Neuroinformatics

Maryann Martone

Amarnath Gupta

Bioinformatics

•a scientific discipline that encompasses all aspects of biological information acquisition, analysis and interpretation

•combines tools and techniques of mathematics, computer science and biology

•depends on large stores of both experimental and derived data

Challenges

• Total amount of data (e.g., 250,000 new articles per year)

• Complexity of data and lack of standardization

• Lack of general-purpose, interoperable tools

• Lack of automation

Information Paradox

Too much data Too little data

“Understanding brain function requires the integration of information from the level of the gene to the level of behavior. At each of these many and diverse levels there has been an explosion of information, with a concomitant specialization of scientists. The price of this progress and specialization is that it is becoming virtually impossible for any individual researcher to maintain an integrated view of the brain and to relate his or her narrow findings to this whole cloth.”

-Stephen Koslow

species discipline modalitytechnique

Too little information:

-missing information

-information that was known at one time but lost

-information that may not be explicit

-information was known but not recorded

-information contained in images, traces etc.

DataPublication

SpecimenInstrument Images

Traditional Method of Data Collection and Presentation

DataPublication

SpecimenInstrument Images

DatabaseDatabase

Human Brain Project: Moving towards an information-centric approach to Neuroscience

Data

SpecimenInstrument Images

Information Sources.Database.Literature.Web sites

Information Sources.Database.Literature.Web sites

Information-centric Neuroscience

• Development of a 3D Cell-centered database. Human Brain Project

• Federation of Brain Data: National Partnership for Advanced Computational Infrastructure

Two Research Efforts:

• Intro to Bioinformatics

• Databases

• Data modeling

• Brain imaging

• Neuronal modeling

• Data integration

Topics

Structure of Course

• Weekly seminar

• Articles or exercises

• Class discussion

• Short paper on neuroinformatics approaches to your own research

http://ncmir.ucsd.edu/NCDB/