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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.
Windows
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.
Linux
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.
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