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Information System for Proteomics Laboratory

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Information System for Proteomics Laboratory MASARYK UNIVERSITY FACULTY OF INFORMATICS Information system for Proteomics laboratory DIPLOMA THESIS Martin Bednařík Brno, 2015 DECLARATION Hereby I declare that this paper is my original authorial work, which I have worked out by my own. All sources, references and literature used or excerpted during elaboration of this work are properly cited and listed in complete reference to the due source. Martin Bednařík Advisor: Mgr. Aleš Křenek, Ph.D. ACKNOWLEDGEMENT I would like to thank my advisor, Mgr. Aleš Křenek, Ph.D., for his patience, guidance and all the practical advice. I would also like to thank doc. RNDr. Zbyněk Zdráhal, Dr., Mgr. David Potěšil, Ph.D. and Mgr. Michal Obořil for their time, support and willingness to coop- erate. KEYWORDS LabKey Server, Proteomics laboratory, Laboratory information and management system, Perun ABSTRACT The main goal of this thesis is to analyze the requirements of Proteomics laboratory for a laboratory information and management system, choose available open-source framework and design and implement a working prototype for this laboratory to use. Another goal is to study the options of external authentication and its usability with chosen framework. This thesis also discusses possible connection to external data storage. CONTENTS 1. Introduction ................................................................................................................................... 1 2. Proteomics Core Facility .............................................................................................................. 3 2.1 Introduction................................................................................................................................. 3 2.2 Involved people and roles ......................................................................................................... 3 2.3 Request processing workflow................................................................................................... 4 2.4 Laboratory requirements ........................................................................................................... 7 2.4.1 Expected user roles .............................................................................................................. 8 2.4.2 System requirements ........................................................................................................... 9 3. Choice of technology .................................................................................................................. 13 3.1 Laboratory Information and Management Systems............................................................ 13 3.1.1 Proteomics laboratory’s reasons for LIMS ..................................................................... 13 3.1.2 LIMS packages ................................................................................................................... 14 3.2 LabKey Server ........................................................................................................................... 16 3.2.1 About ................................................................................................................................... 16 3.2.2 Main features ...................................................................................................................... 17 3.3 Perun .......................................................................................................................................... 20 3.3.1 Introduction ........................................................................................................................ 20 3.3.2 Used and supported technologies ................................................................................... 21 3.3.3 Features ............................................................................................................................... 21 3.4 Data Storage .............................................................................................................................. 23 4. Design and implementation ...................................................................................................... 24 4.1 Introduction............................................................................................................................... 24 4.2 Data model ................................................................................................................................ 25 4.2.1 Introduction ........................................................................................................................ 25 4.2.2 Schemas and queries ......................................................................................................... 26 4.2.3 Used data model ................................................................................................................ 27 4.3 Site structure ............................................................................................................................. 28 4.3.1 Homepage ........................................................................................................................... 28 4.3.2 Projects vs. folders ............................................................................................................. 31 4.4 Users and groups ...................................................................................................................... 32 4.5 Authentication .......................................................................................................................... 33 4.6 File storing ................................................................................................................................. 35 4.7 Collaboration system ............................................................................................................... 36 4.8 Applications .............................................................................................................................. 38 4.8.1 Introduction ........................................................................................................................ 38 4.8.2 General issues ..................................................................................................................... 39 4.8.3 Types of applications......................................................................................................... 39 5. Interaction with implemented system ..................................................................................... 46 5.1 Introduction............................................................................................................................... 46 5.2 Typical system use case scenarios .......................................................................................... 47 6. Conclusion ................................................................................................................................... 50 Bibliography ....................................................................................................................................... 52 Attachment .......................................................................................................................................... 54 1. INTRODUCTION Proteomics Core Facility is a successful facility based under CEITEC. It receives large amount of orders from various customers, its employees successfully publish in scientific magazines and it manages to keep a very good reputation among the academic community. However, this facility could work even more effective. Keeping track of laboratory work requires non-trivial effort. Tens or even hundreds of ex- periments are performed every year and each one requires documentation about who re- quested the measurement, what exactly was requested, how was the measurement per- formed, who was responsible for what, what were the problems that came up during the whole process, etc. Besides paperwork, there are machines that produce data which also need to be put into context, preferably in a way that allows effective look up in case of need. Employees need to know the state of active orders, be able to quickly check their own responsibilities. Doing all this without an information system makes things rather slow and hard to man- age. For years now, an idea of deploying an information system to speed things up has been alive. But the large amount of work, small amount of employees, no employees with either enough IT experience or time to invest to developing this information system resulted into a state when this idea never got realized. The main goal of this thesis is to make the firsts steps and build a foundation for such sys- tem because it is expected that deploying of something that complex will take years. In the second chapter we introduce the Proteomics Core Facility. We describe the way they work and then we present the result of our meetings where we discussed their requirements on laboratory information and management system. The third chapter is more theoretical. We describe laboratory information and manage- ment systems in general, list available open-source packages and present main features of the package (LabKey Server) we decided to use. The next section of this chapter is about Perun, an identity and access management system that we decided to use to test possibilities 1 for authentication to the LabKey Server. At last, we present brief information about the Pro- teomics laboratory’s
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