NetBookingLIMS: Automation of Workflow within Core Genetics Laboratories Using a Novel Internet-Based Information Management System

摘要

NetBookingLIMS is Internet-based software used for the total automation of workflow within core diagnostic or genetics laboratories. NetBookingLIMS organises all data incoming into the laboratory in a flat file and converts it to a relational database that can be used to generate auditing, billing, troubleshooting and usage reports. Also, it generates instrument compatible data and organises the day-to-day management of the laboratory in an efficient and structured manner. It is written using Perl5 and C and designed to run solely using an Internet browser. NetBookingLIMS software as well as a user manual and documentation are available at http://dcs.bbk.ac.uk/～ahamo01blfrontpage.cgi. Previous SectionNext Section INTRODUCTION Pharmaceutical, commercial and academic scientific laboratories deal with enormous amounts of data. Whether this information is related to process, procedures, experimental design or analytical and clinical data, keeping it safe and organized - yet available to those who need it - is a formidable bioinformatics challenge. A core DNA sequencing and genetic analysis laboratory supports many research teams within an organisation and is responsible for the cloning and characterisation of genes. Usually a genetics laboratory employs many staff managed by one manager, has many instruments, supports many applications such as DNA sequencing, genotyping, fluorescent fingerprinting1 and fluorescent mutation detection2 and is used by many users (scientific researchers) with different requirements including high, medium and low throughput usage. Also it is difficult to carry out accurate auditing, billing and troubleshooting with such a complex working model. Thus, within such a laboratory there are many real world issues such as managerial and organisational problems and algorithmically complex problems such as samples scheduling and relational database administration and maintenance. Several commercial genetics laboratory LIMS (Laboratory Information Management System) already exist, such as BioLIMS (http://www.appliedbiosystems.com/informatics/productpages/bl_body.html). However, they are difficult to integrate and use for supporting a multi-user and multi-tasking laboratory and they are not user friendly. NetBookingLIMS (InterNet Booking Laboratory Information Management System) is WWW-based software that automates the management of data within a laboratory. It includes many novel features, is dynamic and flexible, and can fully automate either a laboratory with one instrument and one staff or thousands of instruments and thousands of staff. It uses logical structure to ensure that booking, updating and running the samples is done in a logical sequential order eliminating human errors. This is done by displaying a month-ahead table of all booking on all instruments in the laboratory, as shown in Figure 1. NetBookingLIMS contains many intelligent error checking algorithms and user-friendly forms for data entry. It allows the researcher to cancel bookings when experiments fail. It is platform independent and only requires an Internet browser to run. The system automatically generates instrument compatible sample sheets for the staff. It contains built in intelligent algorithms to modify the state of the web page according to the real world state. For example, it remembers the important information of a client (user, staff or manager) and displays the appropriate “view” according to the client's status. It has an automated scheduling module allowing users to schedule the booking of large numbers of samples. This is implemented using a hybrid first in first out (FIFO)/priority scheduling algorithm.3 It has auxiliary automatic sample generator software that caters to 96 and 384 microtitre plate formats. Its architecture is such that it uses internal centralised ASCII flat files to store booking records information which is then automatically converted to a relational database using an SQL (Structured Query Language)