| | 1 | == Notes Joeri xQTL workbench review meeting 4 march 2011 @ GBIC == |
| | 2 | |
| | 3 | === General === |
| | 4 | * It must be open and clear what exact code is (or will be) executed |
| | 5 | * Having quality control (tools) for the data would be great |
| | 6 | * There must be helpful error reporting in combination with script testing possibilities |
| | 7 | * In general, more tools, visualizations and statistical reports make the system attractive |
| | 8 | * We must find out if and how the latest technologies and formats fit into the system |
| | 9 | * Idea: put 'cross' object as a file in the database with seperate script? Works best with workflows and 'pull' architecture |
| | 10 | * We will get example data and scripts from Yang and Frank soon to testdrive our capabilities and limitations |
| | 11 | * Being able to input raw data formats (machine output) directly into R-ready datamatrices, this would save much time formatting and checking |
| | 12 | * Having a 'universal' importer that supports many specific formats (agilent, illumina, affy, etc) and does all verification/importing would be ideal |
| | 13 | * This importer would be extensible with importers for new formats when needed |
| | 14 | * To start with this, make an inventory of such used/popular formats, estimate how complex the importers would be and how much time it costs for each |
| | 15 | * Being able to (for example) sort in the matrix viewer and get a trait linkout (either to db or external) would already be a great help when interpreting results |
| | 16 | * For biologists, having results plotted on pathways (such as KEGG) would be an immense help for interpretation |
| | 17 | * Having Yang's mislabeled sample scripts in the system would be great as a quality control step |
| | 18 | |
| | 19 | === Top priority === |
| | 20 | * Multifunctional importer, having data ready from raw to R-matrix in a few clicks |
| | 21 | * Interpretation help in the form of pathway visualizations, linkouts, advanced (matrix) browsing |
| | 22 | |
