Prerequisites: NSCI 210 (Introduction to Neuroscience), Psyc 372
(Biopsychology) or permission of the instructor.
Course Goals: This is a hands-on overview of the available and
developing informatics infrastructure for neuroscience research,
recommended for all graduate neuroscience students. The aim is to
provide students with sufficient practical understanding to
appreciate the range of tools and electronic resources that are
part of the contemporary scientific approach to the investigation
of the brain. Students will start using this knowledge
immediately, continuing to update and augment it throughout their
Method of Instruction and Evaluation: Weekly class will consist of
a combination of lectures and live demonstrations. There is no
assigned textbook. Student attendance, punctuality, completion and
reporting of homework assignments, and active participation in
class discussion are all required. Each student will be assigned
individual weekly homeworks as well as a project to be
demonstrated at the end of the semester. Final grades will be
based on 50% class participation and homework discussion, and 50%
project preparation and presentation. Letter grades will be
assigned as follows: A+ and A, 4.00; A-, 3.67; B+, 3.33; B, 3.00;
C, 2.00; F, 0.00.
Instructor: Dr. Giorgio Ascoli - Ph. x3-4383, E-mail:
Office location: Krasnow Institute, Rm. 223
Office hours: Monday 3-4p, Thursday 2:45-3:45p or by appointment.
Technology Requirement: Ability to access the web and email
Honor Code: Mason Academic Policies apply in full
If you are a student with a disability and you need academic
accommodations, please see me and contact the Disability Resource
Center (DRC) at 703-993-2474. All academic accommodations must be
arranged through that office.
(Approx.) Class Schedule of Topics and Readings
1) 1/23: Course goals and format. Overview of neuroinformatics
challenges and opportunities. Preview and brief description of
resources and topics. Discussion of suitable final projects and
presentation assignments. Neuronal morphology: NeuroMorpho.Org
functionality and pipeline.
Last day to add classes & to drop with no tuition penalty:
2) 1/30: Neuronal reconstructions: from image stacks to digital
vector traces. Reconstruction, analysis, visualization, modeling.
ImageJ, Neuron_Morpho plug-in, Neuromantic, Vaa3D, Neuronland,
CVAPP, L-Measure, neuroConstruct, Py3DN. Hands-on activity:
tracing example data set and extract normalized Sholl-like plots.
Useful links here, there,
and in Table 1 of this
article (freely available on campus ethernet; otherwise click).
image stack or one
of these, or else look
for more. Presentation slides
for this class are also available.
6) 2/27: Electrophysiology and biophysics:
Compartmental simulations: a brief historical overview
on the theory, illustrative results and applications. NEURON (more here; also on wikipedia
Check out this
list for many additional relevant resources
including Genesis, Moose, and several
others (see also this and all three sets
of "useful links" in Class 2). Hands-on activity: spike
propagation and synaptic integration in the reconstructed data
set. Presentation slides for
this class are also available. [NEW 3/7: additional
Spring Break 3/13.
8) 3/20: Neuroscience knowledge bases: NIF and NeuroLex; INCF, Neuron Registry and NeuronID; Senselab, Whole Brain Catalog, BrainInfo, and
mining: Pubmed, Google Scholar, google custom search (like
one), and full-text-searches (Textpresso, PMC, Metafinder
or individual publisher' sites, such as this or this). Hands-on activity:
Search and extract hippocampal cell-type connectivity. Alternative
(or additional) hands-on activity: Request and examine available
data from 15 articles (5 published in 2013, 5 in 2008, and 5 in
Students' presentations of selected resources & draft project
proposal pre-presentations (30+5 minutes): Byron (WormAtlas) and
10) 4/3: Neuroscience bioinformatics: NCBI resources (e.g.
BLAST, Swissprot, in-situ hybridization, microarrays, GEO, etc.),
NeuroMab, GENSAT, Allen Brain Expression Maps.
Non-invasive human brain imaging. NeuroVault, LONI resources (ICBM, BIRN, CCP,
ADNI, HCP, MAP, etc.), BraVa,
NITRC. Whole-brain network simulations
and human connectome
project. Hands-on activity: Search and propose activation foci for
value and arousal. Alternative (or
additional) hands-on activity: Search and
compare I_h and NMDA sequences in DG, CA3, CA1.
Students' presentations of selected resources &
draft project proposal pre-presentations (30+5 minutes): Adwait
(Neuron) and Kevin (CellProfiler and/or other ImageJ
11) 4/10: Guest lecture by Dr. Ken P. Smith (MITRE
Corp. & GMU). Does the hypothesis drive the information
architecture or vice versa? When and how to use which
tool: Google, clickstream data, Hadoop, etc. Here are the
slides. See also Science
report on Google
Pre-proposal office hours:
Thursday 4/10 at 11:15a - Justin
Friday 4/11 at 2:45p - Moe
12) 4/17: Project presentations and feedback # 1 (Justin
King) and "Brain in the box" discussion.
Pre-proposal office hours:
Thursday 4/17 at 2:45 - Siva
Thursday 4/17 at 3:30 - Sumit
Friday 4/18 at 11a - Adwait
Monday 4/21 at 11:45 - Kevin
Monday 4/21 at 12:15 - Byron