Timelines

[Simon Heath]

Pierre, Mario,

Would it be possible to get some estimates of timelines for the progress of the operon project?  There are several objectives which we should be working towards, and it is not clear to me how much time is needed to get there.

1) Public instance of Operon that people can browse/download public data. <- I think that regulon.cng.fr already fulfills most of this

2) As above but with restricted access to certain datasets so that people can log in to access private data <- this was what Dominic was meant to be working on but I guess that this is still unfinished

3) Public API that we could start to use to create applications

What Mark (and I guess Florence) would like ultimately would be the release of a 'portable' Operon that collaborators could download, insert their genotype data generated by us or elsewhere, and Operon to manage their data, but this is going to require the API at least to be completed.

Simon

[Pierre Lindenbaum]

> Would it be possible to get some estimates of timelines for the progress of
> the operon project?

I have no clear view of what has to be done. However most of the stuff
written in java can be used to retrieve the data in each database but
I still cannot easily link the numerous databases between each others.
Moreover the C API can also be used to extract and find the results
(but, as you saw at CEPH, the java API is far more powerful)

> There are several objectives which we should be working
> towards, and it is not clear to me how much time is needed to get there.

Let's say I need about two or three days to implement each kind of
'screen' in the operon-cgi.
Please, also note that, as M. Durand may have told you, I'm also
supposed to help Florence's team ( the girl , who was supposed to
replace their DB manager, left them last week too....)

> 2) As above but with restricted access to certain datasets so that people

I need an example for this

> can log in to access private data

My server runs under httpS and requires an authentication.

> 3) Public API that we could start to use to create applications

> What Mark (and I guess Florence) would like ultimately would be the release
> of a 'portable' Operon that collaborators could download, insert their
> genotype data generated by us or elsewhere, and Operon to manage their data,
> but this is going to require the API at least to be completed.

At this time, my API simple reads data from XML and inserts it in the database

Pierre

[Mario Foglio]

Simon,

From the information I have at this moment, I propose to consider first the following:

1. Keep regulon.cng.fr running.
2. Build the new version of Operon in cabernet with my C API (we will need puillac for this).
3. Update the new version of the UMLS  as soon as it is released (it is expected this month).
4. Rename regulon.cng.fr with operon.cng.fr (and rename pulliac's with intranet.operon.cng.fr).
5. Develop the new Operon website with Pierre's java API.
6. Create a httpS site in serverX for downloading the Berkeley dbs as compressed text files.
7. Prepare a java API package for dumping and loading these text files for first relase.
8. Prepare a C API package for dumping and loading these text files for first release.
9. Assign some people to test the new website and the API packages.
10. Debug and repair.
11. Shut down regulon and relase operon.

In order to calculate how long it will take to get to point 11, I would like to discuss with Pierre 
about his requirements to make point 5 posible and plan our schedules. The time will depend a lot
on how many consecutive hours with put on these tasks taking in consideration the are other
projects and jobs on the side.

Mario