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the myTea virtual Lab environment: myTea vLab

The myTea vLab consists of the Report, which functions as an automated but annotatable lab book; (2) the virutal Bench or vBench which provides a mechanism for tracking processes which scientists may wish to have reported to their Report/virtual lab book

A way of imagining the system working is the following scenario: A scientist downloads a sequence from a Web database.

Rather than copying and pasting this sequence into a text editor as they would now, and manually pour through the data to pull out useable sequences they invoke a myTea tool, the sequence editor (a) which automatically parses the sequence into meaningful components (b) a task which the scientist previously did manually.

Opening the sequence alignment editor, a local tool we have developed as part of the myTea system, automatically invokes both the data store and the Bench. The Bench tracks the job being performed – an analysis of a sequence – and the datastore keeps track of what data is used, where it is located, and what manipulations have been performed. At any point in the process, the scientist can pull up the Report to see a record of what processes have been invoked on what (Figure 6).

For example, they might see that before running an alignment on the sequence that was captured in the sequence editor, one part of the sequence collection was turned off, and according to the annotation, it was turned off because it was deemed to be poor data. A link to the source data is also available so that the scientist can recover the original sequence. The Bench transactions, therefore, are automatically recorded in the Report. The Report can then be annotated at the bioinformaticians’ convenience.

The bench maintains the contextual history of all the data gathered. This is a necessary step in re-creating the lab book, but it is not sufficient for a full record of what has been done. To do this adequately, a scientist needs to take notes. Therefore, at any point, the scientists can either choose one of the available annotations, or create their own. Terms from the myTea ontology and myGrid services ontology, which includes general domain concepts from biology are availabe by default. We offer terms that describe the state of work – “finished”, “unsatisfactory”, “useful”, “needs attention”, etc. these will be used to keep track of the state of work. Such semantic annotations can add value to the automatically recorded data such as what was recorded and where the data is from.

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