A. Login
By default, login uses usernames and encrypted passwords stored in the database.
Usernames have associated roles.
Administration by default is defined for user 'admin'
User guest can be defined to login automatically with basic access to unrestricted studies.
B. Browse Tab
The Browse Tab is the usual first page (landing page) displayed.
This page holds metadata about known studies, organised under "Programs".
Studies can have associated Assays, Analyses, Folders and Files.
Studies are linked by STUDY_ID to studies loaded in the Analyze tab.
Search Box
Various searches are available in the text box. The pull-down list defines the search category, listed in alphabetical order. The categories are defined in the searchapp.search_keywords table use dto generate the list in the UI automatically.
| Category | Description |
|---|---|
| All | All fields |
| FreeText | Text fields e.g. Description |
| Country | Country in a Browse Study definition |
| Disease | Disease are in a Browse Study definition |
| File_type | File type stored in a Browse folder |
| Gene | Gene of insterest in a Browse Assay |
| Metabolite | Metabolite of interest in a Browse Assay |
| Mirna | MicroRNA of interest in a Browse Assay |
| Organism | Organism defined for a Browse Study |
| Protein | Protein of interest in a Browse Assay |
Active Filters Box
Searched by controlled vocabularies of Browse Tab attributes offering a choice of all defined values.
| Filter | Description |
|---|---|
| Program Therapeutic Domain | |
| Study Phase | |
| Study Objective | |
| Study Design | |
| Study Biomarker Type | |
| Study Access Type | |
| Assay Type of Biomarkers | |
| Assay Measurement Type | |
| Assay Technology | |
| Assay Vendor | |
| Assay Platform Name | |
| Analysis Measurement Type | |
| Analysis Technology | |
| Analysis Vendor | |
| Analysis Platform Name | |
| File Type |
Program Explorer
The nodes should be expandable and closable.
If loaded, Private Studies may be restricted to Admin users. The usual example if the Cell-Line Use Case from the TraIT project.
C. Analyze Tab
The Analyze tab is the main working area in tranSMART.
Search Box
Active Filters Box
Navigate Terms
Comparison
Builds queries in one or two subsets to explore a cohort or to compare two cohorts.
Any node from the Navigate Terms tree can be dragged to either subset.
A query must have at least one "Include" criterion to identify the study of interest.
Categorical nodes
A single string leaf node (e.g. Demographics: Female) will select those individuals with the term defined
Additional strings can be dragged to the same subquery to select any of the values as matching.
A folder node will include all individuals with that node defined
Numeric nodes
Numeric nodes will offer a choice of value ranges or all nodes with a value defined.
High-dimensional nodes
High-dimensional nodes will offer all nodes with a value defined or allow a search for a single gene and a range of expression values.
Summary Statistics
A default set of i2b2 values is displayed: Age, Sex/Gender, Race.
Any other nodes used in the query definition will also be displayed.
Furher nodes can be dragged into the summary statistics panel, including high-dinmensional nodes.
Grid View
A default set of i2b2 values is displayed: Age, Sex/Gender, Race plus patient ID, sample ID, subset
Additional nodes can be dragged from the Navigate Terms tree.
Column headings are kept unique. If two columns have the same last-level value in their paths fiurther levels are added until the displayed column name is unique.
Advanced Workflows
aCGH Survival Analysis
Box Plot with ANOVA
Correlation Analysis
Frequency Plkot for aCGH
Group Test for aCGH
heatmap
Hierarchical Clustering
IC50
K-Means Clustering
Line Graph
Logistic Regression
Marker Selection
PCA
Scatter Plot with Linear Regression
Survival Analysis
Table with Fisher Test
Waterfall
GWAS Plink
SmartR
Boxplot Workflow
Correlation Workflow
Heatmap Workflow
IpaConnector Workflow
Linegraph Workflow
PatientMapper Workflow
VolcanoPlot Workflow
Data Export
Export Jobs
Analysis Jobs
Workspace
Sample Details
Galaxy Export
Metacore Enrichment Analysis
Genome Browser
Image Viewer
D. Sample Explorer
E. Gene Signature/Lists
F. GWAS
G. Upload data
H. Admin
H.1 Access Log
H.2 Groups
H.3 Users
H.4 Access Control
H.5 Study
H.6 Secure Object Paths
H.7 Roles
H.8 Requestmap Setup
H.9 Package and Configuration
H.9.1 Configuration Detail
H.9.2 Build Information
H.9.3 Status of Support Connections
XNAT Importer
I. Utilities Menu
Help
Contact Us
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