SOCR Videos Dashboard - Revision history

Dinov: /* Protocol */

2018-08-17T18:57:16Z

‎Protocol

Dinov at 18:54, 17 August 2018

2018-08-17T18:54:40Z

Dinov at 18:48, 17 August 2018

2018-08-17T18:48:52Z

Dinov: /* Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE) */

2016-12-20T21:35:00Z

‎Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE)

Dinov: /* Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE) */

2016-12-20T21:34:30Z

‎Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE)

Dinov at 21:32, 20 December 2016

2016-12-20T21:32:20Z

Dinov at 21:27, 20 December 2016

2016-12-20T21:27:30Z

Dinov: /* Test Data */

2016-05-10T16:44:06Z

‎Test Data

Dinov: /* Setting up the Dashboard */

2016-05-10T16:38:08Z

‎Setting up the Dashboard

Dinov at 16:36, 10 May 2016

2016-05-10T16:36:47Z

@@ Line 91: / Line 91: @@
 #	Start the [http://socr.umich.edu/HTML5/Dashboard/ Data Dashboard App]
 #	Select '''Free—Anchored''' Data
-#	Enter the following in teh pop-up dialog box:
+#	Enter the following in the pop-up dialog box:
 ##          Cohort variable name: '''Age'''
 ##          Minimum cohort variable value: '''30'''
@@ Line 115: / Line 115: @@
 A very important feature of the SOCR Data Dashboard is that complies with data privacy protection and regulatory guidelines (e.g., HIPAA) to protect personal information. The Dashboard models the distribution in the entire data archive and simulates from the joint distribution to avoid rendering individualized data. As such, the Data Dashboard is neither an exact representation of the data nor it guarantees that a match/no-match found indicates the presence/absence of a specific participant from the study population.
 ===Reference Materials===

@@ Line 106: / Line 106: @@
 #       For instance, we can add '''Sex''' (Pie chart), '''Weight''' (histogram), '''ResearchGroup''' (Pie Chart), '''VisitID''' (Bar chart), and '''Brainstem computearea''' vs. '''Cerebellum volume''' (Scatterplot)
 #       At this point, the ''Dashboard canvas'' should look something like the image shown below
-[[Image:SOCR_Videos_Dashboard_Fig24.png|500px]]
+<center>[[Image:SOCR_Videos_Dashboard_Fig24.png|500px]]</center>
 #       We are now ready to initiate the process of (1) visual database query and exploratory analytics, and (2) dynamic visualization of intricate multivariate patterns that can be used to formulate new (testable) research hypotheses
 #       Over each chart, using the mouse, you can (1) select a sub-cohort by Clicking on specific chart components, or (2) Choose a range of values (phenotypes) by Right-clicking-and-dragging
@@ Line 112: / Line 112: @@
 #       On each chart, Clicking the '''Reset''' text in the top-left corner removes any prior user stratification based on the specific features included in the chart
 #       The result of one specific data stratification is illustrated on the figure below.
-[[Image:SOCR_Videos_Dashboard_Fig25.png|500px]]
+<center>[[Image:SOCR_Videos_Dashboard_Fig25.png|500px]]</center>
 A very important feature of the SOCR Data Dashboard is that complies with data privacy protection and regulatory guidelines (e.g., HIPAA) to protect personal information. The Dashboard models the distribution in the entire data archive and simulates from the joint distribution to avoid rendering individualized data. As such, the Data Dashboard is neither an exact representation of the data nor it guarantees that a match/no-match found indicates the presence/absence of a specific participant from the study population.

@@ Line 46: / Line 46: @@
-===Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE)===
+===Example Case-Study I: Autism Brain Imaging Data Exchange (ABIDE)===
 This example describes a step-by-step recipe for using the Data Dashboard service to interrogate the [http://fcon_1000.projects.nitrc.org/indi/abide/ ABIDE data archive].
@@ Line 75: / Line 75: @@
 #	Manipulate some of the charts to study the impact on the other plots. [[Image:SOCR_Videos_Dashboard_Fig4.png|500px]].
-====Reference Materials====
 * BagIt/BDBag Data File Format:
 ** [https://github.com/ini-bdds/bdbag Source code] and [https://github.com/ini-bdds/minid Format]

@@ Line 44: / Line 44: @@
 . Navigate to selected address in browser to launch webapp (default is [http://localhost:3000/ http://localhost:3000/]).
 ===Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE)===
@@ Line 67: / Line 68: @@
 #	Add -- Chart (e.g., Pie Chart of DX_Group or DSM_IV_TR) from the Pheno data
 #	Add -- Chart (e.g., Scatter Plot: FIQ vs. ADOS_COMM)
-#	Manipulate some of the charts (e.g., select females, BMIs, etc.) to examine the change in the other features (e.g., FIQ score). [Image:SOCR_Videos_Dashboard_Fig3.png|500px]]
+#	Manipulate some of the charts (e.g., select females, BMIs, etc.) to examine the change in the other features (e.g., FIQ score). [[Image:SOCR_Videos_Dashboard_Fig3.png|500px]]
 #	Import -- Neuroimaging Data (NI), be patient, it will take some time to load the data. After the dialogue box shows up, click “Import”
 #	Add --  NI --  Select a variable of interest (e.g., Volume or SurfArea, as an example of a feature) click “Continue”

@@ Line 55: / Line 55: @@
 ====Protocol====
-(13)	Import -- Neuroimaging Data (NI), be patient, it will take some time to load the data. After the dialogue box shows up, click “Import”
+#	Download the [http://socr.umich.edu/data/ABIDE_Data.zip BDDS ABIDE BagIt data object].
-(14)	Add --  NI --  Select a variable of interest (e.g., Volume or SurfArea, as an example of a feature) click “Continue”
+#	Extract the 4 data files (''neuroimaging_metrics.csv'', ''neuroimaging_metrics_metadata.csv'', ''neuroimaging_metrics_qc.csv'', ''phenotypes.csv''), which contain the relevant (appropriately named) components of the ABIDE dataset
-(15)	Add --  NI --  Select a variable of interest (e.g., Fold_Ind, as an example of a feature) click “Continue”
+#	Start the [http://socr.umich.edu/HTML5/Dashboard/ Data Dashboard app]
-(16)	Add --  NI --  Select a variable of interest (e.g., Primary_Lobe, as an example of a feature) click “Continue”
+#	Select Free—Anchored Data
-(17)	Manipulate some of the charts to study the impact on the other plots.
+#	Enter a new anchor variable subject_ID. [[Image:SOCR_Videos_Dashboard_Fig2.png|500px]]
+#	Import -- Phenotypes data (Pheno)
-<center>[[Image:SOCR_Videos_Dashboard_Fig4.png|500px]]</center>
+#	Select a variable of interest (e.g., Sex)
 ====Reference Materials====
@@ Line 86: / Line 81: @@
 ** [https://github.com/SOCR/SOCR-Dashboard Source code]
 ** [[SOCR_Videos_Dashboard#Video_Tutorial | Videos]]
 ** [http://socr.umich.edu/HTML5/Dashboard/ Service/App]
 === Reference/Citation===

@@ Line 59: / Line 59: @@
 (3)	Start the [http://socr.umich.edu/HTML5/Dashboard/ Data Dashboard app]
 (4)	Select Free—Anchored Data
-(5)	Enter a new anchor variable subject_ID:
+(5)	Enter a new anchor variable subject_ID
 (6)	Import -- Phenotypes data (Pheno)
 (7)	Select a variable of interest (e.g., Sex)
@@ Line 68: / Line 69: @@
 (12)	Manipulate some of the charts (e.g., select females, BMIs, etc.) to examine the change in the other features (e.g., FIQ score)
 (13)	Import -- Neuroimaging Data (NI), be patient, it will take some time to load the data. After the dialogue box shows up, click “Import”
@@ Line 75: / Line 77: @@
 (17)	Manipulate some of the charts to study the impact on the other plots.
 ====Reference Materials====

← Older revision		Revision as of 21:27, 20 December 2016
Line 44:		Line 44:

	6. Navigate to selected address in browser to launch webapp (default is [http://localhost:3000/ http://localhost:3000/]).		6. Navigate to selected address in browser to launch webapp (default is [http://localhost:3000/ http://localhost:3000/]).
		+
		+	===Example Case-Study: Autism Brain Imaging Data Exchange (ABIDE)===
		+	This example describes a step-by-step recipe for using the Data Dashboard service to interrogate the [http://fcon_1000.projects.nitrc.org/indi/abide/ ABIDE data archive].
		+
		+	The Autism Brain Imaging Data Exchange (ABIDE) data includes complex multi-source, incomplete, incongruent and multi-modal data for Autism spectrum disorder (ASD) pediatric cases. Core characteristics of ASD include impairment in social reciprocity, and by repetitive, restricted, and stereotyped behaviors/interests.
		+
		+	These data allow us to peak into the heterogeneous clinical, biological and physio-social characteristics of the ASD phenotypes. Specific biomedical questions that can be addressed via such data include early determination, tracking, diagnosis and prognosis, as well as assessing the clinical impact of alternative treatments.
		+
		+	The Data Dashboard webapp allows us to navigate this very heterogeneous data (n=1,112, k>2,000), graphically explore deep multivariate relations, associations, and trends. In addition, the dashboard service may be used to generate testable research hypothesis about various ASD traits that can be subsequently evaluated using prospective datasets.
		+
		+	====Protocol====
		+	(1) Download the [http://socr.umich.edu/data/ABIDE_Data.zip BDDS ABIDE BagIt data object].
		+	(2) Extract the 4 data files (''neuroimaging_metrics.csv'', ''neuroimaging_metrics_metadata.csv'', ''neuroimaging_metrics_qc.csv'', ''phenotypes.csv''), which contain the relevant (appropriately named) components of the ABIDE dataset
		+	(3) Start the [http://socr.umich.edu/HTML5/Dashboard/ Data Dashboard app]
		+	(4) Select Free—Anchored Data
		+	(5) Enter a new anchor variable subject_ID:
		+	(6) Import -- Phenotypes data (Pheno)
		+	(7) Select a variable of interest (e.g., Sex)
		+	(8) Add -- Chart (e.g., Pie Chart for Sex) from the Pheno data (Variable Sex)
		+	(9) Add -- Chart (e.g., Histogram Chart for BMI) from the Pheno data (Variable BMI) – note that BMI has lots of missing data!!!
		+	(10) Add -- Chart (e.g., Pie Chart of DX_Group or DSM_IV_TR) from the Pheno data
		+	(11) Add -- Chart (e.g., Scatter Plot: FIQ vs. ADOS_COMM)
		+	(12) Manipulate some of the charts (e.g., select females, BMIs, etc.) to examine the change in the other features (e.g., FIQ score)
		+
		+
		+	(13) Import -- Neuroimaging Data (NI), be patient, it will take some time to load the data. After the dialogue box shows up, click “Import”
		+	(14) Add -- NI -- Select a variable of interest (e.g., Volume or SurfArea, as an example of a feature) click “Continue”
		+	(15) Add -- NI -- Select a variable of interest (e.g., Fold_Ind, as an example of a feature) click “Continue”
		+	(16) Add -- NI -- Select a variable of interest (e.g., Primary_Lobe, as an example of a feature) click “Continue”
		+	(17) Manipulate some of the charts to study the impact on the other plots.
		+
		+
		+	====Reference Materials====
		+	* BagIt/BDBag Data File Format:
		+	** [https://github.com/ini-bdds/bdbag Source code] and [https://github.com/ini-bdds/minid Format]
		+	** [http://bd2k.ini.usc.edu/assets/all-hands-meeting/minid_v0.1_Nov_2015.pdf Docs (PDF)]
		+	* Data Dashboard
		+	** [https://github.com/SOCR/SOCR-Dashboard Source code]
		+	** [[SOCR_Videos_Dashboard#Video_Tutorial \| Videos]]
		+	** [http://socr.umich.edu/HTML5/Dashboard/ Service/App]
		+

	=== Reference/Citation===		=== Reference/Citation===

@@ Line 22: / Line 22: @@
 === Test Data===
-The following 2 datasets are used in this specific SOCR Data Dashboard demonstration:
+The following datasets are used in this specific SOCR Data Dashboard demonstration:
-* [http://socr.umich.edu/docs/uploads/MPOWER_Pilot.csv pediatric obesity dataset], and
+* [http://socr.umich.edu/docs/uploads/MPOWER_Pilot.csv pediatric obesity dataset],
-* [http://socr.umich.edu/docs/uploads/PPMI_GSA_FAM_IntegratedDerived.csv Parkinson's disease neuroimaging-phenotypic-genetics dataset]
+* [http://socr.umich.edu/docs/uploads/PPMI_GSA_FAM_IntegratedDerived.csv Parkinson's disease neuroimaging-phenotypic-genetics dataset],
 <center>[[Image:SOCR_Videos_Dashboard_Fig1.png|500px]]</center>

@@ Line 30: / Line 30: @@
 ===Setting up the Dashboard===
 . Ensure the [https://nodejs.org/en/ node framework] has been installed.
 . Install [https://docs.mongodb.com/manual/installation/ MongoDB]. This is not required, but if you want to see the demo using the default CMS, BLS, and Census data you need MongoDB installed.
 . In a command prompt navigate to the ''server/mongodb/bin'' folder, and run mongod:
   mongod --dbpath ../data
 . Navigate to the root directory of the project in node, and run
   npm install
 . Once dependencies are installed, launch node server:
   npm start
 . Navigate to selected address in browser to launch webapp (default is [http://localhost:3000/ http://localhost:3000/]).