NCI CBIIT LIMS ISIG Meeting– Aug. 21,2007 NCI CBIIT LIMS Consortium Interface SIG Mission: focus on an overall goal of providing a library of interfaces/adapters for Instrumentation, Statistical Analysis software, and ERP software which would be available to the cancer research community, would integrate into caLIMS II, and be caBIG compliant. All interested parties are welcome – please help spread the word among colleagues and contact us if interested! Phone: Access code:

NCI CBIIT LIMS Consortium ISIG – Agenda 1)Review of ISIG Mission and Goals 2)Review and discussion of proposed standards – general and specific – reach consensus on recommendation for consortium 3)Discussion of implementation requirements, review, and documentation 4)Discussion related to list of equipment and software for early implementation 5)Meeting Schedule and suggestions for future demo/discussion topics 6)Additional items?

NCI CBIIT LIMS Consortium ISIG – Goals NCI CBIIT LIMS Consortium ISIG: Initial Goals 1)Research and collate known research and health community standards that may be applicable to LIMS interfaces (HL7, 21 CFR Part 11, NCI Biorepository Best Practices, HIPAA, Barcodes) 2)Establish a requirements standard for an adapter (interface)* supported by caLIMS II 3)Establish and prioritize a list of instruments and software most commonly used in both basic research, core facility laboratories, and clinical trials laboratories 4)Explore with consortium members and other interested parties what existing resources are available 5)Explore with commercial vendors whether some partnership could be established to provide interfaces and/or SDKs for their products * Note that while we recognize that the community uses the terms ‘interface’ and ‘adapter’ interchangeably, we have chosen to use the term ‘adapter’ here to avoid any confusion with other types of interfaces (e.g. Graphical User Interface (GUI)).

Components of an Adapter System 1)LIMS – as both input and output (i.e. Bidirectional) 2)Instruments with or without Instrument Data Systems (IDS) 3)Stand alone Software Applications 4)End Users

General Criteria Standards for Adapters General criteria standards are listed in document: InstrumentInterfaceCriteriaList.doc 1)Well defined APIs based Interfacing. 2) Database Interfacing. 3) File exchange based Interfacing. 4)Typed Input/Output parameters 5)Data Constant & Error Codes 6)Exception Handling 7)Time Out 8)Special Environmental requirements, variables etc. 9)Major Issue/Malfunction of the method

High level Adapter Architecture Adapter (written by caLIMSII developer) Example: ABI3730XLSequencin gAdapter Equipment Firm ware (possible future release) Application Software Instrument System Software caLIMS II Server caLIMSII Objects & Utilities File Transporter

Adapter An Adapter is a software interface that connects Instruments Data Systems or External Software Systems to the LIMS. Information can be passed both to and from the LIMS. All adapters of caLIMS II are inherited from gov.nih.nci.calims2.Adapter. Example: An Adapter can be further derived to Specific adapters.

Adapter Standard Criteria – 1 1) Define what needs to be sent to the Instrument Data System (IDS) or External Software Systems from the LIMS and what needs to be sent to the LIMS from the IDS or external software system. Parameters should be strongly typed (Well defined data Type) Example: 1) Sample lists -A Collection of String 2) Run parameters – Parameters declared of Type gov.nih.nci.calims2.domain.Run

Adapter Standard Criteria – 2 2) Define How the data is to be sent between the Instrument Data System or External Software System and the LIMS. External systems may communicate through Application Programmable Interface (APIs)/Web Service, Fixed format data files and/or Database Links (access inter application databases). Example: 1) caLIMS II adapter interfaces to an IDS by exporting and/or importing predefined file formats to and from a given folder. 2) caLIMS II adapter interfaces to a Billing system via data base tables.

Adapter Standard Criteria – 3 3) Error and Exception handling at the interface. Define fatal system error checks. Define a generic error code standard criteria – would apply to all interfaces. Define Specific Error codes to the individual external system. Define Alternate paths for each error code if necessary.

Adapter Standard Criteria – 4 4) Define standards for Documentation and Training materials (To follow caBIG guidelines). Determine requirements for caBIG. Define type and scope of User Guides. Define type and scope of Training guides/presentations/demos. (This topic still needs to be discussed with group!).

Adapter Standard Criteria – Discussion1 Discussion point 1 2) There should be a minimum set of documentation and training documents required. The standards for this set should be determined so that the set is complete enough for the intended use but not a burden for the development or training teams. We intend to leverage off of caBIG Documentation and Training Templates but recognize that these documents may be too ‘heavy’ for most interface applications. We are soliciting comments as to preferred content and format (User Guide, Technical Guide (installation, administration, customization), Training Guide (demo files, PowerPoint, etc.) and/or some combination of the above).

Adapter Standard Criteria – Discussion2 Discussion point 2 3) We continue to welcome comments and suggestions and hope you have had a chance to share our materials with your internal colleagues for additional input. Is there more discussion needed or are we ready to adopt these standards?

Adapter Standard Criteria – Discussion3 Discussion point 3 1)The interface development is independent of the GUI for the LIMS so we will form a GUI SIG that will be a ‘cross-cutting’ working SIG for all parts of the project. Therefore we have taken out the great discussion points we have so far and captured them for a GUI SIG Kickoff meeting – date TBD.

Equipment & Software List u Are we ready to discuss the equipment & software list? u Are there any updates since the last circulation? u Are there volunteers to look at existing interfaces and upgrade to meet caLIMS II (caBIG) compliancy standards? u Suggestions on how to proceed…..

Meeting Schedules and Contacts u Next LIMS Consortium meeting: –August 27, pm EDT (CENTRA) u Next ISIG meeting date: September 18, 2007 u Next OM SIG meeting date: August 23, 2007 u Our thanks to all of you who have volunteered your valuable time and efforts to helping the consortium. We appreciate your participation!

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