Neuroscholar Software

We are very pleased to announce the release of the NeuroScholar system as an installation package. As with any commercial software, download the package, double-click on the installer and the system guide you through the process of installing NeuroScholar. This system should be considered an early (and therefore potentially somewhat fragile) production release.

Note that all downloads are hosted by SourceForge and are therefore anonymous. This means that official reviewers of our work can download and run the software without compromising their anonymity.

We are only releasing the 'core' knowledge model in the NeuroScholar installation package at this time. This system provides the basic functionality of being able to annotate and manage knowledge from the literature in the form of PDF files. This system forms the base for all other subsequent components.

The system is available for Windows, Mac OS X and Linux. Users without MySQL pre-installed on their machine will either need to download the binary with MySQL bundled or download MySQL separately. 

The JRE (Java Runtime Environment) is required in order to run NeuroScholar. Currently NeuroScholar is tested under JRE 1.4 and may not function properly under JRE 1.5. Users without JRE pre-installed on their machine will either need to download the binary verison with JRE bundled or download JRE separately. Users with JRE 1.5 are recommended to download the binary version with JRE bundled.


Mac OS X

Note: After extensive testing, we have found that attempting to bundle MySQL with our MacOSX installation package did not work. For Tiger, and Panther systems, use the following link to download a compatible version of MySQL:

These packages can be installed in the usual way for any application. Users are advised to go through a 'typical' install for MySQL and to remember the root password, since that is what you will be using to initialize NeuroScholar when you run it for the first time.


Note: Due to the great amount of MySQL servers are available for different Linux machines, please use the following link to download the version for your machine:

Knowledge Model

In addition to the 'core' knowledge model, other knowledge models can be downloaded from the following links. They are installation packages as well. You can simply double-click it, the installer will guide you through the setup process, and the knowledge model will be installed into your NeuroScholar system.

The following knowledge models are still under development as prototypes . They are not as stable as the 'core' model. The architecture of these knowledge models can be illustrated in the following diagram:

Connectivity: This is a standalone database concerned with a simple representation of neuroanatomical connectivity. This is a legacy system from Gully Burns doctoral dissertation. [Windows] [Mac OS X] [Linux RPM / Binary]

Diagrammar: This model is built on the basic code model. It contains additional views concerned with importing summary diagrams depicting into the knowledge base. A user may then ‘map’ his/her knowledge graphically and link Knowledge Statements to the elements of the diagram. [Windows] [Mac OS X] [Linux RPM / Binary]

Neuart: This model is built on the basic core model. It describes additional views that are concerned with mapping data into a neuroanatomical atlas, such as the ‘Brain Volume’ view (which simply describes a region of space drawn onto several atlas levels) and a ‘Data Map’ view (which describes the distribution of a set of graphical elements over atlas plates). Both these elements are used extensively to represent data from experiments. [Windows] [Mac OS X] [Linux RPM / Binary]

Notebook: This model is based on the basic core model. It describes additional views that are children of the Resource view and the Fragment view that permit users to build fragments from local image files. These could include image data captured from microscopes or scanned notebook pages. Thus this provides the elements of a rudimentary electronic laboratory notebook. [Windows] [Mac OS X] [Linux RPM / Binary]

Physiology: This is built onto the NeuARt package and contains views that represent the most important features of a physiological experiment designed to implicate a specific neuronal population (which may be scattered across several brain regions) in a behavior, or other global physiological activity involving the whole animal. This includes observation experiments, where changes may be measured in the brain when the animal performs the behavior, or interventional experiments, where some localized manipulation of brain tissue on the part of the experimenter causes a change in the animal’s performance of the behavior. [Windows] [Mac OS X] [Linux RPM / Binary]

TractTracing: This is built onto the NeuARt package and contains views that represent the most important features of a tract tracing experiment: where injections of tracer were made, where the transported labeling was found and what type of tracer was used. This is supported by the knowledge capture module in the fragmenter. [Windows] [Mac OS X] [Linux RPM / Binary]

Whole: This is a composite system made up of all the other available NeuroScholar models: this includes core, notebook, neuart, diagrammar, tracttracing, and physiology. This is principally for developers use and the reader  is referred to the documentation for each of the constituent models for details. [Windows] [Mac OS X] [Linux RPM / Binary]

User Manual

We have written the following documentation as a downloadable PDF file and are working towards importing it into the software as part of the systems help files.

If you encounter problems, please use the Sourceforge discussion groups or submit a bug report. If you like to receive future announcements regarding to the software release, please subscribe the mailing list.