Developer Chat

Scientist Chat

--- Log opened Thu Feb 23 12:54:08 2012
beta_helix	Hello everyone! We will be starting the Scientist Chat shortly, Aaron will be here to talk about the Flu Puzzles and then we'll talk about CASP ROLL.	12:58
frood66	morning! *stands on toes	12:58
u-AQ	awesome!	12:58
brianhixon	morrning!	12:58
@auntdeen2	Attention all players... the developer science chat will start shortly - please use the puzzle channels for all chat that is not related	12:58
DoodelThePlatypus	Nice that it's morning there, it's close to bed time here in Stockholm.	12:58
@tealight-irc	ahh yes teh scientist chat..had actually forgotten about it lol	12:59
@auntdeen2	hi beta :-)	12:59
*** mode/#global [+o beta_helix] by Judecca		12:59
@auntdeen2	and good morning, tea	12:59
phi161	hi all	12:59
BletchleyPark	hi beta	12:59
frood66	present and correct	12:59
mottiger	back	12:59
mottiger	sorry frood that i left, had a little issue here in the flat	13:00
@tealight-irc	passes evryone their coffee and muffin	13:00
frood66	n mott	13:00
frood66	np	13:00
DoodelThePlatypus	I have a quick question, don''t know if it's appropriate here. When I start up FoldIt, I get the error: Unable to write output.	13:00
Aaron	Hi Everyone	13:00
DoodelThePlatypus	Ialso my puzzles were never saved	13:00
@auntdeen2	hi Aaron :-)	13:00
DoodelThePlatypus	I deinstalled and installed again.	13:00
BletchleyPark	hello Aaron	13:00
@marie_s	in windows 7 dont install in programm files	13:00
Flimsor	Too late	13:00
@beta_helix	This is Aaron from the Baker Lab, he's been analyzing all your Flu results!	13:00
DoodelThePlatypus	Oh where to then	13:00
spvincent	Hi Aaaron	13:00
@marie_s	c:\foldit	13:00
DoodelThePlatypus	thanks	13:01
@CFC	Hi Aaron :)	13:01
Aaron	Yes, I'm the graduate student in Baker Lab who has been coming up with and analyzing the flu puzzles	13:01
lamoille	hi Aaron	13:01
frood66	hey	13:01
@mimi2	hiya	13:01
spvincent	So what can you tell us about them?	13:01
karstenw	hellooo	13:01
mottiger	hey aaron, do you know what hilvert contributed to the project?	13:01
Aaron	with the help of beta_helix	13:01
spmm2	can you tell us a bit more about fitness landscapes - like what sort of fitness?	13:02
frood66	baptism by fire lol	13:02
Aaron	So the way the analysis works is I get back the top scoring structures from beta_helix, but they are only numbered	13:03
Aaron	so i don't know who did what	13:03
Aaron	But I generally look at the too100 scoring models	13:03
Aaron	which can be across many different teams	13:03
@beta_helix	(this is the top100 models per puzzle)	13:03
Aaron	whats interesting, is that many of you converge on the same solutions, and it's those convergences that I find useful	13:04
Aaron	so yes, fitness landscapes!	13:04
Aaron	fitness for protein binders is kind of two components	13:04
spvincent	We're always being encouraged to crreate more divergent solutions as a rule.	13:05
Aaron	the first the ability of the protein to fold or it's stability	13:05
Aaron	the second is the ability of the protein to bind to the target	13:05
Aaron	so fitness = stability + binding	13:05
Aaron	@spvincent: yes	13:06
Aaron	we want to try and find as many convergent clusters as possible	13:06
frood66	are the scripts causing the convergence?	13:06
spvincent	Or perhaps the result of group play?	13:06
Aaron	we are basically looking for as many clusters of solutions as possible	13:06
@beta_helix	@mottiger we are unfamiliar with hilvert's contributions to this specific project	13:06
@auntdeen2	or does the fact that many of us converge possibly have to do with our software & tools?	13:06
Aaron	because these clusters are probably local or global minima in the overall fitness landscapes	13:07
@beta_helix	what is interesting is that many different Foldit Groups all converge on the same solutions.	13:07
mottiger	just saw in one article a comment from him, so i thought he is somehow involved	13:07
@tealight-irc	"great minds think alike"	13:08
frood66	but those same groups use (generally )the same scripts beta	13:08
karstenw	is that a good thing, bad thing, or just an observation?	13:08
f1pokerspeed	Does anyone know how I can add recipes to my cookbook from the website? It won't let me	13:08
Aaron	when I see these clusters, it means that many people find a particular solution, and THAT solution might be one(of possibly many) actual real solutionsp	13:08
@CFC	with the mutate designer puzzles, I'm guessing there's a tighter smaller range of convergence - the freedom lies in moving the 'ligand' component	13:08
@auntdeen2	All players - global is being used right now for a developer science chat… please use the puzzle channels for all chat that is not related	13:08
@tealight-irc	log into webiste to be able to get recipes	13:09
f1pokerspeed	thanks	13:09
Aaron	as a puzzle designer, we try to balance convergence with diversity	13:09
Aaron	if everybody converges on the same solution, that really only gives us one thing to try	13:09
BletchleyPark	Does the rule better score = better model apply ?	13:09
Aaron	and if everybody has completely different solutions then that is too many things to try	13:09
TimovdL	How many clusters of solutions did you find?	13:09
mottiger	i'm a bit confused, are we talking about the flu or design puzzles in general or about foldit in general?	13:10
Aaron	but perhaps we've been too restrictive in the puzzles we've given you	13:10
@beta_helix	Right now we are strictly speaking about past Flu Puzzles.	13:10
@CFC	But I am curious if there were specific schains at specific locations, that spawned clusters... say a Phe or Tyr?	13:11
phi161	too restrictive how?	13:11
Aaron	@CFC: YES!	13:11
Aaron	You've noticed	13:11
Aaron	so many of these sidechains are inspired by antibodies that have been shown to bind the flu	13:12
@beta_helix	@TimovdL it depends on the Flu Puzzle, for example the last one (where we just gave you a helix) came back with 1 cluster, but they were all very interesting (for the exact reason CFC just brought up)	13:12
Aaron	we try to use nature as inspiration	13:12
spvincent	How different were the Foldit results compared to those produced by rosett@home, assuming you did that?	13:12
@beta_helix	@phi161 perhaps we put in too many constraints, or in most Flu Puzzles the backbone is completely locked.	13:12
Aaron	@spvincent: I found that the foldit players come up with much more reasonable solutions than by purely computational means	13:13
mottiger	we cannot judge if this is positive or negative if you put so many constraints, this is up to you	13:13
Aaron	both methods have there advantages and disadvantages	13:13
TimovdL	In nature wouldn't the backbone be influenced by the blocker?	13:13
Aaron	We tried doing helix design and docking on our computer clusters(the last flu puzzle) but were unhappy with the results	13:14
mottiger	s	13:15
spmm2	do you try different binding sites or are they optimised already?	13:15
@beta_helix	@BP that seems generally true, 80% of the time the highest scoring models pass Aaron's criteria for what "might be useful"	13:15
BletchleyPark	thanks beta, have you had success yet with a working model ?	13:16
Aaron	@spmm2: we have been trying to go after this same binding site aggressively because it is a location that if we bind to it, we think we can actually inhibit flu virus	13:16
Aaron	so there are other places to bind, but we KNOW there is something interesting about this location	13:16
karstenw	you can keep constraints intact if you give us models, like casp. this way you can control the number of clusters you get	13:16
spmm2	ah ha thanks	13:16
mottiger	do you synthesise some of the solutions or just use them digital?	13:17
Aaron	also, that particular binding spot is highly conserved across many different flu viruses	13:17
Aaron	so if it works for one it might work for others	13:17
Aaron	in terms of the last flu puzzle	13:17
@MikeCassidytoo	It would be good if there was an manual way to gently move parts of the puzzle - maybe the arrow keys	13:17
Aaron	I think it was probably the most useful yest	13:17
Aaron	yet	13:17
spmm2	we had a bit more flexibility on that one	13:18
Aaron	we know that we like a helix in that position but it's really only me in the lab trying to figure out how to fit it	13:18
Aaron	your top100 puzzles were totally awesome in coming up with ways to interact that I hadn't thought of	13:18
Aaron	so we are going to take a few of the top scoring designs, and try to build a protein around it and test if it sticks to the flu	13:19
frood66	good with a hammer here :)	13:19
@marie_s	have you test if they will make an helix with our solutions?	13:19
Aaron	So, do we synthesize the solutions? Well we use them as inspiration on things we do synthesize	13:20
@auntdeen2	when was that last flu puzzle played? during the time that "wiggle" was bugged? if so, you may want to present it to us again	13:20
@auntdeen2	we might be even more awesome ;-)	13:20
mottiger	ah i remmeber the last one, sorry it is some time ago, it was just this little helix, and you think we brought up good solutions but just the helix isnt usefull so you need some decoration on it	13:21
Aaron	and also, as we get better as using and designing puzzles we are trying to streamline moving from foldit players solutions to actually synthesizing them	13:21
frood66	absolutely	13:21
@beta_helix	@auntdeen, it was posted in January: http://fold.it/portal/node/991577	13:21
urlbot	Long URL from beta_helix has been shortened to http://tinyurl.com/7xdkvlx	13:21
spmm2	do you actually look at results in foldit - how do you examine the results?	13:21
@auntdeen2	then really, beta - it may be worth another round	13:21
@beta_helix	in PyMOL	13:21
Aaron	@marie_s: we are going to use a few of the top solutions combined with our computational methods to try and make some new binders, yes	13:21
Aaron	BUT we are also going to give you a puzzle and let you try and do the same thing	13:22
Aaron	which is build the backbone/scaffold of the whole protein around the helix	13:22
BletchleyPark	can the models be quicker with less constraints ?	13:22
BletchleyPark	or by sorting the constraints in a different way ?	13:23
Aaron	@BletchlyPark: What constraints do you not like?	13:23
Aaron	We are basically trying to focus your efforts on a particular area	13:23
frood66	well the mission sounds interesting	13:23
BletchleyPark	I do not know the internals of how constraints are processed, but I can imagine that they are rules	13:23
Aaron	but the next puzzle will have lots of freedom in terms of how to design the scaffold	13:23
Aaron	there are, and it is something that me and beta_helix talk about quite a bit	13:24
@beta_helix	We don't want you to waste your time trying to fit the helix on the other side of the protein for example, because even if that scores better it is utterly useless...	13:24
BletchleyPark	I have some background in raytracing, and one may apply rules there to speed things up regionally. The same methodology might apply to constraints here	13:24
@beta_helix	but we also don't want to constrain you too much, either.	13:24
mottiger	is it possible to make the whole protein 'smaller' so that you don't see all of the flu protein, i had the feeling that this flu puzzle was really hard for old machines	13:24
@beta_helix	we tried to trim it as much as possible, and lock the sidechains that don't interact	13:25
spmm2	maybe an electron density type shape to show us where you want it be be?	13:25
Aaron	so yes	13:25
Aaron	ha	13:25
karstenw	thats what i was thinking, move constraints a bit and give us 5 models. this keeps within your boundaries, but gives us some wiggle room	13:25
Aaron	I have suggested that and we are working on implementing that idea	13:25
Aaron	but really it's an regional area that we want you to be	13:26
@beta_helix	(we need to bug the developers for that one ;-) jflat06, you here? :-) )	13:26
Aaron	the problem is a different the structure prediction because we just want you to be in a particular region but you can do anything you want in that region	13:27
Aaron	unlink structure prediction there is no one solution	13:27
Aaron	If we gave you an 2d image of some designs that already worked, would that be useful as inspiration?	13:28
TimovdL	Don't you want also binding in the surrounding area's?	13:28
karstenw	but the constraint itself can be varied, leave eveything else alone	13:28
spmm2	pictures are always good for me :)	13:28
Aaron	@TimolvdL: There is a particular loop on the target that is used by virus to infect cells, so we try to keep you near that loop	13:29
@beta_helix	would an image as a guide be sufficient for you? then we wouldn't have to enforce any constraints (or a lot fewer)	13:29
BletchleyPark	give it a try beta	13:29
@auntdeen2	definitely worth trying	13:29
spmm2	yes - personally I would stay in that area because it was useful even if people were getting high scores binding in the wrong place	13:30
@MikeCassidytoo	I think that unless the score was tied to the image we would follow the score	13:30
mottiger	in ED puzzles you already have this align to something feature, can't this be implemented to realign the designed protein to that region that you want it to have?	13:30
TimovdL	I the primary target is that loop, but maybe a bigger protein can give an even tighter coupling	13:30
TimovdL	I mean	13:30
karstenw	align to guide wont give you guys too much diversity?	13:31
BletchleyPark	@timo: pins of a powerplug need to connect, but having two ends of the entire plug may yield more stability ?	13:31
@beta_helix	@spmm the issue is if everyone else gets a high score by binding the wrong place, we might miss your solutions :-(	13:31
@beta_helix	this is why we always put in some minimal constraints	13:32
BletchleyPark	then keep those at least	13:32
@marie_s	and recipes will lost our best	13:32
TimovdL	Add bonus points for binding at least the correct place	13:32
@beta_helix	sounds good, really loose constraints (that you might not even notice ;-)	13:32
frood66	sounds sneaky	13:33
karstenw	i like that. loose constraint	13:33
@MikeCassidytoo	Those of us with no bio knowledge can only follow the score	13:33
karstenw	right mike	13:33
@beta_helix	@timovdL it's basically the opposite, if you violate the constraints you get a big penalty, but if you are in the correct zone everything is fine	13:33
@CFC	:) I remember the bond angle puzzles with bonuses... They were an interesting exercise	13:33
TimovdL	same effect	13:33
spmm2	well lets try with mimimal constraints and you can repost if you want to tweak	13:33
@beta_helix	yep...	13:34
@marie_s	no way to make other place not attractive?	13:34
frood66	sounds good	13:34
mottiger	or try different methods	13:34
@beta_helix	@mike that way you can follow the score and know you are at least in the correct place!	13:34
spmm2	x marks the spot :)	13:34
@beta_helix	@marie well, if you try the other place and your score gets horrible, isn't that unattractive enough? or do you mean visually?	13:35
Aaron	@everybody: the overall goal of these puzzles to try to make small proteins that can inhibit the flu, something that has never really done before	13:35
Aaron	it's is very cutting edge	13:35
@MikeCassidytoo	Yes beta the penalty idea would work	13:35
@beta_helix	I think on that note, are there any last questions for Aaron?	13:35
frood66	we have limited computing power - seems sensible to use it wisely	13:35
BletchleyPark	2aaron, would it also bind to the unpublished one that is in the news lately ?	13:35
Aaron	@frood66: ya'll have more than you think	13:36
frood66	haha - we wish lol	13:36
karstenw	more power! lol	13:36
alwen	<-folding on netbook	13:36
Toozinger	westin!!!	13:36
mottiger	installed foldit today on my lab computer and it was amazingly fast	13:36
Aaron	@BletchleyPark: The designs we are doing are against all group I viruses, which include H5, so you never know....	13:36
@CFC	we can only do what we do at the 'frontline' with what you give us, and we thank you for it	13:37
frood66	that's sneaky mott!	13:37
Aaron	@BletchleyPark: The region that you keep see is highly conserved across most all of the viruses, that's why you keep seeing it ;)	13:37
BletchleyPark	thanks Aaron, it will be a high profile discovery if you find it	13:38
@beta_helix	Ok gang, it's time to let Aaron get back to work!	13:38
Aaron	Thanks everybody, I'm gonna head back into the laboratory!	13:38
BletchleyPark	thanks Aaron	13:38
@auntdeen2	thanks, Aaron :-)	13:38
@marie_s	thanks	13:38
karstenw	bye aaron	13:38
lamoille	thanks Aaron for your time	13:38
frood66	thx Aaron - appreciate yr time	13:38
@tealight-irc	thanks for chatting with us aaron :)	13:39
mottiger	enjoy aaron	13:39
@MikeCassidytoo	bye aaron	13:39
BletchleyPark	CASP R12..	13:39
spmm2	I understand a lot more now thanks	13:39
Aaron	Yep, I hope you enjoy the next puzzle, you'll really do a fantastic job.....	13:39
@beta_helix	So one of the promises that we had made in the recent dev. chats was to not post any non-CASP ROLL puzzles until we got the client issues sorted out.	13:39
@tealight-irc	0.o	13:40
frood66	Hmmm	13:40
@tealight-irc	how many are we getting?	13:40
@tealight-irc	lol	13:40
@beta_helix	Hopefully we can post that new Flu Puzzle today!	13:40
@auntdeen2	they are looking sorted, beta	13:40
frood66	u r kidding?	13:40
lamoille	nice	13:40
@auntdeen2	but.....	13:40
tokens	yeah, non-Casp is good	13:40
spmm2	the dev preview is pretty good be nice to get it to main	13:40
@auntdeen2	on quick caution - we didn't realize there was a problem in the last client until endgame	13:41
karstenw	but stagger expiration day pls	13:41
@tealight-irc	i noticed a tremendous improvement with client yesterday, was back to "normal"	13:41
mottiger	same here tealight	13:41
frood66	e have (effectively) 21 current puzzles and u want to add?	13:41
mottiger	much faster, huh?	13:41
@tealight-irc	yes much faster and more consistant	13:41
@auntdeen2	yes - much faster	13:41
@CFC	...but the old rebuild would be a very welcome addition to the 'weaponset'....	13:41
@auntdeen2	second CFC	13:42
@tealight-irc	thirded	13:42
spmm2	they can keep working on the fixes but dev preview imo can go to main now	13:42
mottiger	cannot say anything about the rebuild thing	13:42
@beta_helix	so it would be ok to have 2-3 CASP ROLL puzzles up and 1 design puzzle at the same time (making sure the expiration dates are staggered... it's a bit harder with the CASP ROLL puzzles)	13:42
@auntdeen2	spm - it did	13:42
frood66	ready to hang up my boots here	13:42
karstenw	keep in mind, the more puzzles you send. the less time is spent on each puzzle.	13:42
@beta_helix	@karstenw of course	13:43
BletchleyPark	@beta, CASP roll 12 seems to be 499 long ?	13:43
@auntdeen2	beta - the large casp puzzles are an issue	13:43
@tealight-irc	with staggered dates it shouldnt be too bad	13:43
@beta_helix	that is the issue: do we only post the CASP ROLL puzzles until CASP ROLL is over, or do you have time for design puzzles as well?	13:43
@auntdeen2	even before the 499 comes out	13:43
tokens	I will look forward to a design puzzle for a change	13:43
spmm2	lets have the flu puzzle	13:43
frood66	499 - no way	13:43
spvincent	It's the combination of too many puzzles and a relatively short time to work on each that is a problem.	13:43
@auntdeen2	agree, let's have it	13:43
@beta_helix	don't worry, we will not be doing R0012 (it is 499 residues long and no de-novo, there are many templates for it)	13:44
@auntdeen2	and large & slow	13:44
@mimi2	I don't have the time for what we are getting already unfortunately	13:44
@beta_helix	ok, we'll come back to design puzzle in a second, let's talk about CASP ROLL for a bit:	13:44
frood66	we are already overloaded inmy view	13:44
@tealight-irc	can we have the flu one with a long time frame?	13:44
infjamc	E.g. 30 days?	13:44
@tealight-irc	yeah	13:44
@CFC	and CASP10 isnt here yet frood... :)	13:45
mottiger	multistage flu design like the casp puzzles?	13:45
frood66	either i do my best or not at all	13:45
tokens	30 days is too much I think	13:45
spmm2	it is selecting the template and then feeling anxious about picking the wrong one I don't like :(	13:45
@beta_helix	one way to lighten the puzzle load would be to do away with the TOP Foldit predictions round. Currently, they give us 3 weeks for each target and we basically do: 1 week on 10 server models, 1 week on rosetta models, 1 week on the TOP predictions from the first puzzle.	13:45
@auntdeen2	what are you getting the most out of, beta?	13:45
@CFC	there must be an easy way to cut that to 2 rounds?	13:46
@beta_helix	As I mentioned in this post:	13:46
@beta_helix	http://fold.it/portal/node/991921#comment-15968	13:46
urlbot	Long URL from beta_helix has been shortened to http://tinyurl.com/6u73554	13:46
frood66	something has to give here	13:46
@beta_helix	the important thing for these targets that have no homologs/templates is to try to get as much diversity as possible.	13:46
Voclav	IMAGE: http://fold.it/portal/files/chatimg/irc_404663_1330033610.png	13:46
@auntdeen2	will your foldit submissions suffer if you do away with the top predictions round?	13:46
@auntdeen2	All players - global is being used right now for a developer science chat… please use the puzzle channels for all chat that is not related	13:47
@auntdeen2	thanks players	13:47
@beta_helix	The goal for the TOP predictions round was to take an early version of a high scoring prediction and see if there is a better topology that scores even better.	13:47
frood66	as a self confessed addict i play - but not if I cannot play	13:47
TimovdL	Did that work?	13:48
mottiger	was this idea a success beta?	13:48
@auntdeen2	has that worked, beta? significantly?	13:48
spvincent	And how does it seem to be working so far, beta?	13:48
@beta_helix	@CFC we could post all 15 server predictions in one puzzle but that might be way to overwhelming, and the Rosetta ones usually score better already so the other 10 might be ignored	13:48
@auntdeen2	why not do that and award no global points?	13:49
@auntdeen2	so that everygthing will get looked at?	13:49
@mimi2	timescales are such that unless you have a very powerful system you can only really look at one or two options	13:49
@tealight-irc	many people wouldnt do it if there were no points in it for them	13:49
@Madde	in sense of more diversity wouldn't it be better to get rid of the TOP prediction round and instead add a round de-novo?	13:49
@beta_helix	generally, a better score is found from improving those top predictions, but everyone converges on that same model from the last round.	13:49
frood66	and newbies?	13:49
@auntdeen2	true, tea - but at this stage, many can't even look at one of the current 3	13:50
TimovdL	Beta, I have understood that there are even more models. Maybe in stead of the top predictions, the best 3 of them?	13:50
TimovdL	Of those other models	13:50
karstenw	just stagger puzzles a bit more and introduce new puzzles a tiny bit slower and we can handle it i think, just the way it is.	13:51
@auntdeen2	kars - it's the CASP deadlines	13:51
@auntdeen2	not foldit	13:51
frood66	i can only be blunt - the current situation is alrady too heavy	13:51
@beta_helix	@Madde & spmm's reply to my comment, that is why I always provide an extended chain in the alignment tool for every CASP ROLL puzzle... but freestyle scores rarely get as good as starting from server models	13:51
karstenw	ah, then , idk :D	13:51
frood66	I have not the time to follow through on thing I would like	13:52
@CFC	posting 2 targets a week recently has caused the chaos, but we can only react	13:52
@beta_helix	@karstenw I asked the organizers to push their deadlines and they were able to do that for R0009, @frood66 that is why we are having this chat :-)	13:52
karstenw	ty beta, more time is good	13:52
spvincent	IHow about 10 days on the first 2 stages of the CASP Roll and skip the final stage of refining players solutions then if that doesn't seem to be generating anything new?	13:53
*** mode/#global [+o thomirc8] by ChanServ		13:53
@mimi2	An idea of what we can expect would be helpful It was a shock today to find new puzzles with end dates earlier than the current puzzle	13:53
frood66	@beta - u think I don't know that?	13:53
@beta_helix	So we could do away with the "top predictions/all-hand-ish round" or one way to decrease the amount of puzzles would be to combine that round with the 5 Rosetta Server predictions.	13:53
@tealight-irc	mimi, yes i was surprised last night when i encountered them lol..	13:54
BletchleyPark	everyone will go with the rosetta ones..	13:54
spvincent	That sounds like a possible solution.	13:54
@beta_helix	@mimi I can post a schedule of future CASP ROLL puzzles... I try to give more time on larger targets	13:54
@beta_helix	@BP that is exactly my fear	13:55
@tealight-irc	that would be useful beta :)	13:55
karstenw	i wouldn't combine them	13:55
frood66	qa bit of organisaton would be lovelly	13:55
@MikeCassidytoo	It sounds like I should not be jumping on the alignment giving other people better scores but staying with my low scorinng alignement	13:55
@beta_helix	general question: how much combination are you trying? Is partial threading being used often or do you mostly focus on 1 model at a time?	13:55
@marie_s	one model or 2 for me	13:56
@MikeCassidytoo	I do no partial threading	13:56
BletchleyPark	I hardly use partial, i always try all models	13:56
mottiger	no partial threading here	13:56
spmm2	how many more CASP Roll puzzles/targets are there?	13:56
frood66	partial - no way	13:56
@marie_s	no partial, too hard	13:56
@mimi2	can't get it to work for me	13:56
@beta_helix	http://predictioncenter.org/casprol/targetlist.cgi	13:56
urlbot	Long URL from beta_helix has been shortened to http://tinyurl.com/86p6xu9	13:56
@MikeCassidytoo	I do mess with different alignments	13:56
@tealight-irc	im no good at partial threading so run thru the various models and pick on i like...granted i seem to pick the ones tha dont go far lol'	13:56
@CFC	spmm, it's a rolling process, could be lots, could be some	13:57
frood66	partial is a waste of time	13:57
TimovdL	One model, I just evaluate all and choose one or 2, no partial threading, not time enough	13:57
spmm2	I try every template no partial	13:57
@tealight-irc	it seems many dont use partial......	13:57
@CFC	the fun will be 2 ROLL targets a week, during the madness of CASP10	13:57
@mimi2	I think only infjamc knows how to do partial	13:57
@beta_helix	I always try to give you the most time on the first puzzle (since that one has 10 different starts) but the next 2 rounds only have 5 starts each, so that is another reason why those are shorter	13:57
frood66	try getting through the 10 on 519 first	13:57
frood66	who will do all 10?	13:58
BletchleyPark	I do	13:58
@beta_helix	right, that's why that one has such a long deadline	13:58
spmm2	me too	13:58
bobcat	I've looked at all 10	13:58
TimovdL	Just a startup	13:58
frood66	only 7 days	13:58
@tealight-irc	i look at all, but only play with maybe 2 or 3	13:58
frood66	we have 6 days for 5	13:58
TimovdL	Then a spreadsheet to choose the most promissing	13:59
@MikeCassidytoo	I usually pick the one with the lowest starting score if I can find it	13:59
@beta_helix	generally, would it be better to have a lot longer time (~2 weeks) on the first puzzle (with 10 servers) and then post the Rosetta server puzzle for just 1 week at the very end?	13:59
@Madde	I'd need a few more computers to try all 10 predictions	13:59
@tealight-irc	lol same	13:59
@marie_s	you think the first step is useful for the second?	13:59
frood66	roetta being 5?	13:59
@beta_helix	yeah... I have to admit I didn't think CASP ROLL would have this many targets either... the first 3 targets they gave us months to work on!	14:00
@tealight-irc	yes i think it may be better beta peeps would not feel so pressured	14:00
@auntdeen2	no time for that, beta :-(	14:00
@auntdeen2	I look at all ten - pick one & go - not really evaluate	14:00
@auntdeen2	yes	14:00
Susume2	2 weeks for 10 starts soudns good, more time to try different stuff	14:00
@beta_helix	yes (rosetta=5) @marie would you want them up at the same time?	14:00
@auntdeen2	beta - why 5 predictions from Zhang & quark?	14:00
spmm2	as we all probably elimate several templates quickly - maybe less time on the first ten	14:00
@auntdeen2	someone earlier asked why not just 3 from each....?	14:00
@tealight-irc	maybe they are trying to overwhelm so that computers do better than hoomans.....;)	14:00
Susume2	often there is a quark-zhang pair that are very similar, could leave out one of those	14:01
@beta_helix	The top ranked servers from CASP9 for the Free Modeling category was the ZhangServer & Quark (which is also from Zhang)	14:01
mottiger	evil thoughts you have tealight :D	14:01
frood66	beta: I do all 10 - this takes days for me - it is not fun and I do not have time to do what I would like woth any as a result	14:01
karstenw	2 weeks? seems aweful long to me. burnout. 12 days is plenty	14:01
@tealight-irc	i am evil mott..havent you heard :P	14:01
@beta_helix	@tealight... I never thought of that! :-P	14:01
@CFC	perhaps there's a 'tipping-point' approaching - rather than offering less options beta, we need to recognise that we maybe cant play all puzzles?	14:02
@auntdeen2	but beta - do we need all 5 from each?	14:02
@tealight-irc	well it is a competiton of sorts...and those sorts of tactics wouldnt be unheard of lol'	14:02
@beta_helix	how about 10-12 days for the quark/zhang servers (depending on the length of the protein and how similar each model is to one another) and then 5-7 days for the 5 Rosetta models?	14:03
karstenw	yes beta	14:03
BletchleyPark	7 days rosetta please, we also have private lives.	14:03
@beta_helix	@auntdeen I don't think you want me deciding which server models should be filtered out! Isn't it better for you all to decide that?	14:03
spmm2	so why not an elimination round first - to weed out templates that we just wont use	14:03
@marie_s	why not rosetta first?	14:03
@auntdeen2	lol BP	14:03
karstenw	yes, 7	14:03
@beta_helix	@BP 7 days, got it.	14:04
frood66	is there really no way to concentrate our efforts without compromising our abilities?	14:04
@auntdeen2	beta - in a perfect world where we all have infinite computing power.....	14:04
@beta_helix	@marie the fear with Rosetta first is that since they are already minimized with the same energy function used in Foldit, they already score better and so that might influence players when working on the Quark/Zhang models	14:05
@Madde	couldn't an algorithm filter a prediction out that is too similar to another one?	14:05
@beta_helix	@spmm do you mean a quick round where Foldit players decide which Server Predictions they want to work on?	14:06
spmm2	yes I think so	14:06
@beta_helix	@Madde certainly we could do that, but if they are that similar does it really hurt for you to have those (and just ignore them?)	14:06
mottiger	but how do you decide so fast?	14:06
PIECEofTOAST	this beta has some pretty bad hitboxes, or is a clash tenchnically when they are too close	14:06
@beta_helix	@mottiger that seems to be the issue, it's another time problem	14:07
Susume2	it is not quick in foldit to recognize the near-twins, beta, so we spend time on both while choosing	14:07
@MikeCassidytoo	I think the first round even with ten should be the shortest; we are suppose to be using are intuition to decide what to play; too much time means we are trying to play them all	14:07
@Madde	we could use the slot for another server's prediction	14:07
@tealight-irc	i think it really comes down to player instinct and discretion...the model that gets left out can be the "winner"	14:07
@tealight-irc	i agree with mike	14:07
@beta_helix	@susume & Madde ok...that's not a problem at all. I can easily filter out server models that are "too" similar to one another	14:07
frood66	but the instruction IS to play them all mike	14:07
@auntdeen2	beta - that would be great	14:08
@MikeCassidytoo	I LOOK at them all at most I try 2 maybe 3	14:08
spmm2	yes the extra time is to improve the score for points - templates get eliminated quickly	14:08
@tealight-irc	that may be frood but i actualy dont think that foldit should leave any models out..its up to us to "feel" what needs working on	14:08
@marie_s	I dont follow instruction like this, i am a player	14:08
frood66	that sounds good beta	14:09
@tealight-irc	i just play what i like..i suck..but it keeps it fun lol	14:09
infjamc	Would it be possible to limit each player to a smaller number of models, say 2 out of 10? Of course, scoring would be tricky because you would need a separate ranking for each model	14:09
TimovdL	I would suggest only very simular weeded out	14:09
@beta_helix	at keeping it fun is very important... we don't want anyone (you guys, us) burning out before CASP10 even starts!	14:09
frood66	tealight: we can omly do that if we have the time and computing power	14:09
infjamc	The idea of this approach is to ensure that everyone has enough time to explore the model thoroughly while ensuring that every model is looked at	14:09
BletchleyPark	@amc, i do not want that	14:09
spmm2	@frood - I do the same start routine on every template which takes several hours that eliminates quite a few	14:09
@beta_helix	@TimovdL agreed, just the ones that are obviously toplogically similar	14:10
TimovdL	amc neither do I	14:10
@MikeCassidytoo	I eliminate by looking at them	14:10
rav3n_pl	Hello folders:)	14:11
@tealight-irc	hi rav	14:11
@beta_helix	My other question (with respect to the Top Predictions round) was to bring back the dreaded RMSD filter, to ensure that any improvements to another player's model would end up with a different topology...	14:11
frood66	@spmm: as do I - but that is my point - large protein - how many hrs - and I'm an addict!	14:11
spmm2	well you have been playing for years mike not so easy for us noobs	14:11
@beta_helix	Hi rav, we're talking about CASP ROLL puzzles	14:11
@tealight-irc	yes mike i think it should be the players making the decision which to play	14:11
@MikeCassidytoo	RMSD filter????	14:11
@beta_helix	yes: your score won't count unless your model is structurally different enough from the one you loaded in...	14:12
rav3n_pl	maybe exploration if we are not so creative?	14:12
@MikeCassidytoo	spmm2 your scores are always better than mine	14:12
@beta_helix	RMSD = root mean square deviation	14:12
@auntdeen2	beta - if foldit can live woithout the top predictions round - we surely can	14:12
Datacute	Can the exploration map be available for non-exploration puzzles, so we can see what is untried by others?	14:12
mottiger	feel free to implement such stuff, we deal with everything	14:12
@auntdeen2	without, even	14:12
mottiger	even broken wiggle functions and the proteins are top :D	14:12
@marie_s	one of the problem is that recipes make micro moves with many points	14:13
@tealight-irc	ruddy messy score depriver = RMSD :P	14:13
karstenw	are top predictions round helping, has this been answered already?	14:13
spmm2	but if we are using the same template - timo sp and I all independently started and convereged on the same template no sharing at all	14:14
TimovdL	Another question: can you publish what solutions are sent in with a small explanation?	14:14
spmm2	who get the points?	14:14
@beta_helix	they help at determining which model everyone has converged to	14:14
frood66	soory to sound like a difficult chap - but it sounds like we need two game - one fore two cores - and one for more	14:14
@Madde	beta, is there an official threshold of how different a model has to be from it's parent server prediction to get credit?	14:14
@beta_helix	@Datacute the Exploration Map was turned off when we had too big an influx of players and it took up too much bandwidth... we should be able to bring it back now.	14:15
@mimi2	@ frood - and one for less as well, some people have OLD systems	14:15
Datacute	Ah -- I was part of that influx	14:15
@tealight-irc	yep i still paly mostly n a single core lol	14:15
@tealight-irc	*play	14:15
@marie_s	madde, you remmber the contrinst at the end of casp9 ; it was a nighmare	14:15
BletchleyPark	@frood a client runs on one core, the other core is used to feed the graphics card and chat	14:16
rav3n_pl	Do it on dev and add data counter somewhere	14:16
@beta_helix	@Madde that is a great question... to be honest, there have been so few successes in the Free Modeling Category that it rarely comes up!	14:16
@beta_helix	@marie that's why I did not want to bring that back :-)	14:16
@mimi2	it does make a lot of difference with multistarts as to how many clients you can run	14:16
@auntdeen2	major, mimi, agree	14:16
@tealight-irc	at the end of the day sometimes you just cant do everything..and have to simply pick one and go with that	14:18
spmm2	especially on the bigger puzzles	14:18
@beta_helix	Ok... maybe we should have another CASP ROLL chat in a couple weeks (by then we'll know how many more targets they have released, hopefully it's not 2 new targets every week!) but for now we can do away with the TOP predictions round?	14:18
rav3n_pl	On 3 days rounds I use only one oil f multi starts -that one which looks best for me	14:18
@auntdeen2	yes	14:18
@tealight-irc	worth a shot beta	14:19
@marie_s	ok	14:19
@marie_s	I never paly it anyway	14:19
BletchleyPark	@beta I'd say yes	14:19
spmm2	but that method works well and could be used for other puzzles later - better than all hands	14:19
frood66	BP - noyt worth commrnting on	14:19
@Madde	yes, kill the TOP predictions round	14:19
frood66	jeeze - can'y type	14:19
karstenw	yes, get rid of top predictions, so we can breathe. can always add it on slow weeks, lol.	14:19
TimovdL	Let it deend on the number of coming puzzles	14:20
@beta_helix	and starting with R0010 (which is only 80 residues!) I'll post the first round (10 servers unless they are filtered) for 10 days?	14:20
@tealight-irc	yep	14:20
krulon	What about everyone worked on one server prediction for just one day.	14:20
rav3n_pl	Lol, no	14:20
@beta_helix	@krulon not everyone has 1 day free!	14:20
frood66	now there is a thought	14:20
@CFC	impractical krulon, and will cause riots... :)	14:20
smilingoneIRC	one day isn't enough	14:21
@auntdeen2	and many of us invest much time in hand work that may not pay off until day 3	14:21
TimovdL	some people have jobs	14:21
@tealight-irc	krulon. if people want to do that..it should be their choice..not foisted on everyone :)	14:21
rav3n_pl	1day for 10pts?	14:21
karstenw	grabs pitchfork ;)	14:21
spmm2	yes I like that idea hard to mange maybe two or three days for two or three templates - if we were working as a team we would be trhing to eliminate the duds and then	14:21
frood66	but at least us poor chaps with small computing power are on a relatively even field	14:21
krulon	After all were completed everyone could work on the highest scoring ones.	14:21
spmm2	pushing diversity on a selected set of templates	14:22
@beta_helix	the shortest puzzles we did were the exploration rounds, we would never post anything shorter than that (hopefully!)	14:22
karstenw	nope, gaming rig will kick everyone's butt in one day	14:22
@tealight-irc	oh frood..i play on a single core...you keep going on how hard things are for you..but your ranking belies that, you are on a more level field than you acknowledge	14:22
frood66	and I miss sooo much	14:22
@tealight-irc	thats life	14:22
spmm2	and as CFC pointed out you don't have to play every puzzle it is your choice	14:22
@beta_helix	If that sounds like a plan (for CASP ROLL) we just need to discuss the Flu Puzzle real fast	14:22
@tealight-irc	you can only do what you can do	14:23
infjamc	See, this is exactly why I came up with the "limit each player to n templates" idea. I know that several of you don't like it, but it does make things easier for those with less computing power	14:23
@tealight-irc	but people can make that choice for themselves infj	14:23
infjamc	If the trade-off is between width and depth	14:23
BletchleyPark	it is their choice amc.	14:23
@beta_helix	@infjamc the problem is with the implementation of that...	14:23
karstenw	yes, you do have to play every puzzle. this is a competitive sport :)	14:23
@tealight-irc	why take away other peoples choices?..	14:23
spmm2	agreed infjamc we don't work as a team that way unfortunately	14:23
@auntdeen2	but inf - that would be unfair to people who have teams to work with	14:23
@beta_helix	@karstenw we could make the TOP prediction round worse 0 points :-P	14:23
@tealight-irc	no kartsenw..yu dont have too...you choose too..big difference	14:23
@auntdeen2	I mean that don't have teams	14:24
@marie_s	no karstenw, poitns and score and rank are not so important	14:24
frood66	this is a competitive game - so far	14:24
infjamc	I agree that it's better to give players more choices, but my concern with that is that some models might receive disproportionally less attention	14:24
TimovdL	It is like giving 80% of the people no chance at all it they are unlucky	14:24
infjamc	...as things now stand	14:24
spmm2	what is important is all of us beating the CASP competition	14:24
frood66	remove the competition then much of what is saud is fair	14:24
westrel3	remember KISS	14:24
@tealight-irc	well that comes down to teh people playing infj	14:24
@beta_helix	@infjamc that is the hope with at least giving you 1 day/model (10 days for the first puzzle)	14:24
infjamc	For example, models that are closer to the native but also need to dig out of a deep local minimum	14:24
infjamc	Actually, here's a 2nd idea...	14:25
spmm2	anyway beta probably needs to go to a meeting :) flu	14:25
infjamc	Why not split a puzzle into several "sub-puzzles"?	14:25
infjamc	Say, instead of having one puzzle with 10 templates, have two with 5 each	14:25
@beta_helix	yes, and I did want to ask: is it ok to post a Flu Puzzle with all this CASP ROLL craziness?	14:25
frood66	why not remove teh scoreboards?	14:25
spmm2	ok by me beta	14:25
@tealight-irc	personally i dont think options should be limited...people make their own choices...longer time sframes and better staggering are of more use	14:26
@auntdeen2	yes, beta - if long running	14:26
@tealight-irc	fine with me beta	14:26
@beta_helix	so there will be 3 CASP ROLL puzzles up, 1 beginner puzzle (which none of you should be wasting your time on ;-)) and the Flu Puzzle	14:26
@tealight-irc	if you can make it run long enough	14:26
spmm2	yes infjamc - ten at once is hard to get my head around	14:26
rav3n_pl	Beta: make it small as possible...	14:26
@marie_s	frood , you can competet with pleasurein one puzzle, but not want to do all puzzles, many players play like this	14:26
smilingoneIRC	Beta...some want choice... post it for those that want to play with the flu... personally, I won't be touching it since my plate is full with casp	14:26
frood66	I have no issue with that marie - that is not what I said	14:27
@beta_helix	@infjamc so 1 Quark puzzle (5 models) and 1 Zhang puzzle (5 models) removing any models that are too similar and then the final Rosetta puzzle (5 models)	14:27
@marie_s	give us the flu	14:27
spmm2	yes beta	14:27
frood66	ok - so max 15 models plus 1	14:27
karstenw	many days for flu and i'll squeeze it in when my othe puzzles stall	14:27
rav3n_pl	<- 3 more days off the grid	14:27
lamoille	agreed kars	14:28
@beta_helix	@marie it's very rare to have someone ask "give us the flu" ;-)	14:28
spmm2	design puzzles can stall pretty quickly as well	14:28
@auntdeen2	beta - how many days each then?	14:28
@tealight-irc	ahh but beta this one is one we cant catch :P	14:29
@auntdeen2	if you split to one puzzle for quark & one for zhang? did I understand that correctly?	14:29
@beta_helix	that is the issue (we have 3 weeks, but have to wait 4 days for the server models to come back... and then we need at least 1 day to process/submit everything, that really leaves a bit over 2 weeks)	14:29
TimovdL	We want to kill the flu	14:29
spmm2	not too long for early ones - last few days is just getting points on the pose usually	14:29
karstenw	don't split them. can't compare all ten at once. it will actually take longer if you split them	14:30
@auntdeen2	but krs - then 5 models per puzzle	14:30
@beta_helix	why don't I examine R0010 and R0011 and see how similar the Quark/Zhang models are... maybe we can lower that 10 models down to 5-7 already!	14:30
@auntdeen2	that could be much easier	14:30
@tealight-irc	worth a shot	14:30
frood66	yes beta	14:30
@auntdeen2	good beta	14:30
infjamc	karstenw: Part of the idea of splitting the 10 models into two groups of two is to find the best quark model and the best zhang model...	14:31
@beta_helix	luckily they are both nice and short: 80 & 81 residues :-)	14:31
karstenw	yes beta first see what you can filter out	14:31
@thomirc8	would an exploration puzzle make sense for CASP ROLL?	14:31
@mimi2	yes - better to remove similar and keep models together for comparison	14:31
TimovdL	That will speed up things	14:31
spmm2	agreed infjamc better to split them	14:31
tokens	About the flu puzzle: Some people might find it more fun to work on a design puzzle, so I think it's a good idea to have that along with the casp puzzles	14:31
TimovdL	80 is tiny	14:31
@tealight-irc	nothing wrong with tiny..	14:32
spmm2	how many cystines :)	14:32
@beta_helix	@tokens there should be a Flu puzzle up later today... speaking of which, I should go get that ready!	14:32
tokens	:)	14:32
@auntdeen2	thanks, beta :-)	14:32
mottiger	since there is no deadline for flu puzzles for any competetion why not just release it and make it a long runner ?	14:32
frood66	80 is gorgeous	14:32
BletchleyPark	regarding splitting: you will end up with one puzzle of fairly useless results and another with useful results, yet both will take time	14:32
@beta_helix	@spmm hahahaha, yeah, we'll have to see!	14:32
karstenw	infjamc, you are right, but you are expanding the project by doing so. time is not on our side	14:32
infjamc	80. Good, that means 8 times the processing speed relative to 160	14:32
TimovdL	tx for your time	14:32
lamoille	thx beta	14:32
infjamc	karstenw: I don't see splitting the puzzle as a problem if the due dates are the same. But again, that's just me	14:33
@beta_helix	@infljamc yeah, so hopefully we don't need to split them up... but we'll look into that idea again in a couple weeks.	14:33
rav3n_pl	Ahh looks like I miss nice small puzzles...	14:33
spmm2	exactly and there will be better exploration of the quark models	14:33
@CFC	the reduction of options... from FoldCentrals point of view, with CASP10 approaching, is that a good idea? Or will encourage convergence?	14:33
@beta_helix	hopefully!	14:33
karstenw	you running the puzzle twice. once as zhang and once as quark	14:33
BletchleyPark	and often only one of them is best	14:34
@beta_helix	we are only reducing the final round which was just leading to convergence already	14:34
karstenw	exactly	14:34
BletchleyPark	so one waisted puzzle time	14:34
@thomirc8	also, will the diversity tools make it into the client anytime soon?	14:34
@beta_helix	that is what we are trying to get rid of: wasted puzzle time	14:34
infjamc	BP: That's true, but part of me wonders if that's due to the score function	14:34
@beta_helix	ok gang, I really have to go.	14:34
spmm2	@BP the quark models are in anyway - do you just not use them?	14:34
BletchleyPark	@amc what difference does splpitting then make ?	14:35
karstenw	lol, bye beta	14:35
BletchleyPark	bye beta	14:35
frood66	thx for yr time beta :)	14:35
@beta_helix	Thanks for this great chat... hopefully we can set another one up in a couple weeks!	14:35
spmm2	thanks beta	14:35
@tealight-irc	cya beta!	14:35
@tealight-irc	..now go get the flu :D	14:35
rav3n_pl	Days...	14:35
@beta_helix	I'll try to post up the CASP ROLL puzzle schedule in the Forum soon	14:35
rav3n_pl	;)	14:35
BletchleyPark	@spmm I use all of them.	14:35
infjamc	BP: Fewer models per puzzle = those with lesser computing power can focus on one of the sub-puzzles	14:35
@MikeCassidytoo	bye beta	14:35
spmm2	hi rav having fun :P	14:35
karstenw	bletch, you can't compare starts if you split them	14:36
@beta_helix	bye everyone, thanks again for all your hard work!	14:36
rav3n_pl	I'm only on chat via my phone...	14:36
BletchleyPark	@karsten that is why I am not in favor of slitting	14:36
BletchleyPark	splitting	14:36
f1pokerspeed	Dores anyone have some suggestions for essential scripts that I should have?	14:36
infjamc	karstenw: I'm not familiar with the technical details, but I think that problem is fixable	14:36
infjamc	After all, there are already puzzles that allow you to load solutions from a previous round	14:36
@marie_s	blue fuse, quakeR, DRW, loop rebuid	14:37
karstenw	oh, you meant what's the difference the other way, lol	14:37
infjamc	So it should theoretically be possible to create two concurrent puzzles that are interconnected	14:37
@marie_s	local quake	14:37
infjamc	Namely, you can load the solutions of version A in version B, and vice versa	14:37

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