From W

global links:

1. new NPD admin system (test version)
2. new NPD user system (test version)
3. Reports - weekly reports. setup and test reports, and others
4. Meetings - information on past and future meetings
5. Project plan - the original, and current updates
6. the completed dissertation
7. Original NPD - info and links
8. Web services links

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11:00, Thursday 19th February 2009: Discussed the previous NPD, background to and reasons for the current project, and the requirements/constraints of the project. Received documentation and code for the previous NPD. Agreed to develop the project specification by next meeting.

2:00, Tuesday 3rd March 2009 Cancelled due to short notice hospital visit. However, the initial project report was completed and Wendy and Jano provided feedback for additions and further requirements (which led to the completion of the project plan).

12:00, Monday 4th May 2009: I met Wendy Bickmore again to analyse the administrative functions performed on the NPD. Notes from this meeting will help me in building the new interface.

1:00, Monday 8th June 2009 (week 2): After the problems during the first week accessing the original NPD, I went to see Graeme and Wendy. We found that recent updates to the HGU network had rendered the original NPD admin system inaccessible. All attempts to access the original material from the Access 97 format were unsuccessful. Annotated photocopies will now be used to design the new admin system, and as much data as possible will be pulled from the mysql backups from the online NPD. This system should be ready for Wendy to test by the end of week 3.

3:00, Monday 15th June 2009 (week 3): I have now arranged a weekly meeting with Jano, to take place at 3:00 on subsequent Mondays as required. There will be no meeting with Wendy and Graeme this week. Today I want to ask Jano about how much detail of the work to date could go in the dissertation, a first draft of which should be prepared by the end of this week.

12:00, Monday 22nd June 2009 (week 4): Met up with Graeme to go over the prototype admin system, and discuss the possibilities of altering the schema and dropping some data. The results were good, with quite a few new options to look into. From the admin system, a list of details that can be pulled automatically from sources such as entrez, pubmed etc will be compiled and checked with wendy, and that information can be removed from the NPD if it is not needed for curation. Also, Graeme met with the Gene Ontology people who were interested in sharing data from the NPD to the GO database. Wendy and Graeme are both happy with the prototype system so far, though of course there are further developments to continue. We also found that xdblnnkrecord is a list of all href links used elsewhere in the database. Not sure yet what use that is though. Plus, for attaching proteins, just create a new one each time. There is a possibility that homologous proteins from other species may contain similar data, but would need to find a way to reference to them in the first place. Probably not worth looking into at the moment. More details will be available in the week 4 report.

3:00, Monday 22nd June 2009 (week 4): Met with Jano briefly, and submitted a first draft of the dissertation. It is very sparse, just a framework really, with some intro content from the PRP report and a bit of detail about stage 1 of the project. He will get back to me in a few days with suggestions. Marco Roos was emailed today also, so we are awaiting a reply from him, and I will be working on ogsa-dai this week and if I need to see anyone at KB about that, Jano will be happy to help organise something if necessary.

1:30, Tuesday 30th June 2009 (week 5) Met with Bob and Jano to consider progress so far. Everything seems to be ok. Jano has provided comments on the first draft of the essay which I can go over this week. Slight delays due to the early failure of the original admin system do not seem to be putting too much long term strain on the project plan. Work is now continuing on the grid enabling side of the project, although the admin system still requires tweaking and completion at a later date. But it is important to keep in mind the research goals of the project as well as the technical goals of completing a usable system.

2:00, Friday 3rd July 2009 (week 5) Met Ally Hume from EPCC to discuss the pros and cons of using ogsa-dai for data access on this project. He had already read through my for and against ogsadai report, and was in agreement with the findings mentioned therein. He referred me to a useful section on the ogsadai website, which gives similar reasons for when and when not to apply ogsadai to a data access problem. The conclusion of the ogsadai question is, therefore, that it would not provide useful additional functionality on this project, and would require additional maintenance. Further explanation is in the Week 5 report.

10:30. Monday 6th July 2009 (week 6) I met Jano this morning for the usual weekly meeting. I talked to him about my meeting with Ally and the decisions re. ogsadai. This was all satisfactory, and should provide good content for the dissertation. I will continue to work on that, and try to get something to Jano this week for him to read over next Monday. (we will not be having a meeting next Monday).

2:00, Monday 6th July 2009 (week 6) Met with Wendy to go over the prototype admin system. Narrowed down which content could be pulled automatically, and which had to remain manual. Checked over where drop down lists are required, and what their content should be. Confirmed the search method requirements. Wendy agreed to test the admin system (probably in week 8/9), and to answer some questions comparing it with the original. Also, as she received an email from a person called Derek who is interested in using the NPD data for a project he is working on, Wendy agreed it would be useful for me to contact him and see if there is any potential application there that could link in to my project. Wendy also mentioned that she would eventually like to link some material re. experiments by the mouse atlas people into the NPD data, so this could be mentioned in the dissertation too, for future ideas.

3:00, Monday 20th July 2009 (week 8) The usual meeting with Jano was brief. There are no further updates as I am just continuing with code completion at the moment. Jano is going over draft 2 of the dissertation and will return it in due course. I will continue to work on small sections and submit them as required.

2:00, Thursday 30th July 2009 (week 9) Met with Wendy and Graeme to go over the state of the system. All seemed good, one or two points for me to finalise involving pulling data from the GO sites, and sorting the problem with lowercase search showing some multiple entries, but the system is overall ready for user testing. Wendy will complete the user testing next week and reply with any issues. Graeme mentioned the BioMart talk he was at and their attempts to provide a single query over multiple databases (see the Week 9 report for more details). Also as Graeme will be away from the 14th August, I will need to solve any implementation issues before then, though the attempt to put the service up live could happen when he gets back, on the week of the 24th, as the outcome does not really affect the dissertation content, which has to be completed before then.

10:30, Monday 3rd August 2009 (week 10) Today I met with Bob and Jano for another progress meeting. I updated them about the state of the system, which all seems to be going fine, and agreed that I had to spend some time on writing, which has fallen a bit behind. So the rest of this week will be dedicated to that, in order to catch up before the Friday deadline for feedback comments.