Fri, 05/14/2010 - 18:01
| Time | Name | Message |
|---|---|---|
| 10:43 | zoran | Hi everyone |
| 10:43 | mateuszwlodarski | hi |
| 10:43 | aap2 | hello |
| 10:43 | Renton | Good Morning Brother ! |
| 10:43 | netolk | hi |
| 10:43 | Renton | new threading looks great btw |
| 10:43 | zoran | has anyone tried playing with the new selection threading feature released today? |
| 10:44 | Renton | just started |
| 10:44 | aap2 | a little bit |
| 10:44 | zoran | we think it should change the way threading can be explored, but we would like to hear feedback on it soon so that we can refine in time |
| 10:45 | Renton | It's an amazing feature comepred to the old days, now we can get into the guts of it without having to tiptoe around the basics anymore. 9 out of ten brother ! |
| 10:46 | zoran | good |
| 10:46 | aap2 | i have some other sugestions for the alligment tool |
| 10:46 | aap2 | give the templates a name like A,B C etc |
| 10:46 | TheGUmmer | and please add itto the new interface |
| 10:46 | aap2 | i currently forget which one i have used |
| 10:46 | Renton | perhaps a nameable field? |
| 10:47 | aap2 | also an indication which template im currently using aap2 i currently forget which one i have used |
| 10:46 | Renton | perhaps a nameable field? |
| 10:47 | aap2 | also an indication which template im currently using |
| 10:48 | aap2 | and perhaps an done/not done that shows which templates i have or have not threaded |
| 10:49 | aap2 | perhaps it should even be a counter |
| 10:51 | zoran | we have a long list from yesterday, and i think we can address a good chunk of the improvements on it |
| 10:51 | Madde_irc | I would like a score for parts of the template |
| 10:51 | Renton | I agree Madde. |
| 10:52 | SUCHARD | me too |
| 10:52 | Renton | i kinda thought about the orange and blue line graph above the amino acids in that sequence, to show how many phobic and phillics there are |
| 10:53 | Renton | so we can move them around and see just how strong each seq was on the outside or inside |
| 10:53 | Renton | *of the design given, but score would be great. |
| 10:55 | TheGUmmer | i would like to access the alignments from teh selection interface |
| 10:55 | zoran | we thought you could get alignments from new interface |
| 10:56 | TheGUmmer | not that i can find |
| 10:57 | Madde_irc | no, it's an old interface only feature |
| 10:57 | zoran | ok, that'll be done quickly |
| 10:57 | TheGUmmer | woohoo! |
| 10:58 | zoran | are most people using the new interface now? |
| 10:58 | TheGUmmer | i am |
| 10:58 | mimi | difficult to tell I'm not |
| 10:58 | SUCHARD | most of the time |
| 10:58 | aap2 | not me, used to the old one |
| 10:59 | Dolichwier | i still use the old one |
| 10:59 | zoran | are there other tasks for which old interface is better? |
| 10:59 | Madde_irc | I'm using the old one only for alignments and local wiggling the ends |
| 10:59 | zoran | madde: can you not local wiggle in the new? |
| 10:59 | Renton | i use old one, its still got all the tools in places i can find them quick. |
| 11:00 | Madde_irc | not exactly that way |
| 11:00 | Renton | and an unlock of locks segs easily found. |
| 11:00 | sonnysu | so difficult |
| 11:00 | TheGUmmer | if select a section in the new and hit W. is it local or global wiggle? |
| 11:00 | SUCHARD | move little piece of blackbone is easer on old |
| 11:00 | TheGUmmer | that takes practise in the new |
| 11:01 | Madde_irc | I think it's global wiggle which affects local |
| 11:01 | Renton | can the void crushers and Contenders please leave some scraps for the rest of us to rank up ! thanks... hehe. puzzle hogs... |
| 11:02 | Seth_Cooper | TheGUmmer: it would local wiggle |
| 11:02 | TheGUmmer | So no selection would be global then |
| 11:03 | Madde_irc | I think the local wiggle in old is more powerful than in new |
| 11:04 | zoran | any new suggestions to maximize casp outcomes? especially from those that we haven't heard from yesterday? |
| 11:06 | Dolichwier | more all hands puzzles |
| 11:06 | Renton | um, send us heaps of new folders using threads then upload their designs into our group folders |
| 11:07 | Renton | cannon fodder |
| 11:07 | Renton | um also have cash prizes. (grin) |
| 11:09 | zoran | even if we had cash to award, do you think it would help the outcomes? |
| 11:10 | Renton | i was going to say yes... but realy im just playing the goat. |
| 11:11 | zoran | i mentioned this yesterday briefly: all hands currently does not seem to diversify the solutions. Most people work on improving the current best solution with little cross-borrowing from other solutions |
| 11:11 | Dolichwier | ahh, fair enough |
| 11:11 | Renton | can someone advertise for more folders to come and play so we can increase our teams and solutions to start from |
| 11:11 | TheGUmmer | could you use them as alignments |
| 11:12 | mimi | whenever I tried to copy from one soln to another it didn't work |
| 11:12 | zoran | we will try to change all hands to improve this though |
| 11:12 | zoran | mimi: how did it fail? |
| 11:12 | Christoph | I find all hands very difficult, because so may scripts were applied to the high scoring structures that improving them is nearly impossible |
| 11:13 | Christoph | *many |
| 11:13 | mimi | just came up with a message saying it didn't work |
| 11:13 | TheGUmmer | yes the hig scoring puzzles are very tight |
| 11:14 | zoran | so perhaps doing all hands with earlier structures may be more conducive to mixing |
| 11:14 | TheGUmmer | yes, or use them as alignments and we can mix and match |
| 11:14 | zoran | sometimes when we look at the known solutions, it is clear that two or three solutions have gotten different aspects of the protein right |
| 11:14 | Christoph | copying a part of another solution to an high scoring puzzle will drop the score dramatically and you would have to work for hours to find out if that change would be better |
| 11:14 | Renton | tight is ok, start searching for new shapes if it gets stuck and has brown bits in it otherwise you have a good solution. |
| 11:15 | zoran | ... but merging these parts requires lots of restructuring rather than slight refinements |
| 11:15 | Renton | perhaps making a threaded protein available in the templates in alignments |
| 11:16 | Renton | (from the high scoring one? |
| 11:16 | mimi | Its all very "hands-on" work and difficult to fit in with a lot of other ouzzazles happening |
| 11:16 | mimi | puzzles |
| 11:19 | Dolichwier | sharing the top alignments/threading instead of the whole protein would be interesting |
| 11:19 | zoran | ok, we'll try all hands with all candiates in good performing clusters, but neither fully optimized to encourage mixing |
| 11:21 | Renton | thanks Z and S |
| 11:21 | Renton | how many solutions do we have for casp 1 and 2 now? any with all green segments yet? |
| 11:22 | zoran | we're still analyzing the results |
| 11:23 | Renton | sweet as. |
| 11:24 | Renton | some high scores this year cmpared to last casp8 |
| 11:26 | Renton | any other exciting news? |
| 11:27 | zoran | we're busy trying to do all the improvements, and seeing how the results from the first puzzles can guide what we do next |
| 11:28 | zoran | expect frequent updates this month |
| 11:29 | Renton | thanks guys, its sometimes hard when we dont have direct contact with you to get stuff out of you to keep us motivated to make the earth move. |
| 11:29 | Renton | it's been nice to have betahelix coming into the picture more |
| 11:30 | zoran | yes, next week we'll have David and betahelix on the chat to address some of the protein strategy related questions |
| 11:31 | Renton | did you mean the Big D ? |
| 11:31 | Renton | *prof David Baker* |
| 11:31 | TheGUmmer | no hasselhoff |
| 11:32 | zoran | yes, "big D" ;) |
| 11:32 | Renton | YEAH !!!! finally. |
| 11:32 | Christoph | cool |
| 11:32 | CharlieFortsConscience | which one brought the Berlin wall down,? I always forget... |
| 11:32 | Renton | Gummer, KIT is now threading proteins at the university. watch out for turbo boost |
| 11:33 | TheGUmmer | hehe |
| 11:34 | Renton | i have to go and buy a pokadot bow tie to wear to the David Baker meeting. |
| 11:35 | Renton | *tinfoil hat already on standby* |
| 11:35 | mib_5gw8gd | anything else CASP related? |
| 11:35 | Seth_Cooper | oops, that was me |
| 11:36 | Renton | *holds back frothing goat on chain* easy girl... it's just seth. |
| 11:37 | Seth_Cooper | does the partial threading work alright? |
| 11:37 | Renton | all jokes aside, we need more time to try out your changes |
| 11:37 | Seth_Cooper | okay |
| 11:37 | Seth_Cooper | it hasn't been too long since the update |
| 11:38 | Renton | we almost need a new beginner puzzle to test it out on or another casp one. |
| 11:38 | Madde_irc | There are some big casp targets for humans, what is the max. number of residues foldit can deal with properly? |
| 11:38 | Seth_Cooper | typically we try to limit to < 200 |
| 11:39 | Seth_Cooper | we are planning on trying some of the shorter server targets |
| 11:39 | Seth_Cooper | so that we can have more! |
| 11:39 | aap2 | how many casp puzzles are there going to be? |
| 11:39 | TheGUmmer | per day per week |
| 11:39 | aap2 | casp proteins |
| 11:39 | Christoph | I saw there is one with ~65 residues, will we work on that one? |
| 11:40 | Renton | ide sure like the chance to eat the servers up with the new threading component |
| 11:42 | Seth_Cooper | most likely we'll post the 65 residue one |
| 11:42 | Renton | buddaboom |
| 11:43 | Renton | if we can proove ourselves worthy of our workmanship after this casp results are out, will we go forward with making folding by Human a Reality in the global playground? |
| 11:44 | Renton | (marketplace) |
| 11:44 | CharlieFortsConscience | you after a job again aot? |
| 11:44 | Renton | not me, david hasslehoff. |
| 11:45 | Renton | and tattoo from fantasy island. The Plane, The Plane... |
| 11:45 | Seth_Cooper | aap2: we don't really have control over the number of CASP puzzles |
| 11:45 | Seth_Cooper | it's based on what get released, but you can sort of guess from what's been psoted so far |
| 11:46 | Seth_Cooper | however, we want to reduce the number of a,b,c by posting more templates in a single puzzle |
| 11:47 | Renton | who designed the new threading component btw? |
| 11:49 | Seth_Cooper | we had help from some alignment experts in the Baker Lab (such as tex) and beta_helix and myself worked on it |
| 11:49 | Renton | fantastic concept !!! |
| 11:49 | Seth_Cooper | thank you! |
| 11:50 | Renton | its always refreshing watching people working on the business rather than working in the business. if that makes sense. |
| 11:50 | Seth_Cooper | I think so |
| 11:50 | Seth_Cooper | okay, I have a class I need to get to |
| 11:50 | Seth_Cooper | thanks for chatting again everyone! |
| 11:51 | Renton | Thanks Seth, Thanks Zoran. |
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This looks suspiciously like the log from Wednesday...