SIGLa is a LIMS focused on the workflow of laboratory activities. It guides the user through the execution of each activity, informing the next activity/activities that can be executed. For each activity SIGLa stores its attributes as an eletronic notebook. In just one view the user can visualize all the activities executed in a experiment. The details of each activity can be accessed by just clicking on the activity. SIGLa adapts its interface to each laboratory as it is capable of managing workflows defined in the XPDL standard. This is possible because SIGLa uses a workflow management system to control which activities have been executed and which ones are available for execution.
It is an application with an easy to use interface that is easily adaptable to different types of laboratories, in contrast to most LIMS that support a single type of laboratory. To store and manage data on laboratory activities SIGLa uses workflows. In workflow based systems users define activities, transitions, actors and rules of transitions. In SIGLa it is possible (through the Together Workflow Editor) also to define further details for each entity. For example, during the laboratory workflow definition, the user can define the attributes of each activity, its types, the range of values that each attribute can assume, its formats or define auto-calculated attributes from other attributes. It’s also possible to define the inputs and outputs of each activity, to define the number of inputs and outputs, as well as the relation of these inputs and outputs with the experiments. In the workflow definition it is also possible to assign to each activity a documentation that contains standards, instruments calibration, procedures and registers associates to the activities.
It’s important to notice that to successfully manage a laboratory it’s necessary to create a well defined workflow. It must contain all the experiments with its attributes, inputs and outputs clearly declared with its types, formats and specified sizes. The definition of workflow is a very important step in the process of quality assurance given by SIGLa. Once the activities, rules and procedures have been defined, the workflow editor generates a XPDL file with all the definitions. This file is loaded in SIGLa, then the LIMS will be ready to manage the laboratory activities. With this mechanism, practically any type of laboratory can define its activities and rules in an XPDL file and use SIGLa to manage all the laboratory information. For SIGLa’s initial development the workflow of a proteomics laboratory was defined . Proteomics is the process of identification and quantitative analysis of proteins expressed in different conditions or life stages of a cell or organism. Several analytical methods are used in proteomic analysis generating large amounts of data that varies significantly depending on the experiment type and conditions used. By using this kind of experiment as an model for SIGLA’s initial development we have shown how SIGLa’s can manage real complex experiment data.
After defining the proteomic workflow and implementing the main functionalities of SIGLa we have defined a second workflow to validate the capability of SIGLa of adapting to multiples laboratories. With the support of UFMG Microarray Laboratory we have defined the microarray workflow. The technique of DNA microarrays is used to study gene expression on a large scale in several species. DNA microarrays are usually layers of glass, plastic or nylon which is deposited series of thousands of microscopic spots of oligonucleotides or cDNAs, each containing picomoles of a specific DNA sequence. The microarray slide is then used to detected expression level of mRNA related to the DNA printed on its surface by incubatiing of the microarray with a solution containing cDNA or RNA obtained from biological samples. .
Microarray technique generates a large number of information, both laboratory data and image and data files. The microarray process has several steps, requiring the storage of information for each one of them. Usually this information is stored in lab books, which makes it difficult to access the information, since they are in chronological order only. After scanning microarray slides and image analysis, new and large image data and data files are produced and the number could reach hundreds of files. The organization of these data using laboratory notebooks or basic text files becomes very time-consuming. By using a single platform as SIGLa for this task is possible to keep all data organized making its manipulation more reliable. Moreover, the use of a web based platform such as SIGLas provides access to data for all members of a research group in a fast and efficient way.
The current version of SIGLa is able to manage all the activities of a workflow and their attributes. An important feature that is not currently available, however, is the ability to call an external program to perform an automatic analysis such as gene sequence annotation. In this case, the analysis has to be performed externally. Its result, however, can be stored in SIGLa as an attribute of type file, and can be used later in the workflow. Automatic analysis execution will be available in the next version of SIGLa.