee this neuroscience application to me used in undergraduate, graduate, and post-graduate medical sciences (psychiatry, neurology, nursing), basic sciences (neuroscience, neurobiology, molecular psychiatry), and clinical psychology instruction.


08/22/04 Flash MX designed; new screenshots

Visual Brain Application Screenshot 3

Visual Brain Application Screenshot 4

Render 1

Render 2


  • Increase the ratio of the "Summary of Research" box relative to the "List of Articles".

  • Add a text box on top of "Search for Articles" button, that allows the user to enter (and manipulate) search strings.

  • Add Clinical Search Queries intended for clinicians, such as Systematic Reviews, Therapy, Diagnosis, Etiology, and Prognosis (Based on Haynes RB, et. al.).

  • Integrate or link database from the NCBI (National Center for Biotechnology Information) called OMIM (Online Mendelian Inheritance of Man").


08/22/04 Added Clinical Search Queries and Systematic Reviews support

Visual Brain Application Screenshot 5

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