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  1. lpgLIMS 1.3 Overview 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)

  2. Training Environment SELF-LED COMPUTER/WEB-BASED TRAINING (CBT/WBT)

  3. 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

  4. 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….]

  5. 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

  6. 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

  7. Lesson 1: Introduction/History of lpgLIMS 1.3Lesson 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

  8. Lesson 1: Introduction/History of lpgLIMS 1.3Application 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)

  9. Lesson 1: Introduction/History of lpgLIMS 1.3History 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

  10. Lesson 1: Introduction/History of lpgLIMS 1.3Goals 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

  11. Lesson 1: Introduction/History of lpgLIMS 1.3Architecture for 1.3 Diagram description of the 1.3 Architecture indicating the 4 layers: client, presentation, object, and data source layers.

  12. Lesson 1: Introduction/History of lpgLIMS 1.3Improved 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

  13. Lesson 1: Introduction/History of lpgLIMS 1.3Review 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

  14. Lesson 2: lpgLIMS 1.3 OverviewLesson 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

  15. Header Change Lab Login Info Log Out Functional Tabs *Administration, Projects, Inventory Back Button Main Window Footer 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.

  16. Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Basic Modules Administration Inventory Project Three key modules: Administration, Inventory, & Project

  17. Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Users and Authority Levels Define login and contact info for each user Log skills for each user Designate Lab & authority level for each user 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. 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.

  18. 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.

  19. 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).

  20. 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 Assay outputs More assays protocols

  21. Lesson 2: lpgLIMS 1.3 Overview lpgLIMS 1.3 Adapters lpgLIMS 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

  22. Lesson 2: lpgLIMS 1.3 OverviewReview 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

  23. Lesson 3: Administration ModuleLesson 3 Overview Lesson 3 gives a brief description of the Administration Module • Administration Module Overview • Administration Module Functions • Administration Module Users

  24. Lesson 3: Administration ModuleAdministration Overview The Main Page for Administration displaying the links available to a superuser. Links to Admin functions

  25. Lesson 3: Administration ModuleAdministrative 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

  26. Lesson 3: Administration ModuleAdministrative Functions (2) User defines new unit • 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

  27. Lesson 3: Administration ModuleAdministrative 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

  28. Logged in as superuser Logged in as manager No link to Auditing or Toggle Debug links to Auditing & Toggle Debug lpgLIMS 1.3 Administration page for superuser (left) and lab manager (right). Note accessibility to different functions per user type and authority. Lesson 3: Administration ModuleAdministrative Users

  29. Lesson 3: Administration ModuleReview Lesson 3 gave a brief description of the Administration Module • Administration Module Overview • Administration Module Functions • Administration Module Users

  30. Lesson 4: Inventory ModuleLesson 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

  31. No Upload Project Samples available for technician Upload Project Samples available for manager Lesson 4: Inventory Module lpgLIMS 1.3 Inventory overview Inventory has links to key functions: supplies, supply types, samples, sample types, cartons, containers, container types, Upload Project Samples. Depending on authority level, views may vary by user: Inventory Main Page as viewed by a technician (left) and a manager (right).

  32. Lesson 4: Inventory Module lpgLIMS 1.3 Cartons and Containers Container types, Containers,and Cartons Cartonsare Containers created for a supply, reagent, sample, working stock, or aliquot. Cartons can hold other cartons or containers of different container types (e.g.: a box of tubes containing reagent aliquots). Carton Search Criteria To define a Container, choose the container type and enter a container name. Create new container: enter name and select type 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.

  33. Lesson 4: Inventory Module lpgLIMS 1.3 Inventory Search Inventory Search for Supplies 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. Search criteria for inventory supplies Links to log new purchases or new reagents made in lab

  34. Information for a new supply Lesson 4: Inventory Module Inventory Functions: Supplies and Reagents User can enter new supply information into inventory.

  35. Laboratory inventory functions include: • adding and/or editing different types of inventory (samples, cartons, supplies, reagents) • searching inventory • viewing inventory information • creating working stocks and performing plate comparisons. Sample Parser Tool Lesson 4: Inventory ModuleInventory Functions: Sample Management Upload samples Batch sample file Samples can be entered through Inventory or Project tabs. Batch sample information can be uploaded using the sampleParser tool and specifically formatted files.

  36. Sample file selected for import Sample position indicated in plate layout Sample working stocks (aliquots) created for assay runs Samples color coded 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.

  37. Lesson 4: Inventory ModuleReview 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

  38. 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

  39. 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 Predefined Template Project Select to create a new Project Select Project Module functions

  40. 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.

  41. File location To create a project, a manager creates the assays and protocols for the project, assigns the appropriate level of approval, and adds each component to the project tree. The project tree represents all personnel, laboratories, assays, protocols, and samples affiliated with a project. Carton Type Sample Type Lesson 5: Project Module Project Creation Project Details Project Details Tree Navigation Assays

  42. 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

  43. Select project for execution Lesson 5: Project Module Project Execution Tree Log results files to project Project Execution Tree Set approvals 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.

  44. Lesson 5: Project Module Project Results Tree Results details Data on run Data on sequence files 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.

  45. Lesson 5: Project ModuleReview Lesson 5 gave a brief description of the Project Module • Project Overview • Project Management • Project Creation • Project Execution • Project Results

  46. Lesson 6: caLIMS II IntroductionLesson 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

  47. 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.

  48. DB DB DB DB DB Research Data Repository Services caArray Analytical Services Gene pattern, caIntegrator Clinical Trial Services C3D, C3PR caGRID LIMS Services caLIMS II Sample Repository caTissue, caTies File System Lesson 6: caLIMS II Introduction Integration with caBIG caLIMS II fills the gap between tissue repositories and analytical tools in the caGRID.

  49. 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

  50. 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