gs lims implementation guide - brigham young universitydna.cs.byu.edu/bio465/454/gs-flx lims...

GS LIMS Implementation Guide

–– Table of Contents ––

Preface............................................................................................................................................. 2 About this Guide ......................................................................................................................... 2 Related Publications.................................................................................................................... 2

1. Introduction............................................................................................................................. 3 2. Implementation ....................................................................................................................... 3

2.1 System Requirements...................................................................................................... 3 2.2 Configuration .................................................................................................................. 3

2.2.1 LIMS Connector ..................................................................................................... 3 2.2.2 LIMS Simulator ...................................................................................................... 4

2.3 Pre-wash.......................................................................................................................... 5 2.3.1 Description.............................................................................................................. 5 2.3.2 Stimulus/Response Sequences ................................................................................ 6

2.4 Sequencing Run .............................................................................................................. 7 2.4.1 Description.............................................................................................................. 7 2.4.2 Stimulus/Response Sequences ................................................................................ 8

3. Appendix A: Glossary........................................................................................................... 10 4. Appendix B: Sequencer Messaging Schema ........................................................................ 11 5. Additional Information About this Manual .......................................................................... 14

5.1 Revision History ........................................................................................................... 14 5.2 Intended Use ................................................................................................................. 14 5.3 Notice to Purchaser ....................................................................................................... 14 5.4 Trademarks ................................................................................................................... 14 5.5 Assistance ..................................................................................................................... 15

USM-00023.D – December 2007


PREFACE

About this Guide

This document describes the LIMS lookup feature of the Genome Sequencer System, a simple method of extracting the Run parameters that are associated with a PicoTiterPlate barcode in a Laboratory Information Management System (LIMS), and applying them as settings for a sequencing Run to be carried out on the Genome Sequencer Instrument. The Guide will enable customers and their Roche Representative to set up the necessary communication interface between the Genome Sequencer Instrument and a LIMS server. More details on how to use the LIMS lookup feature to set up and launch a sequencing Run are available in the GS FLX Sequencing Method Manual.

Related Publications

A full suite of publications are available that describe in detail the components and usage of the Genome Sequencer System:

• Genome Sequencer FLX Operator’s Manual • Genome Sequencer FLX System Methods Manual, including:

o GS FLX Shotgun DNA Library Preparation Method Manual o GS FLX Paired End DNA Library Preparation Method Manual o GS FLX Amplicon DNA Library Preparation Method Manual o GS FLX emPCR Method Manual o GS FLX Sequencing Method Manual o A Quick Guide version of each Method is also available.

• Genome Sequencer FLX Data Analysis Software Manual • Genome Sequencer System Site Preparation Guide – this manual

All Genome Sequencer Manuals, Guides and Bulletins are available three ways: in hardcopy form, on a CD from your Roche representative, or downloaded from the customer restricted access area of www.genome-sequencing.com.

http://www.genome-sequencing.com/


1. INTRODUCTION

The LIMS lookup feature of the Genome Sequencer System is a simple method of extracting the Run parameters that are associated with a PicoTiterPlate barcode in a Laboratory Information Management System (LIMS), and applying them as settings for a sequencing Run to be carried out on a Genome Sequencer Instrument. This reduces the time and errors associated with manual data input. The LIMS lookup feature is ideal for LIMS-based, high-throughput environments. The LIMS lookup feature connects the information in the clients’ LIMS to the Run parameters for the Genome Sequencer Instrument. A network interface is required for the LIMS messaging. If the LIMS server is not available, an error message will appear telling the user that the LIMS information cannot be retrieved because the LIMS server is unavailable. The operator can still set up a Run manually if this occurs.

2. IMPLEMENTATION

2.1 System Requirements

• Genome Sequencer Software version 1.0.52 or above must be installed. • A preconfigured limslookup.properties file must exist in the config directory. • A LIMS connector must be installed and configured in the limslookup.properties file. • The LIMS system must be customized to receive and send the XML messages defined by

the sequencer.xsd schema. • The LIMS system must respond with valid Run script information before the Run can

start. • The existing preRunRinse.xml file can be used as an example for the response message.

2.2 Configuration

2.2.1 LIMS Connector

The LIMS lookup feature communicates with a LIMS server to get the Genome Sequencer Instrument Run script information required. The Run information is keyed on the PicoTiterPlate ID. Before executing a Run, the Run information should have been entered into the LIMS system. By the time the instrument operator is ready to set up a Run, the information should be retrievable from the LIMS system. The LIMS Lookup is implemented as a socket connection to the LIMS server from the Genome Sequencer Instrument. The lookup mechanism sends an XML request to the server and waits for a response XML message. The server address needs to be specified in the file /usr/local/rig/config/limslookup.properties.


Here is an example entry: lims.connectionURI=http://oracle.454.com:80 It is the customer’s responsibility to create a server process that will listen on a socket for a connection and receive a LIMS Lookup request in XML. The process then queries the LIMS system and creates the Lookup Response message and sends it on the socket connection back to the requesting process.

2.2.2 LIMS Simulator

A LIMS Server Simulator application is distributed with the application. Under normal operation, this software is not activated. It is provided for testing and developing customer LIMS connectors. To start the server, run: /usr/local/rig/bin/startLimsSimServer.sh This will run a server on port 1234 on the local host. To change the port number, pass a number to the java application as a command line parameter. Edit the startLimsSimServer.sh to pass in the port number.


2.3 Pre-wash

2.3.1 Description

The Pre-wash action selected from the GS Sequencer application’s Run Wizard allows the user to start a pre-wash.


2.3.2 Stimulus/Response Sequences

The GS Sequencer application presents the Run Wizard modal dialog when the Start button is pressed in the Global Action Area. The Pre-wash option is selected and the Next button clicked. At the next prompt, the ‘Start’ action will start the pre-wash Run; and the ‘Cancel’ action will negate the request.


2.4 Sequencing Run

2.4.1 Description

The Configured Sequencing Run selection from the the GS Sequencer application’s Run Wizard allows the user to start a sequencing Run based on the LIMS information that matches the specified PicoTiterPlate ID. Potential error conditions are:

• No LIMS adapter installed • No LIMS connection available • Communication timeout • Bad message format received • LIMS error (formatted and returned from LIMS) • Store requirements exceeded • No style sheet found • Invalid style sheet • Invalid response document

There are three style sheets that aid in the formatting of the outgoing and incoming messages:

• lookupmessage.xsl • limsresponse.xsl • limsresponseerror.xsl


2.4.2 Stimulus/Response Sequences

The GS Sequencer application presents the Run Wizard modal dialog when the Start button is pressed in the Global Action Area (see above). The Configured Sequencing Run option is selected and the Next button is clicked. At the next prompt, the user must enter a PicoTiterPlate ID in the field and retrieve the Run settings associated with it from the LIMS server. This enables the ‘Start’ button. The ‘Start’ action will start the sequencing Run; and the ‘Cancel’ action will negate the request.


3. APPENDIX A: GLOSSARY

LIMS Server The server containing the Run script parameters associated with the PicoTiterPlate ID.

LIMS Connector The software adapter used to connect and communicate the barcode and Run information.

LIMS Simulator A testing server that simulates the responses to a PicoTiterPlate ID lookup from a LIMS server.

Lookup A message containing the PicoTiterPlate ID, sent to the LIMS server.

PTP Abbreviation for PicoTiterPlate.

PTP ID The PicoTiterPlate identification; a unique identifier for the LIMS system. ID and barcode in this case are synonymous. However, the term ID is more general: clients may use any identification techniques besides barcoding, such as RFID, magnetic strips, etc.

PTP Barcode The PicoTiterPlate barcode that correlates to the PicoTiterPlate ID. Synonymous with the PicoTiterPlate ID.

Pre-wash Run The action that invokes the Genome Sequencer Instrument pre-wash Run script.

Response A message returned from the LIMS server in response to a Lookup message. This response will either be the Run information or an error message.

Sequencing Run The action that presents a dialog for barcode entry, validates the Run information received from the LIMS (in response to a loopup message), and starts a sequencing Run script based on the PicoTiterPlate ID.


4. APPENDIX B: SEQUENCER MESSAGING SCHEMA

Data passed to and from the LIMS adapter is XML based on the schema below. This XML provides a flexible and adaptive interface between the Genome Sequencer Instrument and any LIMS systems.

Send a lookup message from the Genome Sequencer Instrument to the LIMS

<?xml version="1.0" encoding="UTF-8"?> <Sequencer xmlns:fn="http://www.w3.org/2005/02/xpath-functions" xmlns:fo="http://www.w3.org/1999/XSL/Format" xmlns:xdt="http://www.w3.org/2005/02/xpath-datatypes" xmlns:xs="http://www.w3.org/2001/XMLSchema"> <Instrument> <Name>454 Sequencer</Name> <Host>MyRigHost</Host> <Version>1.x</Version> <SerialNumber/> </Instrument> <LIMSLookup> <PtpId>1</PtpId> </LIMSLookup> </Sequencer>

Receive a LIMS lookup error <?xml version="1.0" encoding="UTF-8"?> <Sequencer xmlns="http://www.454.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.454.com sequencer.xsd"> <Instrument> <Version>Version 1.2</Version> <SerialNumber>1234</SerialNumber> <Name>TheInstrumentName</Name> </Instrument> <LIMSLookup> <PtpId>3</PtpId> </LIMSLookup> <Error> <Message style="limsresponseerror.xsl"><b>No information found for PicoTiterPlate ID 3.</b></Message> <Severity>1</Severity> <Id>100</Id> </Error> </Sequencer>


Receive a valid LIMS lookup

<?xml version="1.0" encoding="UTF-8"?> <Sequencer xmlns="http://www.454.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.454.com sequencer.xsd"> <Instrument> <Name>Instrument Name</Name> <Host>SomeHostName</Host> <Version>Version 1.0</Version> <SerialNumber>serial#123</SerialNumber> </Instrument> <Run> <ShortRunName>TheShortRunName</ShortRunName> <RunId>1</RunId> <RunDirectory></RunDirectory> <GroupName>TheGroupName</GroupName> <PTP> <Id>PTP!D123</Id> <Size>25x75</Size> <PadLayout></PadLayout> </PTP> <AnalysisType></AnalysisType> <NukeFlowOrder>TACG</NukeFlowOrder> <CycleCount>42</CycleCount> <Backup>true</Backup> <UserName type="Administrator"> <First>Jon</First> <Last>Johnson</Last> </UserName> <Email type="Notification">[email protected]</Email> <FilePath type="RunScript"></FilePath> <FilePath type="AnalysisParse"></FilePath> <FilePath type="BackupScript"></FilePath> <FilePath type="EndOfRunScript"></FilePath> <Message style="limsresponse.xsl" type="String">This is the information for PicoTiterPlate ID 1.</Message> </Run> <LIMSLookup> <PtpId>1</PtpId> </LIMSLookup> </Sequencer>


Sequencer Messaging Schema (sequencer.xsd)


5. ADDITIONAL INFORMATION ABOUT THIS MANUAL

5.1 Revision History

Manual Version Instrument Version Software Version Revision Date FLX.01 – USM-00023.B GS FLX 1.1.01 December 2006 FLX.02 – USM-00023.C GS FLX 1.1.02 June 2007 FLX.03 – USM-00023.D GS FLX 1.1.03 December 2007 Every effort has been made to ensure that all the information contained in this document was correct at the time of printing. However, Roche Diagnostics GmbH reserves the right to make any changes necessary without notice as part of ongoing product development. No part of this document may be reproduced or transmitted in any form or by any means, electronic or mechanical, for any purpose, without express written permission. Questions or comments regarding the contents of this manual can be directed to the address below or to your Roche Representative or to the customer support address below:

Roche Diagnostics GmbH Roche Applied Science Customer Support Nonnenwald 2 82372 Penzberg, Germany

5.2 Intended Use

The Genome Sequencer System is intended for life science research applications and must be used exclusively by laboratory professionals trained in laboratory techniques and having studied the instructions for use of its various associated kits. The Genome Sequencer System is not intended for use in diagnostic procedures.

5.3 Notice to Purchaser

RESTRICTION ON USE: Purchaser is only authorized to use the Genome Sequencer Instrument with PicoTiterPlate devices supplied by 454 Life Sciences Corporation and in conformity with the procedures contained in the Operator’s Manual. Made in USA for Roche Diagnostics by 454 Life Sciences Corporation, Branford, CT, USA.

5.4 Trademarks

454, GENOME SEQUENCER, PICOTITERPLATE, and emPCR are trademarks of 454 Life Sciences Corporation, Branford, CT, USA. Other brands or product names are trademarks of their respective holders.


5.5 Assistance

If you have questions or experience problems with the Genome Sequencer System, please call, write, fax, or e-mail us.

When calling for assistance, be prepared to provide the serial number of your Genome Sequencer Instrument and/or lot number of the kit(s) you are using. The instrument’s serial number is located on the label found on the back of the instrument cart.

If you are located in… Please contact Roche Applied Science Technical Support via: USA or Canada phone: 1-800-262-4911

(toll-free) e-mail: [email protected]

Europe, Middle East, Asia Pacific, Mexico, South America or Africa

phone: +49-8856-60-6457 or toll-free +800SEQUENCE

e-mail: [email protected]

Japan phone: +03-5443-5287 e-mail: [email protected]

mailto:[email protected]



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