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Magnus Mengelbier Director. An Open Source Reporting System for Life Sciences. Topics. Introduction Traditional process Library Analysis Reporting Connections Summary. Listings. Derived. Tables. Graphs. Source. Listings. SDTMs. ADaMs. Tables. Graphs. Define. Tradition.

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An Open Source Reporting System for Life Sciences


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topics
Topics
  • Introduction
  • Traditional process
  • Library
  • Analysis
  • Reporting
  • Connections
  • Summary
tradition

Listings

Derived

Tables

Graphs

Source

Listings

SDTMs

ADaMs

Tables

Graphs

Define

Tradition

Source

templates and specifications

Specifications

Templates

Shells

Data Sets

Tables

Listings

Define

SAP

Programs

Shells

Data

Sets

Data

Sets

SAP

Templates and Specifications
library

SAP

Library

Library

Specifications

Programs

Shell

Data Sets

Tables

Listings

Define

TLGs

Data

Sets

Data

Sets

organizing content
Organizing Content
  • Directory Trees
  • No restriction on the number of levels
  • No restriction on naming conventions
  • Contexts
  • Aware of parent directory
  • Contexts have to be consistent within a directory tree
  • Directory tree can be your departmental drive or network share
default defintions
Default Defintions
  • Data Sets
  • Tables
  • Listings
  • Graphs
definitions and inheritance
Definitions and Inheritance
  • Types of definition controlled for each level
  • Definitions can be inherited from parent to child levels
specifications
A Specification is just a set of links to content in the Library

All Definitions have to be in the Library

Specification

Specifications

Library

repository
Repository

Data Sets

Tables

Listings

Graphs

Simple Meta-Data Engine

  • Model – View – Controller (MVC) design pattern
    • Model – Meta-data
    • View – Graphical and programming interface
    • Controller – ”Administrator” of the meta-data
  • Very primitive and flexible meta-data engine
repository definitions
Repository - Definitions
  • Defintions
    • Type, e.g Data Set, Table, etc.
    • Identified by Type and Name
  • References and associations to other meta-data items
    • Look-up
    • Ordered list
  • Versions
    • Increment
    • Construct for a unique reference to variations of the same item
    • More than one version is selectable
    • Future plans include major/minor versions
repository data set

Sequence

Reference

1

NAME

2

SEX

Collections

3

AGE

4

HEIGH

5

WEIGHT

Repository – Data Set
repository table 3

N

  • MEAN_SD
  • MEDIAN
  • MIN-MAX
  • MEAN
  • SD
  • MIN
  • MAX
Repository – Table (3)
  • N
  • MEAN_SD
  • MEDIAN
  • MIN-MAX
analytics

Code library

  • Code generators
  • Statistics “meta-data” interface
  • Requires an analytics engine (SAS/R/S-Plus)
Analytics
  • Meta-data driven
  • Standard statistics
analytics1

Code Generator

DataSets

Data Sets

Tables

Listings

Define

Specifications

Non-standard

Programs

SAP

  • N
  • MEAN
  • SD
  • MIN
  • MAX
Analytics

Library

Code

TLGs

Data

Sets

  • MEAN_SD
  • MEDIAN
  • MIN-MAX
reporting by elements
Reporting By Elements
  • Data
    • Input Data Set
    • Select Parameter(s)
    • Subset
  • Summaries & Statistics
    • Compute
    • Append
    • Format
  • Render Table
    • Report structure
    • Format
    • Sort & Order
    • Render

Library

Analytics

Reporting

reporting by elements1
Reporting by Elements

ADAE

ADLB

ADVS

Analysis Data Sets

StatisticsData Sets

STAE

STLB

STVS

STSUBSET

Outputs

analytics repository

PK Analytics

Non-standard

Programs

Code Generator

Code Library

Analytics Repository

Analytics Repository

reporting results

Non-standard

Programs

Code Generator

Code Library

Tables

Listings

Graphs

Submission files

Portals

Reporting Results

PK Analytics

Analytics Repository

other outputs
Other Outputs

Data Sets

Tables

Listings

Graphs

Simple Meta-Data Engine

  • Model – View – Controller (MVC) design pattern
    • Model – Meta-data
    • View – Graphical and programming interface
    • Controller – ”Administrator” of the meta-data
  • Very primitive and flexible meta-data engine
  • Adding an output starts with a Model, View and Controller(s)
tracking and status
Track status

Track and enforce dependencies

Code Generator

DataSets

Data Sets

Tables

Listings

Define

Specifications

Non-standard

Programs

Common Work Flow

Tracking and Status

Library

Code

TLGs

Data

Sets

organization revisited
Organization Revisited
  • Directory Trees
  • No restriction on the number of levels
  • No restriction on naming conventions
  • Contexts
  • Aware of parent directory
  • Contexts have to be consistent within a directory tree
  • Directory tree can be your departmental drive or network share
connections

Code Generator

DataSets

Data Sets

Tables

Listings

Define

Specifications

Non-standard

Programs

Network

Subversion

SAS Server

SDD *

R

* SAS Drug Development

Connections

Library

Code

TLGs

Data

Sets

Common Work Flow

web services

Code Generator

DataSets

Data Sets

Tables

Listings

Define

Specifications

Non-standard

Programs

SDD *

* SAS Drug Development

Web Services

Library

Code

TLGs

Data

Sets

Common Work Flow

PC SAS

S-Plus / R

SAS Server

Anything really

conclusion
Conclusion

Data Sets

Tables

Listings

Graphs

Simple Meta-Data Engine

  • Model – View – Controller (MVC) design pattern
    • Model – Meta-data
    • View – Graphical and programming interface
    • Controller – ”Administrator” of the meta-data
  • Very primitive and flexible meta-data engine
  • Adding an output starts with a Model, View and Controller(s)
conclusion1

Code Generator

DataSets

Data Sets

Tables

Listings

Define

Specifications

Non-standard

Programs

Network

Subversion

SAS

SDD *

S-Plus / R

* SAS Drug Development

Conclusion

Library

Code

TLGs

Data

Sets

Common Work Flow

questions comments
Questions & Comments

Magnus MengelbierDirectorLimelogic Ltd

mmr@limelogic.com+44 208 144 5701

  • Introduction
  • Traditional process
  • Library
  • Analysis
  • Reporting
  • Connections
  • Summary