NOTES

3:46pm start

?: Have we delivered on the promise to have markers clearly delineating the euchromatic regions?
Danny Zamir: basically, yes

Zamir: we have to look at segmental duplications, once you have some of those, there are many biological questions you can ask.  We need to keep our heads down and stay focused on our current goals, and try to do some biology with what we have now.

Giovanni Giuliano: if we have a small pilot shotgun project at 0.1x - 1x, it would give us a much better idea of the whole picture

Lukas: wouldn't it be better to do fosmid ends right now?  it would fit with both projects

Gerard: that fits with both projects, it's a good idea

Lukas: I think Giovanni will have to devote some resources to doing the fosmid ends, it's a great start to 

Zamir: there's another topic that's more urgent, and that's the paper that we want to write.  We have to put in some biological highlights, like comparisons to other species, segmental duplications, etc.  Take some of these things, turn them out into a figure, publish it either in journals or on the web.  This is what will get us over the hump.

Stephane Rombauts:  some catchy things.

DZ: exactly.

Rene K-L: I kind of doubt that we have enough data to make a good high-quality paper, but if we can do it, great.

Mondher Bouzayen: what do you think about GG's shotgun proposal.

RKL: I think it's very dangerous at this time.  Not everyone has the situation of guaranteed funding you have in Italy.

Jim Giovannoni: I think everyone agrees that the fosmids are going to be very useful.  If you have too much stuff, you run the risk of making it look like you have everything done and it doesn't need to be funded.  Whether it's done or not, especially NSF, they'll just pull out.  At the same time, I think it's fine to capture that picture.  I'm not saying not to do any shotgun.  If you can do it in the context of giving me what that picture looks like, great.

GG:  My feeling is if we put in a request for funding for another chromosome, our funding agency would balk.

MB: Why don't you do the fosmids then?

GG: It's very technical, not the sort of thing you write a proposal for.  It could be just an aspect of a proposal, though.

DZ:  You could say OK, we've done chr 12, let's go sequence chr 12 from a bunch of other species.  We can't give the message that we're going for the heterochromatin, we're already behind schedule.

GG:  The WGS is not sequencing the heterochromatin, it's different.  WGS at an exploratory level, with fosmids, is in my view useful to understand what piece in the puzzle we're missing.

JG: I think that doing a WGS is OK as long as it's presented very carefully, that it's being done in support of the existing project.

SR: Might not the WGS at low coverage help for rapidly closing gaps in phase I BACS?

GG: Indeed it would.  Rene, how flexible is the current funding to start taking BACs from orphan chromosomes, and which ones do we consider orphan chromosomes?

DZ:  I suggest that we let the US go on with what they are doing, not starting yet to farm out their BACs until they tell us.  Let's wait and see.  When we prepare the data for the paper, we should also prepare a powerpoint with all the highlights of the project, so that anyone has the opportunity to present it in their own country.  I review projects, and my impression is that it's a great project.  There is beautiful work being done here, I feel confident.  We just have to make sure that we let the community know about it as much as possible.  A paper, a powerpoint, sequencing like crazy, and submitting.

JG:  I think it would be helpful for SGN if we had a small community of users, sort of a standing focus group.

DZ:  I think we are underestimating the importance of phase I BACs, they are very useful for people.  Material should really always be released as soon as possible.