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== [[SOCR_News | SOCR Events]] - INCF/IBRO 2017 Neuroscience Summer School and 2017 Malaysia Telemedicine Conference==
  
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[[Image:SOCR_D3_JavaScript_Viewer.png|250px|thumbnail|right| INCF/IBRO Summer School]]
  
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=== Logistics ===
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* [http://ibro.info/events/applications-open-for-ibro-aprc-school-on-neuroinformatics-and-brain-network-analysis/ IBRO-APRC/INCF School on Neuroinformatics and Brain Connectivity Analysis 2017], Kuala Lumpur,  Malaysia
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* Dates: Sunday, August 06, 2017 09:00 PM -- Saturday, August 19, 2017 05:00 AM
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* Location: [http://cape.utp.edu.my/contact-us/ Centre For Advanced And Professional Education (CAPE), Menara Kembar Bank Rakyat]
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* [https://www.trelliscience.com/#/group-home/1576 IBRO/INCF 2017 Summer School Trellis Forum] (protected)
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* Webcast: [https://www.youtube.com/watch?v=ptMCu4mIbI8&t=0s&list=PLWYWUwcywqfgW868At5pXdOOy_q2XcWhy&index=4 (archived YouTube) videos]
  
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Dinov Lecture Notes Organization
 
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INCF/IBRO 2017 Neuroscience Summer School
 
  
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'''Outlines of Prof. Dinov's lectures are listed below.'''
  
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Aug 10 Ivo Dinov (Statistical Computing)
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===Aug 10, 2017 (Statistical Computing) ===
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• Data Science and Predictive Analytics (http://DSPA.predictive.space)
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[[Image:SMHS_SciVisualization_V2.png|250px|thumbnail|right| Statistical Computing]]
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o Motivation
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* [http://DSPA.predictive.space Data Science and Predictive Analytics]
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o I. Foundations of R
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/00_Motivation.html Motivation]
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o II. Data Management
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/01_Foundation.html I. Foundations of R]
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o III. Visualization
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/02_ManagingData.html II. Data Management]
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o X. Black Box Machine-Learning Methods: Neural Networks and Support Vector Machines
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/03_DataVisualization.html III. Visualization]
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o XVII. Regularized Linear Modeling and Controlled Variable Selection
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/10_ML_NN_SVM_Class.html X. Black Box Machine-Learning Methods: Neural Networks and Support Vector Machines]
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o XIX. Text Mining and Natural Language Processing
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/17_RegularizedLinModel_KnockoffFilter.html XVII. Regularized Linear Modeling and Controlled Variable Selection]
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o XX. Forecasting and Prediction with Statistical Cross-Validation
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/19_NLP_TextMining.html XIX. Text Mining and Natural Language Processing]
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o XXII. Deep Learning and Neural Networks
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/20_PredictionCrossValidation.html XX. Forecasting and Prediction with Statistical Cross-Validation]
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o Datasets & Case-Studies: https://umich.instructure.com/courses/38100/files/folder/Case_Studies  
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** [http://www.socr.umich.edu/people/dinov/2017/Spring/DSPA_HS650/notes/22_DeepLearning.html XXII. Deep Learning and Neural Networks]
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** [https://umich.instructure.com/courses/38100/files/folder/Case_Studies Datasets & Case-Studies]
  
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Aug 11 Ivo Dinov (High Throughput Processing of Big Neuroscience Data)
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===Aug 11, 2017 (High Throughput Processing of Big Neuroscience Data)===
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• Pipeline Environment http://pipeline.loni.usc.edu  
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[[Image:PL_GSA_Schematic.png|250px|thumbnail|right| Statistical Computing]]
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• Pipeline Client GUI – data, modules and workflow objects
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* [http://pipeline.loni.usc.edu Pipeline Environment]
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• Module definition (http://pipeline.loni.usc.edu/learn/user-guide/creating-modules/#Simple%20modules) and workflow construction (http://pipeline.loni.usc.edu/learn/user-guide/building-a-workflow/#Building%20a%20workflow)
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* [http://pipeline.loni.usc.edu/learn/user-guide/ Pipeline Client GUI] – data, modules and workflow objects
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• Pipeline workflows documentation: https://wiki.loni.usc.edu/index.php/Main_Page
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* [http://pipeline.loni.usc.edu/learn/user-guide/creating-modules/#Simple%20modules Module definition] and [http://pipeline.loni.usc.edu/learn/user-guide/building-a-workflow/#Building%20a%20workflow workflow construction]
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• Pipeline Workflow Library: http://pipeline.loni.usc.edu/explore/library-navigator/
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* [https://wiki.loni.usc.edu/index.php/Main_Page Pipeline workflows documentation]
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• Pipeline workflow miner: http://pipeline.loni.usc.edu/files/miner/  
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* [http://pipeline.loni.usc.edu/explore/library-navigator/ Pipeline Workflow Library]
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• Case-studies
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* [http://pipeline.loni.usc.edu/files/miner/ Pipeline workflow miner]
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o Global Shape Analysis (GSA)
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* Case-studies
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Simple 3 cohort study of dementia
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** [https://wiki.loni.usc.edu/index.php/Global_Shape_Analysis_(GSA)_Workflow Global Shape Analysis (GSA)]
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/ifs/loni/ccb/collabs/2017/INCF_IBRO_SummerSchool
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*** Simple 3 cohort study of dementia
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GSA workflow (ADNI_11AD_11_MCI_11HC_CaseStudy_DM.csv)
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*** ''/ifs/loni/ccb/collabs/2017/INCF_IBRO_SummerSchool''
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• https://wiki.loni.usc.edu/index.php/Global_Shape_Analysis_(GSA)_Workflow
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*** GSA workflow ([https://umich.instructure.com/files/5062660/download?download_frd=1 ADNI_11AD_11_MCI_11HC_CaseStudy_DM.csv])
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• http://bit.ly/1Djhihs  
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* [https://wiki.loni.usc.edu/index.php/Global_Shape_Analysis_(GSA)_Workflow GSA Doc]
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Try-It Now server; Cranium LONI Global Shape Analysis - Two Groups (Complete) workflow
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* [http://bit.ly/1Djhihs GSA Try-It-Now], Try-It Now server; Cranium -> LONI -> Global Shape Analysis - Two Groups (Complete) workflow
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o Minimum deformation template (MDT): https://wiki.loni.usc.edu/index.php/MDT_Atlasing_Workflow
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* [https://wiki.loni.usc.edu/index.php/MDT_Atlasing_Workflow Minimum deformation template (MDT)]
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o Tensor-Based Morphometry (TBM): http://pipeline.loni.usc.edu/explore/library-navigator/  
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* [http://pipeline.loni.usc.edu/explore/library-navigator/ Tensor-Based Morphometry (TBM)]
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o PLINK Association: http://pipeline.loni.usc.edu/explore/library-navigator/
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* [http://pipeline.loni.usc.edu/explore/library-navigator/ PLINK Association]
  
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===Aug 15-16, 2017 3<sup>rd</sup> Malaysia Telemedicine Conference (2017)===
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[[Image:Dinov_BigData_Schematic.png|250px|thumbnail|right| Statistical Computing]]
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The theme of the [http://med.monash.edu.my/campaign/telemed/index.html 2017 Malaysia Telemedicine Conference] is ''Healthcare for Tomorrow - The Disruptions Begin''. Prof. Dinov's Keynote Presentation is titled ''Predictive Data Analytics'', Tuesday, 15 August 2017 at 9.00-9.45 AM, Sunway Medical Centre, Hospital Pusat Perubatan Sunway, 5, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor
  
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Aug 15-16 Dinov Keynote, Plenary 1- Predictive Data Analytics scheduled on Tuesday, 15 August 2017 at 9.00-9.45 am (45 minutes), at the Sunway Medical Centre, Hospital Pusat Perubatan Sunway, 5, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor
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* [http://socr.umich.edu/docs/uploads/Dinov_PredictiveDataAnalytics_2017_MalaysiaTelemedicine.pdf Lecture notes (PDF)]
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• Lecture notes: http://socr.umich.edu/docs/uploads/Dinov_PredictiveDataAnalytics_2017_MalaysiaTelemedicine.pdf  
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* Outline
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• Driving biomedical problems and motivational health challenges
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** Driving biomedical problems and motivational health challenges
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o Neurodegeneration
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*** Neurodegeneration
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o Pheno-Geno-Enviro
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*** Pheno-Geno-Enviro
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• Common Characteristics of Big (Biomedical and Health) Data
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**Common Characteristics of Big (Biomedical and Health) Data
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• Data science
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** Data science
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• Predictive analytics
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** Predictive analytics
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• Case-studies
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** Case-studies
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• Tomorrow’s Healthcare:  The Age of Disruptions
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** Tomorrow’s Healthcare:  The Age of Disruptions
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*** Open Problems
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*** Future Healthcare Innovation & Delivery
  
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Aug 18 Ivo Dinov (Neuroimaging-genetics)
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=== Aug 18, 2017 (Neuroimaging-genetics)===
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• Predictive Big Data Analytics (PBDA/PD): https://github.com/SOCR/PBDA  
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[[Image:PL_GenomicsComputing.png|250px|thumbnail|right| Statistical Computing]]
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• PLINK association workflow
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* Use [http://wiki.stat.ucla.edu/socr/uploads/8/84/R_invocationExample.pipe.zip these data and a skeleton of an R-script] to generate a batch mode R invocation that runs in the pipeline as a module, computes some models (ALS dataset is included in the ZIP file) and saves the results locally in a file. See also the [http://bit.ly/1Djhi0Q Pipeline R-invocation example].
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o https://wiki.loni.usc.edu/index.php/PLINK_GWAS_Workflows
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* [https://github.com/SOCR/PBDA Predictive Big Data Analytics (PBDA/PD)]
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o http://bit.ly/1BuiI5j  
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* PLINK association workflow
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• Pipeline bioinformatics and Genomics computing pipeline workflows https://wiki.loni.usc.edu/index.php/LONI_Pipeline_Genomics_and_Informatics_Workflow_Solutions
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** https://wiki.loni.usc.edu/index.php/PLINK_GWAS_Workflows
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• Examples of published studies
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** http://bit.ly/1BuiI5j  
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o Moon, S., Dinov, ID, Kim, J, Zamanyan, A, Hobel, S, Thompson, PM, Toga, AW (2015) Structural Neuroimaging Genetics Interactions in Alzheimer's Disease. Journal of Alzheimer's Disease, 48(4):1051-63, doi: 10.3233/JAD-150335 (PMID: 26444770)
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* [https://wiki.loni.usc.edu/index.php/LONI_Pipeline_Genomics_and_Informatics_Workflow_Solutions  Pipeline bioinformatics and Genomics computing pipeline workflows]
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o Moon, SW, Dinov, ID, Hobel, S, Zamanyan, A, Choi, YC, Thompson, PM, Toga, AW and Alzheimer's Disease Neuroimaging Initiative (ADNI) (2015) Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment. Journal of Neuroimaging, 25(5):728–737,. DOI: 10.1111/jon.12252
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* [http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression#Volume_Multiple_Linear_Regression_Usage Design Matrices] and [http://pipeline.loni.usc.edu/learn/user-guide/building-a-workflow/#Study Study-Modules]: e.g., [https://umich.instructure.com/files/5062660/download?download_frd=1 12_ADNI_11AD_11_MCI_11HC_CaseStudy_DM.csv]; save this CSV file locally, open the pipeline client, drag-and-drop the CSV into the workflow canvas, specify the second column as carrying the references to the imaging volumes, construct the study-module and plug it into the GSA workflow as input data
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o Moon, SW, Dinov ID, Zamanyan, A, Shi, R, Genco, A, Hobel, S, Thompson, PM, Toga, AW and Alzheimer's Disease Neuroimaging Initiative (ADNI) (2015) Gene Interactions and Structural Brain Change in Early-Onset Alzheimer's Disease Subjects Using the Pipeline Environment . Psychiatry Investigation, 12(1):125-135. DOI: 10.4306/pi.2015.12.1.125
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* Examples of published studies
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•
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** Moon, S., Dinov, ID, Kim, J, Zamanyan, A, Hobel, S, Thompson, PM, Toga, AW (2015) [http://dx.doi.org/10.3233/JAD-150335 Structural Neuroimaging Genetics Interactions in Alzheimer's Disease]. Journal of Alzheimer's Disease, 48(4):1051-63, doi: 10.3233/JAD-150335 (PMID: 26444770)
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** Moon, SW, Dinov, ID, Hobel, S, Zamanyan, A, Choi, YC, Thompson, PM, Toga, AW and Alzheimer's Disease Neuroimaging Initiative (ADNI) (2015) [http://dx.doi.org/10.1111/jon.12252 Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment]. Journal of Neuroimaging, 25(5):728–737,. DOI: 10.1111/jon.12252
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** Moon, SW, Dinov ID, Zamanyan, A, Shi, R, Genco, A, Hobel, S, Thompson, PM, Toga, AW and Alzheimer's Disease Neuroimaging Initiative (ADNI) (2015) [http://dx.doi.org/10.4306/pi.2015.12.1.125 Gene Interactions and Structural Brain Change in Early-Onset Alzheimer's Disease Subjects Using the Pipeline Environment]. Psychiatry Investigation, 12(1):125-135. DOI: 10.4306/pi.2015.12.1.125
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** Torri, F., Dinov, ID, Zamanyan, A, Hobel, S, Genco, A, Petrosyan, P, Clark, AP, Liu, Z, Eggert, P, Pierce, J, Knowles, JA, Ames, J, Kesselman, C, Toga, AW, Potkin, SG, Vawter, MP, Macciardi, F. (2012) [http://dx.doi.org/10.3390/genes3030545 Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows], Genes, 3(3):545-575; doi:10.3390/genes3030545.
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<hr>
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* SOCR Home page: http://www.socr.umich.edu
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{{translate|pageName=http://wiki.socr.umich.edu/index.php/SOCR_News_IBRO_INSF_Malaysia_2017}}

Latest revision as of 07:15, 4 October 2018

SOCR Events - INCF/IBRO 2017 Neuroscience Summer School and 2017 Malaysia Telemedicine Conference

INCF/IBRO Summer School

Logistics


Outlines of Prof. Dinov's lectures are listed below.

Aug 10, 2017 (Statistical Computing)

Statistical Computing

Aug 11, 2017 (High Throughput Processing of Big Neuroscience Data)

Statistical Computing

Aug 15-16, 2017 3rd Malaysia Telemedicine Conference (2017)

Statistical Computing

The theme of the 2017 Malaysia Telemedicine Conference is Healthcare for Tomorrow - The Disruptions Begin. Prof. Dinov's Keynote Presentation is titled Predictive Data Analytics, Tuesday, 15 August 2017 at 9.00-9.45 AM, Sunway Medical Centre, Hospital Pusat Perubatan Sunway, 5, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor

  • Lecture notes (PDF)
  • Outline
    • Driving biomedical problems and motivational health challenges
      • Neurodegeneration
      • Pheno-Geno-Enviro
    • Common Characteristics of Big (Biomedical and Health) Data
    • Data science
    • Predictive analytics
    • Case-studies
    • Tomorrow’s Healthcare: The Age of Disruptions
      • Open Problems
      • Future Healthcare Innovation & Delivery

Aug 18, 2017 (Neuroimaging-genetics)

Statistical Computing

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