Topic in Neuroscience: Neuroinformatics

NEUR 689                        Thursdays 12n-2:45p, Krasnow 229

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 professional development.

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 communication.

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: Wednesday 1/29.

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). Try this image stack or one of these, or else look for more. Presentation slides for this class are also available.

3) 2/6: Dr. Laurence C. Bray: Neocortical Simulator.
Please read the last NCS publication ahead of class! [New 4/1 presentation slides!]


5) 2/20: Dr. Ruben Armananzas: Machine Learning for Bioinformatics.
Read here for a primer. Class material is available here.

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 and scholarpedia) and ModelDB. 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 tools here]

7) 3/6: Hippocampus, hippocampal circuitry (while the link is broken, look at this, including especially the supplementary interactive material!), neuron types, the Hippocampome and functional hippocampal models. System neuroanatomy, contours, surfaces, and volumes: Cytoarchitecture and Hippocampus3D. The rest of the brain: Brain maps and Allen Brain Reference Atlas (see class 10 for expression maps), VIAS, Reconstruct, tract-tracing. Hands-on activity: Quantify cytoarchitectonic gradients in mouse, rat, and monkey hippocampus. Presentation slides for this class are also available.

 Spring Break 3/13.

8) 3/20:
Neuroscience knowledge bases: NIF and NeuroLex; INCF, Neuron Registry and NeuronID; Senselab, Whole Brain Catalog, BrainInfo, and BAMS. Literature mining: Pubmed, Google Scholar, google custom search (like this 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 2003).
Students' presentations of selected resources & draft project proposal pre-presentations (30+5 minutes): Byron (WormAtlas) and Moe (FlyCircuit).

9) 3/27: 
 Students' presentations of selected resources & draft project proposal pre-presentations (30+5 minutes): Justin (ImageJ plugins), Siva (Brian simulator), and Sumit (Trees tool box).

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 plugins).

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 flu[ke].
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

13) 4/24: Project presentations and feedback # 2 & 3 (Moe Allaham + Adwait Lonkar).

14) 5/1: Project presentations and feedback # 4 & 5 (Siva Venkadesh + Sumit Nanda).

15) 5/6 (TUESDAY!
Make-up class...): Project presentations and feedback # 6 & 7 (Byron Price + Kevin Armengol).

16) 5/7 (WEDNESDAY! Extra guest-lecture!) at 1:45p: Dr. Steven Bressler (Florida Atlantic University
), Beta Synchrony in Visual Expectation.

5/8: grades posted on Patriot Web.