# Presentation: 579139

## Session Date: 	August 2007
Session Length:	Approximately 1 hour

Target Audience:	
Developers, Lab Personnel, and Project Leads interested in Laboratory Information Management Systems

Trainer:	
Jenny M. Kelley (LPG)/Robert J. Clifford (LPG)

Developer Subject Matter Expert: 
Jenny M. Kelley  (LPG)/Robert J. Clifford (LPG)

- Session Date: 	August 2007
- Session Length:	Approximately 1 hour
- Target Audience:
- Developers, Lab Personnel, and Project Leads interested in Laboratory Information Management Systems
- Trainer:
- Jenny M. Kelley (LPG)/Robert J. Clifford (LPG)
- Developer Subject Matter Expert:
- Jenny M. Kelley  (LPG)/Robert J. Clifford (LPG)

## Training Environment

**SELF-LED COMPUTER/WEB-BASED TRAINING (CBT/WBT)**

## Session Details

- This training is designed to introduce you to the design and concepts of the lpgLIMS 1.3 application.
- Target Audience:
-  Laboratory personnel
-  Project leads
-  Software developers
-  Anyone with an interest in LIMS applications
- Prerequisites: none

## Session Details:Navigating the Learning Environment

- Navigation is through the common Power Point navigation process
- In Slide Show view, to progress to the next slide, the user can click on the right arrow or the down arrow or the Enter key; to go back to the previous slide, the user can click on the left arrow or up arrow.  To exit Slide Show View, the user can click the Escape key.
- In Normal View, the user can click on the slide at the left to choose which one to view or with the cursor in the slide area, use the arrow and/or enter keys.  The User can also click on the scroll bar regions to select forward or backward.
- [this may change with the audio version....]

## Session Details: Session Goals

**By the end of this training, you will be able to:**
- Understand the historical context of the lpgLIMS 1.3 application
- List the system requirements for installation and running lpgLIMS 1.3
- Describe the key modules of the lpgLIMS 1.3 application and the process for using lpgLIMS 1.3
- Understand the key features of the new caLIMS II project and where to find additional information
- Know where to find downloads and contact information

## Session Details:Lesson Plan

- Lesson 1:  Introduction and History
- Lesson 2:  lpgLIMS 1.3 Overview
- Lesson 3:  Administration
- Lesson 4:  Inventory
- Lesson 5:  Project
- Lesson 6:  caLIMS II Overview
- Lesson 7:  Review

## Lesson 1: Introduction/History  of lpgLIMS 1.3Lesson 1 Overview

**This lesson describes the purpose and goals of the lpgLIMS 1.3 application. **
- Purpose and description of lpgLIMS 1.3
- History of caLIMS 1.0 – lpgLIMS 1.3 development
- Goals for lpgLIMS 1.3
- Architecture Design and Technology for lpgLIMS 1.3

## Lesson 1: Introduction/History of lpgLIMS 1.3Application Description

**lpgLIMS 1.3 is an open source Laboratory Information Management System***
-  lpgLIMS 1.3 is a web application based on J2EE technology
-  lpgLIMS 1.3 allows researchers to manage
- 	personnel
- 	equipment
- 	samples
- 	supplies
- 	workflows
- 	results
- *(not caBIG compliant)

## Lesson 1: Introduction/History of lpgLIMS 1.3History of development

**The LIMS for the LPG was produced by SAIC ca. 2000**
**Is a web application based on J2EE technology**
**Data about users, inventory, etc. stored in Oracle**
**Experimental results and project files stored on an FTP server**
**Accessed through a web browser**
-  lpgLIMS 1.0 was designed prior to the establishment of the caBIG guidelines
-  lpgLIMS 1.0 is not based on a data model and used obsolete technology (Tomcat3.x/Java 1.3)
-  lpgLIMS 1.0 is difficult to configure, build and install

## Lesson 1: Introduction/History of lpgLIMS 1.3Goals set for lpgLIMS 1.3

**Upgrade technology stack**
**	****Java 1.3****	****->****	****Java 1.4**
**	****Tomcat 3****	****->****	****Tomcat 5**
**	****Oracle 8****	****->****	****Oracle 10**
** **Stabilize code base (use caLIMS 1.2 as a foundation)
-  Simplify configuration, compilation and installation
-  Provide new adaptors (e.g. ABI 3730XL)
-  Recommended a Three-tiered deployment: development, staging, production

## Lesson 1: Introduction/History of lpgLIMS 1.3Architecture for 1.3

- Diagram description of the 1.3 Architecture indicating the 4 layers: client, presentation, object, and data source layers.

## Lesson 1: Introduction/History of lpgLIMS 1.3Improved Installation for 1.3

**Compile the application using Apache Ant**
**	****single configuration file**
**	****builds in ~2.5 minutes on Windows**
-  The build process generates two files
- 	LIMS RMI server (*.jar file)
- 	LIMS application (*.war file)
-  Installs in 5 minutes
-  Tested on Solaris, Linux, Windows
-  Tested in Tomcat 4, Tomcat 5, JBoss 4 +/- Apache

## This lesson described the purpose and goals of the lpgLIMS 1.3 application.  
Purpose and description of lpgLIMS 1.3
History of caLIMS 1.0 – lpgLIMS 1.3 development
Goals for lpgLIMS 1.3
Architecture Design and Technology for lpgLIMS 1.3

- Purpose and description of lpgLIMS 1.3
- History of caLIMS 1.0 – lpgLIMS 1.3 development
- Goals for lpgLIMS 1.3
- Architecture Design and Technology for lpgLIMS 1.3

- Lesson 1: Introduction/History of lpgLIMS 1.3Review

## Lesson 2:  lpgLIMS 1.3 OverviewLesson 2 Overview

**Lesson 2 provides an overview of the lpgLIMS 1.3 organization and features:**
- lpgLIMS 1.3 Overview: Web page navigation and features
- Three Basic Modules: Administration, Inventory, Project
- Additional Features: Equipment and Supplies, Assays and Protocols, and Adapters

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Overview and Navigation

- The Welcome page for Lab Manager login.  Note the three main module tabs: Administration, Project, & Inventory*.  Additional navigation points include: LogOut button, Back button, and Change Lab button.

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Basic Modules

- Administration

- Inventory

- Project

- Three key modules: Administration, Inventory, & Project

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Users and Authority Levels

-  There are differences in the links and data presented to the users based on their user authority level.  Examples are shown later in this presentation.

**There are multiple User Authority Levels**
- The privileges assigned to authority levels are defined in a configuration file which may be modified to customize a lpgLIMS 1.3 installation.

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Authority Levels Examples

**The default authority levels for users are:**
**Superuser**: has global privileges in the system.
**Administrator**: installs and maintains the system, has global privileges.
**Manager**: can create, execute, & review projects, create assays & protocols, modify template assays, enter inventory, and give approvals as specified.
**Technician**: can execute runs, read/write data, enter inventory, and give limited approvals as specified.
**Customer**: can read data as specified.
**Collaborator**: can read/write data as specified.
**Guest**: can read only specified data.

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Equipment and Supplies

**The default lpgLIMS 1.3 installation includes seed data for common laboratory supplies, reagents and equipment to enable immediate use. **

- There are also scripts available for uploading supply and equipment information in batch format (*.csv).

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Assays and Protocols

**Assays are the experiments performed in the laboratory.  Assays can have multiple steps which are defined as Protocols.  lpgLIMS 1.3 includes pre-defined laboratory assays and protocols for:**
** **PCR Amplification
-  RFLP Genotyping
-  AB Sequencing
-  AB Genotyping
-  Affymetrix GeneChip
-  Affymetrix HuSNP + 10K
-  MALDI-TOF Mass Spec

- assay

- protocols

- Assay outputs

- More assays

## Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Adapters

**l****pgLIMS 1.3 includes modules for importing and parsing data files associated with:**
** ****	**ABI 3100 sequencing and genotyping assays
-  	ABI  3730XL sequencing and genotyping assays
-  	Affymetrix expression microarrays
-  	U95A and U95Av2
-  	U133A, U133B, and U133p2 microarrays
-  	Affymetrix genotyping microarrays
-  	HuSNP and 10K SNP

## Lesson 2 provided an overview of the lpgLIMS 1.3 organization and features: 
lpgLIMS 1.3 Overview: Web page navigation -  tabs for modules; Back, Next, and Logout buttons; drop-down selection boxes
Three Basic Modules: Administration, Inventory, Project
Additional Features: Equipment and Supplies, Assays and Protocols, and Adapters

- lpgLIMS 1.3 Overview: Web page navigation -  tabs for modules; Back, Next, and Logout buttons; drop-down selection boxes
- Three Basic Modules: Administration, Inventory, Project
- Additional Features: Equipment and Supplies, Assays and Protocols, and Adapters

- Lesson 2: lpgLIMS 1.3 OverviewReview

## Lesson 3: Administration ModuleLesson 3 Overview

**Lesson 3 gives a brief description of the Administration Module**
- Administration Module Overview
- Administration Module Functions
- Administration Module Users

## Lesson 3:  Administration ModuleAdministration Overview

- The Main Page for Administration displaying the links available to a superuser.

- Links to Admin functions

## Lesson 3: Administration ModuleAdministrative Functions (1)

**Laboratory Administration**
- Allows a manager to create a laboratory within a domain and assign CAN/grant/cost/billing numbers
- Provides a summary of users assigned to a laboratory

**Personnel Administration**
**Permits a manager to assign authorities, skills, and laboratories to each user**
- A user can be affiliated with multiple laboratories
- A user can have different authorities in different laboratories

## Lesson 3: Administration ModuleAdministrative Functions (2)

**Skills/Roles**
-  A skill is a particular expertise that a user possesses or can perform
-  A role is a user’s function in a project
-  A user can have different roles in different projects
**Organizations/Customers/Technical Support**
-  Allows a manager to record customer/collaborator contact information, organizations, and technical support contacts

**Units of Measurement**
-  Allows a manager to specify the unit of measure (ml, ul, etc.) for a unit type (volume, concentration, mass) for protocol directions and inventory calculations

## Lesson 3: Administration ModuleAdministrative Functions (3)

**Equipment and Storage Devices**
-  Allows a manager to define the types of equipment used in the laboratory, the output type(s) associated with a piece of a equipment, and whether a LIMS adapter is available for an equipment type
-  Allows a manager to define the equipment or storage device used to store samples, cartons and supplies

**Auditing**
-  Allows a superuser or administrator to enable or disable LIMS auditing
**Toggle Debug**
-  Allows a superuser or administrator to enable or disable Debugging

## Lesson 3: Administration ModuleAdministrative Users

## Lesson 3 gave a brief description of the Administration Module

Administration Module Overview
Administration Module Functions
Administration Module Users

- Administration Module Overview
- Administration Module Functions
- Administration Module Users

- Lesson 3:  Administration Module Review

## Lesson 4: Inventory ModuleLesson 4 Overview

**Lesson 4 gives a brief description of the Inventory Module**
- Inventory Module Overview
- Inventory Module Function: Cartons and containers
- Inventory Module Function: Inventory search
- Inventory Module Function: Supplies and reagents
- Inventory Module Function: Samples and working stocks

## Lesson 4: Inventory Module lpgLIMS 1.3 Inventory overview

- Depending on authority level, views may vary by user: Inventory Main Page as viewed by a technician (left) and a manager (right).

**Inventory has links to key functions: supplies, supply types, samples, sample types, cartons, containers, container types, Upload Project Samples.**

## Lesson 4: Inventory Module lpgLIMS 1.3 Cartons and Containers

**C*****artons**** *are **Containers** created for a supply, reagent, sample, working stock, or aliquot. C*artons *can hold other *cartons or containers *of different *container types *(e.g.: a box of tubes containing reagent aliquots).

**Container types, Containers,** **and Cartons**

***Container Types***** – **examples include:* kit, 9x9 Freezer Box, 10x10 Freezer Box, 96 well 0.5ml plate, 96 well 2ml plate, 1.5ml screw top tube, 2ml screw top tube, 96 PCR Plate, 384 PCR plate, 96 UV plate, 14 ml tube, 96 well filter plate, AffymetrixChip*.

- To define a ***Container*****,** choose the *container type* and enter a *container name*.

- Create new container: enter name and select type

- Carton Search Criteria

## Lesson 4: Inventory Module lpgLIMS 1.3 Inventory Search

- Lesson 4: Inventory Module lpgLIMS 1.3 Inventory Search

**Inventory Search Page**:
- search by lot #, supply type, laboratory, storage device, project, origin, and dates into
- inventory or depleted with additional filters of depleted, QC’d, and case sensitivity.
- User can also enter a new purchased supply or a new reagent made in the lab.

**Inventory Search for Supplies**

- Search criteria for inventory supplies

- Links to log new purchases or new reagents made in lab

## Lesson 4: Inventory Module Inventory Functions: Supplies and Reagents

**User can enter new supply information into inventory.**

## Lesson 4: Inventory ModuleInventory Functions: Sample Management

## Lesson 4: Inventory Module Inventory Functions: Working Stocks

**Samples can be associated with plates when uploaded into inventory and working stocks (aliquots) of the plate can be created for assay runs.  Information about a single sample can be viewed by clicking on the sample well position.**

## Lesson 4 gave a brief description of the Inventory Module

Inventory Module Overview
Inventory Module Function: Cartons and containers
Inventory Module Function: Inventory search 
Inventory Module Function: Supplies and reagents
Inventory Module Function: Samples and working stocks

- Inventory Module Overview
- Inventory Module Function: Cartons and containers
- Inventory Module Function: Inventory search
- Inventory Module Function: Supplies and reagents
- Inventory Module Function: Samples and working stocks

- Lesson 4: Inventory ModuleReview

## Lesson 5: Project Module Lesson 5 Overview

**Lesson 5 gives a brief description of the Project Module**
- Project Overview
- Project Management
- Project Creation
- Project Execution
- Project Results

## Lesson 5: Project Module Lesson 5 Project Module Overview

**Project Main Page: **On the left, links to Project Creation, Project Execution, Project Results, Project Personnel, Project Laboratory, Assays, Protocols, Process Types, and Search Projects.

- Use the *Projects *main page to begin or continue the work of a project by selecting a pre-existing *project *to delete or edit or by creating a new project with the *New *button

- Select existing Project

- Select to create a new Project

- Predefined Template Project

- Select Project Module functions

## Lesson 5: Project Module Project Management

**A project is the work carried out in the laboratory.**
-  A project consists of ***Assays,***** **designated samples, equipment, laboratory/personnel, and supplies.
-  An ***Assay*** is an experiment to perform within a project.
-  An ***assay*** consists of ***inputs*** (samples, reagents, plate record), ***outputs*** (run data file, image file, PCR product), and ***protocols***.
-  A ***protocol*** is a series of steps to be followed in order to conduct an ***Assay***.  ***Protocols*** within a project may also have ***processes/sub-processes***.
- A group of pre-defined common genomic assays and protocols are available in the lpgLIMS 1.3 via the template project.
- Key Project functions include: 1) project creation, 2) project execution, and 3) project results.

## Lesson 5: Project Module Project Creation

## Lesson 5: Project Module Project Execution

- Laboratory researchers can only work on projects assigned to them by their laboratory manager
-  *Multiple researchers can work on a project*
- Experiments are conducted by following the assays, protocols, and processes outlined in the project tree
-  The researcher creates a run for each assay, creates working stock from the samples affiliated with the project, and performs the assay
-  *Multiple runs can be created for each assay*
-  The researcher logs the status and results (reports, files, images) of each step in the assay

## Lesson 5: Project Module Project Execution Tree

- Each Assay is performed in 1 or more Run(s) which include designated samples and protocols.
- The project tree is color coded to reflect the current project status.
- Project results can be uploaded via the LIMS ftp client to the lpgLIMS 1.3 FTP server.  Project results can be logged for cartons or samples.

## Lesson 5: Project Module Project Results Tree

- Project results are available to project participants and assigned customers or collaborators.
- Project results can be displayed by data type, cartons and samples, and assay.
- Project results can include summaries and reports in addition to data files.

## Lesson 5 gave a brief description of the Project Module

Project Overview
Project Management
Project Creation
Project Execution
Project Results

- Project Overview
- Project Management
- Project Creation
- Project Execution
- Project Results

- Lesson 5: Project Module**Review**

## Lesson 6: caLIMS II IntroductionLesson 6 Overview

**Lesson 6 gives a brief description of the caLIMS II project**
- caLIMS II Introduction/caBIG integration
- caLIMS II Project Design Principles
- caLIMS II Project Communication and Contacts

## Lesson 6: caLIMS II Introduction Purpose of caLIMS II Project

-  To Create a general-purpose LIMS that seamlessly integrates with caBIG data sources and analytical tools (silver/gold level compliancy).
-  To develop a generic Core LIMS infrastructure that could be used by multiple laboratory types.
- To build a basic LIMS that allows easy customization to a specific Laboratory domain.

## Lesson 6: caLIMS II Introduction Integration with caBIG

**caLIMS II **fills the gap between tissue repositories and analytical tools in the caGRID.

## Lesson 6: caLIMS II Introduction caLIMS II Advantages and Features

- Advantages
- Open source
- caBIG integration
- Consortium-based development
- Rapid development / revision cycles
- Customization – design custom lab specific objects
- Expandable – APIs allow ease of adding new functionalities
- Features
- FileTransporter tool
- Customizable UI
- Security management (fine grain)
- Workflow management
- MetaData management

## Lesson 6: caLIMS II Introduction caLIMS II Design Principles

**Design principles for caLIMS II **
- Model Driven Architecture (roundtrip UML artifacts)
-  Service Oriented Architecture
-  caBIG silver/gold compliance
-  Semantically (caDSR/EVS), syntactically interoperable well defined APIs
-  Security - CSM/UPT
-  Reuse of existing caBIG tool / functionalities / components
-  Workflow management – import standard workflows
-  Platform independent
-  Modularity
-  Ease of customization
-  Ease of installation
-  Usability standards based UIs
-  Documentation and training available

## Lesson 6: caLIMS II Introduction caLIMS II Major Components

- caLIMS II has 5 key modules: Administration, Inventory, Workflow, Report, & Analysis

- Lesson 6: caLIMS II Introduction caLIMS II Architecture

**CLIENT**

**BUSINESS LOGIC **
**LAYER**

**PERSISTENCE**
**LAYER**

**ENTERPRISE INFORMATION**
**SYSTEMS **
**LAYER**

**PRESENTATION **
**LAYER**

*Browser / Webservice /*
*API client*

*HTTPS*

*Scanner *

**Components of the 5 layers for caLIMS II**

## Lesson 6: caLIMS II Introduction NCI CBIIT LIMS Consortium

**LIMS Consortium meetings:**
- LIMS Consortium General Meeting: 4th Monday of month at 1 pm Eastern Time
- LIMS Interface Special Interest Group:  3rd Tuesday of month at 1 pm Eastern Time
- LIMS Object Model Special Interest Group:  3rd Thursday of month at 1 pm Eastern Time
- LIMS User Interface Special Interest Group: TBD
- Meetings are held by teleconference and CENTRA* and notices are sent out through the list-serve: _[https://list.nih.gov/archives/nci-lims-consortium.html](https://list.nih.gov/archives/nci-lims-consortium.html)_
- **those in Washington DC metro area are welcome to come to our (NCI CBIIT and LPG) offices at 2115 E. Jefferson, Rockville, MD 20852, for the meetings.*

## Lesson 6: caLIMS II Introduction caLIMS Project Information

- caLIMS II Project site:
- _[http://gforge.nci.nih.gov/projects/calims2](http://gforge.nci.nih.gov/projects/calims2)__ _
- NCICB LIMS Consortium LISTSERV:
- _[https://list.nih.gov/archives/nci-lims-consortium.html](https://list.nih.gov/archives/nci-lims-consortium.html)_
- Web based Design artifacts
- _[http://lpgws.nci.nih.gov/calims2/index.htm](http://lpgws.nci.nih.gov/calims2/index.htm)__ _
- Contacts:
**LPG Development Team (LPGLIMS_TEAM@list.nih.gov )**
**Bob Clifford – LPG **
**Jenny Kelley – LPG**

## Lesson 6 gave a brief description of the caLIMS II project

caLIMS II Introduction/caBIG integration
caLIMS II Project Design Principles
caLIMS II Project Communication and Contacts

- caLIMS II Introduction/caBIG integration
- caLIMS II Project Design Principles
- caLIMS II Project Communication and Contacts

- Lesson 6: caLIMS II IntroductionReview

## Session Summary:Review

- In Summary, we presented:
- An introduction and history of lpgLIMS 1.3
- An overview of the lpgLIMS 1.3 application
- A more detailed description of the 3 key Modules
- Additional information on a caLIMS II project (redesigned according to current caBIG silver/gold compliancy standards)

## Session Summary: lpgLIMS 1.3 Overview Review of lpgLIMS 1.3 Overview

**Now that you have successfully completed this**
**training, you should be able to:**
- Understand the historical context of the lpgLIMS 1.3 application
- List the system requirements for installation and running lpgLIMS 1.3
- Describe the key modules (Administration, Inventory, and Project) of the lpgLIMS 1.3 application and their main functions
- Understand the key features of the new caLIMS II project and where to obtain additional information on caLIMSII

## Session Summary:Next Steps: lpgLIMS 1.3 Distribution

**lpgLIMS 1.3 can be downloaded from **
**	**_[http://gforge.nci.nih.gov/projects/lpglims](http://gforge.nci.nih.gov/projects/lpglims)__ _
- The distribution includes:
- source code
- lpgLIMS 1.3 Installation Guide
- lpgLIMS 1.3 Quick Start Guide (a detailed User Guide for setting up a project)
- seed data
- Distributions are provided for Windows, Linux, and Solaris

## Session Summary:Next Steps: Contact Information

**lpgLIMS 1.3 Support**
**NCI CBIIT Support****	**
- NCI CBIIT Applications Support
- Email: _[ncicb@pop.nci.nih.gov](mailto:ncicb@pop.nci.nih.gov)__ _
- Toll-Free: 888.478.4423
- Local: 301.451.4384
- _[http://ncicbsupport.nci.nih.gov](http://ncicbsupport.nci.nih.gov/)_
**LPG Development** **Team **(_[LPGLIMS_TEAM@list.nih.gov](mailto:LPGLIMS_TEAM@list.nih.gov)__ )_
- Bob Clifford – LPG
- Jenny Kelley – LPG
- Cu Nguyen – LPG
- Sashi Thangaraj –  LPG/SAIC

## Session Summary:Course Evaluation

- A Training Evaluation form is included on the Training Portal.