Chromatography integrates well

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The way to interface and integrate chromatography data systems is a major theme in this issue's review of laboratory information management systems, writes Phillip Hill

One of the latest developments in the interfacing between a laboratory information management system (LIMS) and a chromatography data system (CDS) is the emergence of 'configurable interfaces'. With a configurable interface, set-up screens can be used to identify key parameters that are specific to the CDS. Drop down menus and check boxes can be used to set default parameters such as servers, instrument methods, databases, and logon routines, that are being used by the CDS. Being able to configure these defaults without having to 'reprogram' the interface provides maximum flexibility.

Working in conjunction with major CDS developers, Labtronics has introduced configurable interfaces for ChemStation Plus, Chromeleon, EZChrom Elite, Millennium 32, Empower, Turbochrom and TotalChrom. All of these interfaces can be used to interface the CDS with any LIMS.

The two key portions of a bi-directional CDS/LIMS interface are collecting sample information from the LIMS and using that to create a sequence in the CDS, and then capturing the CDS results and transferring them to the LIMS. Check-boxes on the sequence set-up screen identify the fields that are being transferred to the CDS.

The Report Set-up screen provides a quick and efficient means for selecting the fields that are going to be requested from the CDS after the samples have been run (see Fig. 2 below).

  • Fig.1 Sequence set-up: identifying fields for transfer to the CDS

  • Fig.2 Reporting back: selecting fields requested from the CDS

Until recently, creating an interface between the CDS and LIMS meant implementing a separate program to connect the two systems. Embedded integration gives the analyst access to the interface at the most logical point - from the application that is running the analysis, at the time of analysis. Because the interface becomes an integral part of the CDS application, it is able to use the CDS security and audit trail. This, combined with the file-less transfer of information between the CDS and LIMS, simplifies compliance with 21 CFR Part 11 and reduces validation requirements.

In a related development, Varian and Labtronics have announced that they are partnering to develop and market the integration of Labtronics' LimsLink CDS with Varian's Galaxie CDS. The latter is a client/server solution that can control a wide range of liquid chromatographs and gas chromatographs, including other manufacturers' models, and allows analyses to be viewed from anywhere on the network, through a common user interface. The latest version of LimsLink CDS can also display Waters Millennium 32 or Empower chromatograms from inside a LIMS.

For its part, Thermo Electron has released the latest version of its Chromatography Data System, Atlas 2003, calling it 'the most significant release of Atlas in recent years'. The CDS offers full control for Thermo's Finnigan Surveyor LC and SpectraSystem LC, plus control of its Trace GC and Focus GC instruments.

Atlas 2003's support for Photo Diode Array (PDA)/3D data acquisition improves productivity, for example through rapid determination of the best detection wavelength and automated peak purity assessment. Atlas now supports the creation of a spectral library database, enabling chromatographers to search for matching spectra to confirm peak identity. Oracle technology chosen

Thermo Electron has worked with other major chromatography instrument vendors to incorporate control of their systems into Atlas 2003 CDS. Atlas also enables seamless integration with LIMS, and solutions for data archival and electronic record keeping. The company offers CDS, LIMS, and data archival systems, integrated as a single informatics solution. Atlas supports full compliance with the 21 CFR Part 11 on electronic signatures and records.

Thermo Electron has also started shipping the latest version of its LIMS, Nautilus 2003 Release 1. The most significant changes over previous versions relate to functions for Result Entry and Auditing. Result Entry is now more flexible, with improved row ordering and switchable row/column highlighting. Barcode navigation has also been simplified.

Auditing now enables audit tables of, for example, instrument or operator records in the LIMS database to be displayed in a hierarchy. This allows users to see more easily the relationships between tables and therefore view the audit trail. Users are also able to audit tables with primary keys that consist of more than a single field. Nautilus Auditing uses the latest Microsoft.NET Framework technology. With version 2003, Nautilus has been updated to operate with the Oracle 9i database. Applied Biosystems, too, has chosen the Oracle-9i Application Server as the platform for its SQL*LIMS. Oracle software has been an integral part of the SQL*LIMS since it was first released 15 years ago.

Running SQL*LIMS on a multi-tiered architecture, based on the Oracle-9i Application Server, will bring particular benefits to laboratories needing to address and meet stringent regulatory requirements, the company believes. The LIMS is multilingual and offers excellent organisational security, for example, across virtual and physical sites, for different projects or different classes of users.

Applied Biosystems sees one fruitful area of application in forensics laboratories. A solution based on SQL*LIMS has recently been installed at the DNA unit of the Criminalpol at the Ministry of the Interior in Italy. Based on systems initially developed for the pharmaceutical and biotechnology industries, the Applied Biosystems' system for forensic laboratories combines a basic LIMS with two or three additional components, depending on the laboratory and the customer's specific requirements. Despite similar workloads, these can vary considerably, according to Dr Renato Biondo, Chief of the DNA unit in the Criminalpol. He said: 'Members of staff from a hospital in France recently visited us and were generally impressed by our solution, in particular by the barcode management. However, a forensic specialist from Lausanne did not understand this approach at all! Every group working in a forensic laboratory has different needs and working procedures, and I would recommend that they gain as much experience of other groups as possible.' The minimum requirement that forensics customers have asked of Applied Biosystems is a UNIX database, so that all the information and relevant data can be stored in the same repository. Strong casework and management systems are also important and, due to the sensitive nature of the work, good security is essential.

Partnerships
Other recent LIMS developments highlight the increasing trend for partnerships between LIMS providers and their customers or corporate providers.

For instance, LabVantage Solutions has attained Advanced Member status in IBM's PartnerWorld for Developers Business Partner Programme. As an Advanced Member, LabVantage gains access to IBM platforms, middleware, and computing infrastructure capabilities. Dorman Followwill, Vice President of Healthcare and Life Sciences for market analysts Frost & Sullivan, said: 'This partnership is a boon for the drug discovery and development community. LabVantage's Enterprise LIMS and Life Sciences LIMS, with seamless data sharing across a wide variety of computing platforms, combined with IBM Life Sciences' hardware and global service offerings, represent an end-to-end information leveraging solution that will save precious time in the race to discover new drugs.'

Galileo Genomics has signed a software and services agreement for LabVantage Sapphire Life Sciences LIMS. Galileo will initially use Sapphire to manage information relating to microsatellite and SNP genotyping. It expects that, once it has implemented Sapphire, it will be able to expand and perform dense genome-wide scans on at least 40 diseases within the next three years, followed by fine mapping of small candidate regions and identification of disease-related sequence variations. This process includes over three billion genotypes on DNA samples from approximately 60,000 patients, relatives, and controls, generating terabytes of raw and derived data.

But LabVantage is not alone in joining up with IBM. LabWare too has attained Advanced Member status in IBM's PartnerWorld for Developers Programme. With the shared goal of providing enterprises with a total information management solution, LabWare and IBM will integrate their solutions to enhance regulatory compliance, increase productivity and link all critical data throughout the enterprise. LabWare and IBM will join in strategic initiatives, and also create market-specific solutions by leveraging LabWare's expertise in conjunction with IBM technologies. LabWare expects to benefit from a close working relationship with IBM and will have access to a wider array of IBM resources.

Before its IBM announcement, LabWare introduced a new product, LabWare Web LIMS, that makes full use of the advantages of the Web without requiring customers, who use the existing Client/Server LIMS product, to make any configuration changes. Users can now choose to interact with the LIMS either via Web LIMS, or the Client/Server LIMS, or a combination of both. The new system is designed to run on any J2EE-based Web Application Server without requiring the deployment of any applets. The Web user interface runs on the existing LIMS configuration, and therefore honours all the business rules, template configurations, and security settings the customer has established.

BASF and Creon Lab Control have announced a new data management system supporting combinatorial materials research. This is the outcome of a strategic cooperation agreement between the partners that began in March 2002. BASF expects that combinatorial materials research will drastically cut cost and time in the development of novel or improved polymers and materials. The automated technique offers parallel, small-scale synthesis, formulation, application and testing of many materials.

AstraZeneca, for its part, has implemented the Watson LIMS from InnaPhase Corporation in its Adlerley centre in the UK. AstraZeneca is also using the Watson LIMS product within its facilities in: Charnwood, UK; Lund, Sweden; and Wilmington, Delaware, USA. Watson LIMS, a solution within the Pharma LIMS suite, is specifically designed to support DMPK/Bioanalytical studies in drug development while ensuring regulatory compliance with 21 CFR Part 11 guidance on electronic records and signatures.

Biogen, the world's oldest independent biotechnology company, has also signed a licence agreement to implement InnaPhase's Watson LIMS. This most recent agreement provides Biogen with Watson licences for their Cambridge, Massachusetts, and Research Triangle Park, North Carolina, facilities in the US.

In another example of cross-site hook-ups, Aventis Pharmaceuticals has implemented SciQuest's LifeCycle Biologicals Manager at two European sites. Aventis has licensed LifeCycle for its industrial operations business unit, which is involved in the development and scale-up of microbial strains and vectors for producing therapeutic compounds through fermentation and cell culture methods. During the first phase of implementation, Aventis will use the materials management solution to track more than 2,500 unique microbial strains in more than 20,000 individual containers throughout Aventis process development facilities in Frankfurt, Germany and Vitry-sur-Seine, France.

Aventis is the first company to implement all three of SciQuest's materials management solutions; it has also installed Reagent Manager to track and monitor chemicals and reagents used in the discovery processes, as well as Substance Manager to manage proprietary compounds.

  • An analyst no longer needs to leave the CDS to interact with the LIMS

Data management
ABS Labs Ltd, a pharmaceutical development and occupational testing company based in London, has chosen the NuGenesis Scientific Data Management System (SDMS) for company-wide operations. ABS Labs processes highly sensitive chromatographic-mass spectrometric assays for a variety of compounds in biological samples. NuGenesis SDMS accurately and automatically captures, catalogues and stores lab instrument data and information from business applications and facilitates the seamless integration of information within the organisation.

ABS Labs believes that the NuGenesis SDMS platform will increase analyst productivity. The system will also provide ABS Labs with data archival and easy access to data and documentation to prepare regulatory submissions.

Mira Doig, technical director of ABS Labs, said: 'NuGenesis SDMS reduces the time analysts now spend manually moving data from instrument reports into spreadsheets, taking a three-hour process down to five minutes. This means we can significantly boost output without increasing internal resources. The system will pay for itself in less than a year.'

On document and record management, Thermo Electron has made several significant extensions to its product eRecordManager. Launched in 2002, eRecordManager helps customers capture, store and index large volumes of original raw instrument data, reports and documents, while also converting the content of these records for storage as XML (eXtensible Mark-up Language) files. The new version, Release 2, focuses on enhanced security of electronic records and further ease of use. It offers new XML converters for file formats including Applied Biosystems/ MDS SCIEX Analyst, Dionex Chromeleon CDS, and Thermo's Multichrom CDS.

Enhancements to existing file converters in the new eRecordManager release include those for Micromass Masslynx, Bruker XWIN-NMR, and Perkin Elmer's AccessChrom, Turbochrom, and Totalchrom instruments.

eRecordManager allows scientists to archive electronic records and to share information with colleagues. It translates instrument data into a platform-neutral format called GAML (Generalized Analytical Markup Language), based on XML, which frees the data from reliance on the original instrument software for its retrieval.

A consistent theme of the LIMS business in recent years has been the interest of LIMS' vendors in applying their skills and techniques more widely in the life sciences. One example of a company moving to marry its LIMS business with other software for life sciences is Applied Biosystems, which is marketing the Celera Discovery System (Applied Biosystems and Celera are sister companies within the Applera Corporation). The Celera Discovery System goes way beyond conventional LIMS and an enhanced version of the online platform has recently been released. A key feature is the offer of individual subscriptions for academic researchers, who could save time and money through online access to an integrated set of high quality data and analysis tools, thus eliminating the need for data infrastructure development and maintenance.

The new release has an interactive Map Viewer, updated to give customisable graphic displays for comparative genomics studies. It also allows researchers to conduct BLAST searches in batch mode and customised data views, from entire chromosomes to the single nucleotide level.

Other features include curated human and mouse gene databases, updated sequence analysis tools, protein libraries for functional predictions and links to the Human Gene Mutation Database (HGMD), Online Mendelian Inheritance in Man (OMIM), Swiss-Prot and LocusLink databases. These enhancements are intended to aid high throughput analysis and allow subscribers to analyse biological relationships within any region of the human or mouse genomes.