Can you help me with some database for neuroscience, for example fMRI database, or database which show underlying mechanisms of the brain, show the connection between brain and behavior, psychiatry database and other things which related to brain, if you were familiar with genetics we have for example Reactome, KEGG, STRING and other database which show lots of pathway and cell connection, I wonder if we have sth like that in neuroscience, a big database which help us to better understand the brain.
Here is a list of great readings addressing the topics you have mentioned: -fMRI:
1) "Introduction to Resting State fMRI Function Connectivity" by JANINE BIJSTERBOSCH, STEPHEN SMITH, and CHRISTIAN BECKMANN.
ISBN: 978–0–19–880822–0.
2) "fMRI Techniques and Protocols" by MASSIMO FILLIPPI. ISBN: 978-1-60327-918-5
- Underlying mechanisms of the brain; psychiatry basis:
1) "Comprehensive Developmental Neuroscience Neural Circuit Development and Function in the Healthy and Diseased Brain" by JOHN L. RUBENSTEIN and PASKO RAKIC. ISBN: 978-0-12-397266-8.
2) "Neurobiology of Brain Disorders - Biological Basis of Neurological and Psychiatric Disorders" by MICHAELJ. ZIGMOND, LEWIS P. ROWLAND, and JOSEPH T. COYLE. ISBN: 978-0-12-398270-4.
- A better understanding of the brain; links between brain and behavior:
1) “Fundamentals of Cognitive Neuroscience (Second Edition)” by NICOLE M. GAGE. ISBN: 978-0-12-803813-0.
2) "Understanding the Brain From Cells to Behavior to Cognition" by JOHN E. DOWLING. ISBN: 978-0-39371-258-2.
- Pathways and cell connections:
1) "Genetic Dissection of Neural Circuits and Behavior" by STEPHEN F. GOODWIN. ISBN: 978-0-12-374836-2. *Personal Favorite*
2) "Neurotransmitter Transporters Investigative Methods" by HEINZ BöNiSCH. ISBN 978-1-4939-3763-9.
Good Luck,
Seth
Hi Ali Motahharynia ,
Actually you can use those databases that you mentioned to conduct research and understand mechanisms of brain activity in health and disease in computational neuroscience!
We recently used KEGG and STRING to study gene networks in different psychiatric diseases.
However, if you are mainly interested in using fMRI and imaging databases in your research, please check the following as well:
1. Blue Brain project by EPFL has a great database in at circuit level that can be used:
https://bbp.epfl.ch/nmc-portal/welcome
2. Human Connectome Project (HCP) is a great database comprised of scans and analyses of more than 1100 subjects:
http://www.humanconnectomeproject.org/data/
3. Allen Brain Atlas
4. BIRN: https://openfmri.org
and many other databases that you may find and use depending on your main focus in neuroscience.
I am sorry but I don't think such a site/database exists for fMRI. I always had to do all the litterature research for a specific task, area or structure...
For a begining, some interresting data can be found here : https://www.nitrc.org/projects/task_fmri_atlas/
Dear Seth Shirazi
Thank you for such a detailed answer, I appreciate that.
Dear Bahman Sadeghi
I appreciate your taking the time to answer my question. It has really helped me, and one more question is that how can I relate these molecular databases and computational neuroscience together?
Hi Ali Motahharynia ,
Actually there is no direct or independent way or medium to relate these databases to any subject. Thus, these databases can be used for any goals in any studies from neurogenetics to computational and imaging studies.
It depends on the hypothesis and the aim of your own study which can be different from my own for instance and therefore we may both use the same data but with different approaches and disparate results.
You need to know what factors, parameters or dependent/independent variables you will be employing in your study and then match them with the variables or data available to choose how may you relate your own computational data with the databases and how they may help you.
For example: you may need to model a cortical neuron activity based on its magnitude of response, delay and the region it projects to or receives APs. You may need to design if it is excitatory or inhibitory... then you can select which database can be useful.
In another example, you may need to model a neuronal activity in a specific pathway (e.g. dopaminergic, serotonergic, etc.) in a specific psychiatric disorder (schizophrenia or OCD for instance). You see that by narrowing down your search via configuration of further variables you can use those mega databases such as KEGG or STRING in a much efficient way and relate the available data and refer to them or compare them in your own study.
Hope this helps.
Hi Bahman Sadeghi
yeah thanks your detailed and informative answer, that really helps.
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