Difference between revisions of "SOCR News IBRO INSF Malaysia 2017"
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* Location: [http://cape.utp.edu.my/contact-us/ Centre For Advanced And Professional Education (CAPE), Menara Kembar Bank Rakyat] | * Location: [http://cape.utp.edu.my/contact-us/ Centre For Advanced And Professional Education (CAPE), Menara Kembar Bank Rakyat] | ||
* [https://www.trelliscience.com/#/group-home/1576 IBRO/INCF 2017 Summer School Trellis Forum] (protected) | * [https://www.trelliscience.com/#/group-home/1576 IBRO/INCF 2017 Summer School Trellis Forum] (protected) | ||
| + | * Webcast: [https://www.youtube.com/watch?v=ptMCu4mIbI8&t=0s&list=PLWYWUwcywqfgW868At5pXdOOy_q2XcWhy&index=4 (archived YouTube) videos] | ||
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===Aug 11, 2017 (High Throughput Processing of Big Neuroscience Data)=== | ===Aug 11, 2017 (High Throughput Processing of Big Neuroscience Data)=== | ||
[[Image:PL_GSA_Schematic.png|250px|thumbnail|right| Statistical Computing]] | [[Image:PL_GSA_Schematic.png|250px|thumbnail|right| Statistical Computing]] | ||
| − | * [http://pipeline.loni.usc. | + | * [http://pipeline.loni.usc.edu Pipeline Environment] |
* [http://pipeline.loni.usc.edu/learn/user-guide/ Pipeline Client GUI] – data, modules and workflow objects | * [http://pipeline.loni.usc.edu/learn/user-guide/ Pipeline Client GUI] – data, modules and workflow objects | ||
* [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] | * [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] | ||
| − | * [https://wiki.loni.usc.edu/index.php/ | + | * [https://wiki.loni.usc.edu/index.php/Main_Page Pipeline workflows documentation] |
* [http://pipeline.loni.usc.edu/explore/library-navigator/ Pipeline Workflow Library] | * [http://pipeline.loni.usc.edu/explore/library-navigator/ Pipeline Workflow Library] | ||
* [http://pipeline.loni.usc.edu/files/miner/ Pipeline workflow miner] | * [http://pipeline.loni.usc.edu/files/miner/ Pipeline workflow miner] | ||
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===Aug 15-16, 2017 3<sup>rd</sup> Malaysia Telemedicine Conference (2017)=== | ===Aug 15-16, 2017 3<sup>rd</sup> Malaysia Telemedicine Conference (2017)=== | ||
[[Image:Dinov_BigData_Schematic.png|250px|thumbnail|right| Statistical Computing]] | [[Image:Dinov_BigData_Schematic.png|250px|thumbnail|right| Statistical Computing]] | ||
| − | The theme of the [http://med.monash.edu.my/campaign/telemed/index.html 2017 Malaysia Telemedicine Conference] is ''Healthcare for Tomorrow - The Disruptions | + | 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 |
* [http://socr.umich.edu/docs/uploads/Dinov_PredictiveDataAnalytics_2017_MalaysiaTelemedicine.pdf Lecture notes (PDF)] | * [http://socr.umich.edu/docs/uploads/Dinov_PredictiveDataAnalytics_2017_MalaysiaTelemedicine.pdf Lecture notes (PDF)] | ||
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=== Aug 18, 2017 (Neuroimaging-genetics)=== | === Aug 18, 2017 (Neuroimaging-genetics)=== | ||
[[Image:PL_GenomicsComputing.png|250px|thumbnail|right| Statistical Computing]] | [[Image:PL_GenomicsComputing.png|250px|thumbnail|right| Statistical Computing]] | ||
| + | * 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]. | ||
* [https://github.com/SOCR/PBDA Predictive Big Data Analytics (PBDA/PD)] | * [https://github.com/SOCR/PBDA Predictive Big Data Analytics (PBDA/PD)] | ||
* PLINK association workflow | * PLINK association workflow | ||
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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 | ** 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 | ||
** 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 | ** 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 | ||
| − | ** 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. | + | ** 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. |
<hr> | <hr> | ||
Latest revision as of 07:15, 4 October 2018
Contents
SOCR Events - INCF/IBRO 2017 Neuroscience Summer School and 2017 Malaysia Telemedicine Conference
Logistics
- IBRO-APRC/INCF School on Neuroinformatics and Brain Connectivity Analysis 2017, Kuala Lumpur, Malaysia
- Dates: Sunday, August 06, 2017 09:00 PM -- Saturday, August 19, 2017 05:00 AM
- Location: Centre For Advanced And Professional Education (CAPE), Menara Kembar Bank Rakyat
- IBRO/INCF 2017 Summer School Trellis Forum (protected)
- Webcast: (archived YouTube) videos
Outlines of Prof. Dinov's lectures are listed below.
Aug 10, 2017 (Statistical Computing)
- Data Science and Predictive Analytics
- Motivation
- I. Foundations of R
- II. Data Management
- III. Visualization
- X. Black Box Machine-Learning Methods: Neural Networks and Support Vector Machines
- XVII. Regularized Linear Modeling and Controlled Variable Selection
- XIX. Text Mining and Natural Language Processing
- XX. Forecasting and Prediction with Statistical Cross-Validation
- XXII. Deep Learning and Neural Networks
- Datasets & Case-Studies
Aug 11, 2017 (High Throughput Processing of Big Neuroscience Data)
- Pipeline Environment
- Pipeline Client GUI – data, modules and workflow objects
- Module definition and workflow construction
- Pipeline workflows documentation
- Pipeline Workflow Library
- Pipeline workflow miner
- Case-studies
- Global Shape Analysis (GSA)
- Simple 3 cohort study of dementia
- /ifs/loni/ccb/collabs/2017/INCF_IBRO_SummerSchool
- GSA workflow (ADNI_11AD_11_MCI_11HC_CaseStudy_DM.csv)
- Global Shape Analysis (GSA)
- GSA Doc
- GSA Try-It-Now, Try-It Now server; Cranium -> LONI -> Global Shape Analysis - Two Groups (Complete) workflow
- Minimum deformation template (MDT)
- Tensor-Based Morphometry (TBM)
- PLINK Association
Aug 15-16, 2017 3rd Malaysia Telemedicine Conference (2017)
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
- Driving biomedical problems and motivational health challenges
Aug 18, 2017 (Neuroimaging-genetics)
- Use 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 Pipeline R-invocation example.
- Predictive Big Data Analytics (PBDA/PD)
- PLINK association workflow
- Pipeline bioinformatics and Genomics computing pipeline workflows
- Design Matrices and Study-Modules: e.g., 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
- Examples of published studies
- 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)
- 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
- 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
- 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) Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows, Genes, 3(3):545-575; doi:10.3390/genes3030545.
- SOCR Home page: http://www.socr.umich.edu
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