Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics, Indiana University June 2005 / The large volume of data generated by commercial and research laboratories, along with requirements mandated by regulatory agencies, have forced companies to use laboratory information management systems (LIMS) to improve efficiencies in tracking, managing samples, and precisely reporting test results. However, most general purpose LIMS do not provide an interface to automatically collect data from analytical instruments to store in a database. A scientific data management system (SDMS) provides a “Print-to-Database” technology, which facilitates the entry of reports generated by instruments directly into the SDMS database as Windows enhanced metafiles thus to minimize data entry errors. Unfortunately, SDMS does not allow performing further analysis. Many LIMS vendors provide plug-ins for single instrument but none of them provides a general purpose interface to extract the data from SDMS and store in LIMS. In this project, a general purpose middle layer named LabTechie is designed, built and tested for seamless integration between instruments, SDMS and LIMS. This project was conducted at American Institute of Technology (AIT) Laboratories, an analytical laboratory that specializes in trace chemical measurement of biological fluids. Data is generated from 20 analytical instruments, including gas chromatography/mass spectrometer (GC/MS), high performance liquid chromatography (HPLC), and liquid chromatography/mass spectrometer (LC/MS), and currently stored in NuGenesis SDMS iv (Waters, Milford, MA). This approach can be easily expanded to include additional instruments.

Indiana University-Purdue University Indianapolis (IUPUI) / Proof of Concept - An Academic LIMS application: The aim of this project is the creation of an open-source, freeware LIMS application that can be used in an academic setting as a teaching tool for both chemistry and computer science students. The LIMS package will combine an application, developed using VB.NET, to manage the data with other open-source or freeware programs such as MySQL and WEKA. The numerous commercial chemical informatics applications available are useful tools to learn how to manage data from a user's standpoint. However, they are not readily available to the average student, nor do they offer a great understanding into how they were developed from a programmer's frame of mind. There is a great void here that, if filled can greatly help the academic community.

Philosophiae Doctor - PhD / A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open source LIMS are available. The decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. However, to find a LIMS that incorporates all possible requirements of a biobank may often be a complicated endeavour. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the development of Baobab LIMS, an open source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. Baobab LIMS is based on the Plone web-content management framework, a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines. The Baobab LIMS components were tested and evaluated in three human biobanks. The testing of the LIMS modules aided in the mapping of the biobanks requirements to the LIMS functionalities, and furthermore, it helped to reveal new user suggestions, such as the enhancement of the online documentation. The user suggestions are demonstrated to be important for both LIMS strengthen and biobank sustainability. Ultimately, the practical LIMS evaluations showed the ability of Boabab LIMS to be used in the management of human biobanks operations of relatively different biobanking workflows.

L'objectif de mon travail de thèse était de développer des outils bio informatiques permettant d'améliorer la traditionnelle gestion de l'information scientifique au sein d'un grand centre de recherche et en particulier au sein d'une plateforme de génomique. Trois outils ont été développés: un cahier de laboratoire électronique, un système de gestion de l'information de laboratoire pour des applications de génomique dont le séquençage de nouvelle génération, ainsi qu'un système de gestion des échantillons pour de grandes bio-banques. Ce travail a été réalisé en étroite collaboration avec des biologistes, épidémiologistes et informaticiens. Il a également inclus la mise en place d'interactions entre les différents outils pour former un système informatique intégré. Les trois outils ont été rapidement adoptés par l'ensemble des scientifiques du centre de recherche et sont désormais utilisés au quotidien pour le suivi de toutes les activités de laboratoire mais aussi plus globalement pour les autres activités scientifiques du centre de recherche. Ces outils sont transposables dans d'autres instituts de recherche / The aim of my thesis work was to develop bioinformatics tools to improve the traditional scientific information management within a large research centre and especially within a genomics platform. Three tools have been developed: an electronic laboratory notebook, a laboratory information management system for genomics applications including next generation sequencing, as well as a sample management system for large biobanks. This work has been conducted in close collaboration with biologists, epidemiologists and IT specialists. It has also included the setup of interactions between the different tools to make an integrated IT system. The three tools have been rapidly adopted by all the scientists of the research centre and are now daily used for the tracking of all the laboratory’s activities but also more globally for the research centre’s other scientific activities. These tools are transposable in other research institutes