1. OMERO.editor Where next? (After Beta3)

2. Goal of Editor? (1) To record a complete description of the experiment. Like a lab notebook that someone else can understand! (Not just the protocol description)? Lab note-book Fix and Stain Cells Prepare formaldehyde by dissolving 1.85g powder in 10mls PBS. Warm in fume cupboard till solution is clear. Filter through 0.2uM filter. This is 37% solution… Word documents, Spreadsheets etc Web sites http://lamondlab.com/f7immunostainprotocol.htm

3. Goal of Editor? (2) To make a nice UI for viewing protocols (text / tables etc) within insight?

4. Goal of Editor? (3) To develop a data-model for an experiment or at least a format for recording an experiment? e.g. MAGE-TAB Eg usefulchem(wiki) Experiment: Objective Procedure Results Discussion Conclusion

5. Goal of Editor? (4) To be an electronic lab notebook? (The experiment is the “home”, link to the data) UsefulChem http://usefulchem.wikispaces.com/ ChemTools http://chemtools.chem.soton.ac.uk/projects/blog/ eCAT http://www.axiope.com

6. What Editor does now: (Should it continue to do these?) Separates Experimental variables from Protocol description –Clear fields, load defaults etc. –Easy to view the important metadata Hierarchy Simple data types (Text, number, table, date, time, link, image, Ontology term, checkbox, drop-down menu)

7. Problems Protocols and Experiments in Editor don’t look like biologists expect: Experimental variables not in context. Editor files not nicely displayed by other software. Editor files not “understood” by other software. Which of these should I aim to solve? Solving any of these requires a change in OMERO.editor file format…

8. File Format Options? MAGE-TAB –Protocols with parameters –Software can “understand” format (although protocols are free-text) –Easy to edit in other software (Excel) –Other reasons for using Tabs are not applicable to OMERO.editor –MAGE-TAB document consists of several TAB files: 1 for protocols, the others describe microarray set-up and workflow. Wiki / semantic wiki –Semantic wiki is an overkill? –Could use markup to identify parameters. –Save as html / database?

9. File Format Options? XML –This is current format. –Can include other XML with no changes. –Difficult to read without OMERO.editor –Reading “imported XML” is dependent on the format of the XML. Some easy (eg OME-XML), most are much harder (eg GelML, MAGE-ML etc). GelML in OMERO.editor

10. File Format Options? XHTML –All the advantages of XML, but can be displayed by any browser. –Can place parameters in context within text. –Supports tables, hierarchy etc.

11. Mapping MAGE-TAB to editor/XML

12. MAGE-TABEditorText protocol One Experiment is one IDF file (with SDRF file(s)) One Editor file could be many exps or part of an exp. Text file is usually one protocol / experiment Defined fields for Person, Experiment. No defined fieldsSome conventions for experiment, not for protocol Protocol NameField Name- Protocol Type-- Protocol DescriptionField DescriptionStep Description Protocol Parameters (Named) Variable (Data-types). Named? Within text OR as list. Not named. SDRF file (refs protocols)Order of steps is impliedOrder as described Parameter values in separate (SDRF) file Values (& defaults etc) are parameter attributes Within text No Hierarchy. SDRF file describes workflow as a DAG HierarchyNo Hierarchy