Lina: a Laboratory Inventory System for Oligonucleotides, Microbial Strains, and Cell Lines Ahmed F
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University of New Haven Digital Commons @ New Haven Electrical & Computer Engineering and Computer Electrical & Computer Engineering and Computer Science Faculty Publications Science 2011 Lina: A Laboratory Inventory System for Oligonucleotides, Microbial Strains, and Cell Lines Ahmed F. Yousef Masdar Institute of Science and Technology Ibrahim Baggili University of New Haven, [email protected] G. Bartlett Bartlett Consulting, Indianapolis Michael D. Kane Purdue University Joe S. Mymryk University of Western Ontario Follow this and additional works at: https://digitalcommons.newhaven.edu/ electricalcomputerengineering-facpubs Part of the Computer Engineering Commons, Electrical and Computer Engineering Commons, Forensic Science and Technology Commons, and the Information Security Commons Publisher Citation Yousef, A. F., Baggili, I. M., Bartlett, G., Kane, M. D., & Mymryk, J. S. (2011). Lina: A laboratory inventory system for oligonucleotides, microbial strains, and cell lines. Journal of the Association for Laboratory Automation, 16(1), 82-89 Comments Dr. Baggili was appointed to the University of New Haven’s Elder Family Endowed Chair in 2015. Copyright (c) 2011 by the Society for Laboratory Automation and Screening. Software available at http://linasoft.weebly.com. See also http://publish.uwo.ca/~jmymryk/LINA.html Innovation Brief LINA: A Laboratory Inventory System for Oligonucleotides, Microbial Strains, and Cell Lines A.F. Yousef,1 I.M. Baggili,2 G. Bartlett,3 M.D. Kane,4 and J.S. Mymryk1* 1Department of Oncology and Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada 2College of Information Technology, Zayed University, Abu Dhabi, UAE 3Bartlett Consulting, Indianapolis, IN 4Department of Computer and Information Technology, Purdue University, West Lafayette, IN n this article, we present the Laboratory Inventory INTRODUCTION Keywords: Network Application (LINA), a software system that I Biomedical research has become ever more data biomedical systems, assists research laboratories in keeping track of their intensive.1 The rapid development of biological tech- laboratory collections of biologically relevant materials. This open nology has similarly resulted in the production of inventory, source application uses relational Microsoft Access new laboratory reagents, including DNA constructs, relational database database technology as a back end and a Microsoft .NET antibodies, and cell lines, at an exponential rate. application as a front end. Preconstructed table templates Generating and maintaining reagent records have are provided that contain standardized and customizable always been vital aspects of successfully running data fields. As new samples are added to the inventory, a research laboratory, and this was traditionally each is provided with a unique laboratory identifier, which organized using paper records. However, the days is assigned automatically and sequentially, allowing rapid when academic scientists could efficiently keep track retrieval when a given reagent is required. The LINA of all the reagents in their laboratory using a note- contains a number of useful search tools including book and pen have come to an end. The use of computer databases to maintain and a general search, which allows database searches using up access laboratory reagent records was the obvious to four user-defined criteria. The LINA represents an next step in the evolution of modern laboratory prac- easily implemented and useful organizational tool for tices. Indeed, many programs have been developed in biological laboratories with large numbers of strains, industry that are very useful in cataloging, and ac- clones, or other reagents. (JALA 2011;16:82–9) cessing records related to experiments performed and reagent inventories. These industry-produced programs include software such as the Cryotrack in- ventory management system (by Cryotrack, Ltd., *Correspondence: J. S. Mymryk, Ph.D., Department of Oncology Los Altos, CA), Inventory Workgroup (by Cam- and Microbiology & Immunology, University of Western Ontario, 790 Commissioners Road East, London, Ontario N6C 4L6, bridgeSoft, Cambridge, MA), LABCOLLECTOR Canada; Phone: þ1.519.685.8600, ext. 53012; Fax: (by Chemistry Software Ltd., Houston, TX), and ez- þ1.519.685.8616; E-mail: [email protected] Freezer (by ATGC labs, Frederick, MD). All these 2211-0682/$36.00 systems are comprehensive and allow scientists to or- Copyright c 2011 by the Society for Laboratory Automation and ganize their inventories efficiently. However, one Screening drawback to these software programs is the high cost doi:10.1016/j.jala.2009.07.004 82 JALA February 2011 'RZQORDGHGIURPMODVDJHSXEFRPDW81,92)1(:+$9(1/,%5$5<RQ2FWREHU Innovation Brief of acquiring them. Although this cost may not be substantial a product that satisfied all the concerns raised by the authors. to industrial labs with considerable resources, such large ex- Due to time limitations, all the prototype and Beta versions penditures are prohibitive to academic laboratories. Indeed, were created using the Visual Basic .NET programming a recent survey of the computational needs of biological lab- language. The .NET technology is advantageous when devel- oratories identified the financial burden of acquiring currently oping usable applications in a short period of time because it available software as a common barrier experienced by small is a Rapid Application Development tool. The database back laboratories.2 To this end, we have developed the open source end for LINA is a single MDB Microsoft Access file. Any database program Laboratory Inventory Network Applica- computer capable of running the .NET Framework is capable tion (LINA), which will be available free of charge to all lab- of running LINA. oratories in academic institutions. The LINA project was developed with the following data and functional requirements in mind: 1. Separate Database Tables for Different Reagents. Four PROGRAM DESCRIPTION database tables were created: oligonucleotides, bacteria The LINA is ‘‘laboratory inventory management’’ software (plasmid), yeast, and cell lines (Fig. 1). A detailed de- for academic laboratories developed at the University of scription of each of these tables and the entries available Western Ontario, and Purdue University from January 2007 in each is summarized in Table 1. The data types for each until February of 2008. The programming was performed by field are typically in text format with the exception of Bartlett Consulting pro bono publico. The authors provided date fields. Text field sizes were initially set at 50 charac- Bartlett consulting strict direction with respect to user require- ters, but in some cases were increased as deemed neces- ments and design evaluation. Furthermore, continuous feed- sary during beta testing. Sizes can be increased to back was provided during the testing phase to ensure a maximum of 255 characters by editing the table in Figure 1. Screenshot of all four tables in the Laboratory Inventory Network Application. The four separate tables can be opened simultaneously and manipulated in individual windows. They can be tiled vertically, horizontally, and cascaded using the ‘‘Windows’’ pull-down menu. 'RZQORDGHGIURPMODVDJHSXEFRPDW81,92)1(:+$9(1/,%5$5<RQ2FWREHU JALA February 2011 83 Innovation Brief Table 1. Summary of the entries in the four tables that make up the Laboratory Inventory Network Application database ‘‘Oligonucleotides’’ table Description of entry Lab name This is assigned a sequential numerical designation automatically. Former name This is the name of the oligo before it was entered into the database. Date This is easily entered using a pop-up calendar. Purpose Indicates the intended use of the oligonucleotide. Sequence The nucleic acid sequence of the oligonucleotide is entered here. Length This is automatically generated as the sequence is entered. Restriction sites Any restriction site present in the sequence can be entered here. Gene The name of the gene for which the sequence anneals to. Species The species from which the target gene was derived from. Donor The person who designed or donated the oligonucleotide is entered here. Strand Top/bottom strand to which the oligonucleotide anneals to can be designated here. Position The location of annealing (e.g., 59 or 39 end, base pair X) can be entered here. Stock concentration The concentration of the laboratory stock can be entered here. Supplier The company from which the oligonucleotide was acquired. Comments Any additional comments can be inserted here. ‘‘Yeast’’ table Description of entry Lab name This is assigned a sequential numerical designation automatically. Former name This is the name of the strain before it was entered into the database. Date This is easily entered using a pop-up calendar. Plasmid Plasmids harbored by the yeast strain can be indicated in this field. Genotype The yeast strain’s genotype can be entered here. Mating type Mat a or Mat alpha can be entered here. Donor The source of the yeast strain. Comments Any additional comments can be inserted here. ‘‘Bacteria’’ table Description of entry Lab name This is assigned a sequential numerical designation automatically. Former name This is the name of the strain/plasmid before it was entered into the database. Date This is easily entered using a pop-up calendar. Host strain The strain of the bacteria (e.g., DH5alpha) is entered here. Markers The antibiotic marker of the plasmid (e.g., ampicillin) is entered here. Plasmid size The size of the plasmid