Our perception:

Project – a larger unit research with a defined objectives and aims, relating to one area of study. A project will contain multiple experiments.

Experiment – a smaller unit of research performed in order to achieve of the objectives of a research project. In the MyGrid context we perceive an experiment to be an instance of a workflow. i.e. A record of an input data set, a reference to the workflow that was used and the resulting intermediate and final datasets (including annotations).

Workflow - A set of linked services that are enacted automatically or semi-automatically. Exists as a definition.

Visualisation and interaction requirements for the GD scenario.

In order to demonstrate the GD scenario it is necessary for the user to be able to both interact with the labbook and also to visualise data (inputs or outputs).

See also GDScenarioReqsWithWP6Annotation

1st section of the scenario:

1) User needs to interact with labbook to create a new project.

2) User needs to interact with labbook to upload a collection of AffyIds^? to the new project

3) The user will be required to visualise the uploaded collection of AffyIds^?

4) User interacts with labbook to create a new experiment - involves a subset of interactions, to specify starting dataset and the appropriate workflow definition. In the first case the workflow used in the GD scenario is workflow 1, the annotation pipeline.

5) The user interacts with the labbook to run the defined experiment.

6) The user requires a method of visualising the results of experiment 1. In the case of the annotation pipeline these results will be as a minimum, for each AffyId^? in the input collection,:

The original AffyId^?, a single line annotation, EMBL id, SwissProt^? id, Omim id, PubMed^? id, and the GO term.

A Tabular view is one suggested method for viewing the results of this experiment.

(These ‘results’ are derived from the output of intermediate services in the workflow. The GO term is the final output of the workflow. The workflow will store the intermediate results of each service in the IR)

2nd section of the scenario

1) The user needs to interact with the client to select which gene (AffyID^? or EMBL id) they want to take through the second experiment. Ideally this will be selected from the results of experiment 1.

2) The labbook will need to visualise the features associated with a particular gene. As a minimum this should be the positions of exons, introns and snp’s on the sequence. (it has been suggested that this could be performed using Artemis. This would require the SNP information to be added to an embl entry which is the desired input file for Artemis. Artemis could then display the SNP entries as variation features.)

3) The user will need to interact with the client in order to select a given SNP.

(I don't think it would be very easy to do this in Artemis, but may be wrong, features are clickable but how does this feed back to the client?).

4) The labbook will need to visualise the sequence of the suggested primers.

5) The labbook will need to visualise the name of the suggested enzyme and its recognition sequence in the context of the SNP containing sequence.

3rd section of the scenario

Requirements for the third section of the scenario are similar to the first.

1) The user needs to interact with the client to select which gene (AffyID^? or EMBL id) they want to use as input to the third experiment. Ideally this will be selected from the results of experiment 1. The third experiment produces more annotation about the proteins encoded by the ‘interesting genes’

2) The user requires a method of visualising the results of experiment 3. In the case of the annotation pipeline these results will be as a minimum, for each AffyId^? in the input collection,:

The original AffyId^?, the SwissProt^? id, a link to Interpro, a link to some PESTO output and a PDB id (if present).

A Tabular view would be ideal for viewing the results of this experiment. However, a PDB entry should be viewable in Rasmol or as text.

-- AnilWipat - 24 Apr 2003