![]() ![]() The plug-in also supports connections to other databases, Excel spreadsheets, and Google Fusion Tables. After the DNA barcode sequence data have been obtained and deposited into the LIMS, Geneious performs automated sequence alignments-trimming low-quality data from sequence ends in the process-as well as base calling, which accelerates the workflow, reduces personnel demands, and makes it easier to trace problems identified during sequence analysis back to the relevant reactions and reagents. The LIMS keeps a record of all of the samples, reagents, primers, procedures, and data generated during the barcoding process, from DNA extraction to PCR to DNA sequencing. Solution: The Moorea Biocode Project contracted Biomatters Ltd., a New Zealand–based bioinformatics company, to develop the open-source Biocode LIMS plug-in for use with Biomatters’ Geneious sequence analysis software ( Methods Mol Biol, 858:269-310, 2012). The team also needed a tool to help automate some of the routine tasks associated with DNA barcoding, such as sequence analyses and uploading the data to public repositories. Furthermore, collaborators around the world needed to be able to view, edit, and share the data. Problem: Multiple labs are processing the genetic data using different equipment, protocols, and workflows, making it difficult to track all the project data. ![]() “It’s an attempt to build a digital signature, or phone book, for every species so we can monitor this ecosystem and understand it better,” Meyer says. Project: Since 2007, the Moorea Biocode Project has been obtaining DNA barcode sequences-short sequences from standard and widely agreed-upon regions of the genome-for every animal, plant, and fungal species living on and in the waters surrounding the tropical island of Moorea, French Polynesia. Research Zoologist, Smithsonian Institution National Museum of Natural History The Scientist spoke with three researchers about how they are using LIMS to manage the particular type of data generated in their labs. Buyers should also consider the system’s capacity to adapt as the lab’s requirements change over the years. LIMS shoppers should also look out for how much customization will be required, which influences the cost and time needed to get your LIMS up and running. Of particular importance are the frequency and quality of services such as system updates, bug fixes, and new-feature rollouts, he says. In addition to evaluating LIMS based on the features that your lab requires, Dolan recommends that prospective buyers try to learn as much as possible about a prospective vendor. Since there is no “standard” LIMS, choosing a system can be difficult. Many LIMS are also equipped with data-mining and trending tools that can provide unique insights into the data. Once the analysis is done, the LIMS can compile and generate custom data reports using information generated by multiple instruments and personnel. Features like these can improve efficiency by saving researchers the task of manually recording and entering data, and can reduce data transcription errors. This not only allows data to flow directly into the LIMS as it is generated, but also enables the system to direct the workflow with specifically tailored instructions. Many LIMS can be configured to communicate with laboratory equipment, including analytical instruments and liquid-handling robots. “A LIMS today is defined by what it can achieve,” says Tom Dolan, Director. Today, a plethora of commercially licensed and open-source options are available, ranging from application-specific tools to multipurpose solutions. The first LIMS came on the scene more than 30 years ago as custom-made applications designed to increase productivity and to reduce the errors associated with routine laboratory functions. As a result, many researchers are turning to computerized laboratory information management systems (LIMS)-database applications that can help collect, organize, and track information about the samples being analyzed and the data being generated in the lab. ![]() The traditional approaches to data management-notes jotted in lab notebooks, multiple spreadsheet files tucked away in computer folders, and images of gels and computer printouts stashed in 3-ring binders-no longer suffice. © RYCCIO/ISTOCKPHOTO.COM With today’s high-throughput technologies and state-of-the-art tools, laboratories around the world are generating mountains of data at unprecedented rates. ![]()
0 Comments
Leave a Reply. |
Details
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |