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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.

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.

CategoryDescription
AllAll fields
FreeTextText fields e.g. Description
CountryCountry in a Browse Study definition
DiseaseDisease are in a Browse Study definition
File_typeFile type stored in a Browse folder
GeneGene of insterest in a Browse Assay
MetaboliteMetabolite of interest in a Browse Assay
MirnaMicroRNA of interest in a Browse Assay
OrganismOrganism defined for a Browse Study
ProteinProtein of interest in a Browse Assay

Active Filters Box

Searched by controlled vocabularies of Browse Tab attributes offering a choice of all defined values.

FilterDescription
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

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

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