Posts by Tarx

21) Message boards : Cafe Rosetta : Oh Canada? (Message 18591) Posted 13 Jun 2006 by Tarx Post: Bye-bye Ars Technica! Yes, we've moved up to 7th overall! And Phoenix Rising is just about to join them :) After XPC, then TeAm AnandTech (sic) will have to be the next target, but we'd need to be alot stronger (at least double) than we currently are! With that level of performance, we should also be able to shake off SETI.USA. That said, we've gone from mid 40s to mid 60s in the last two weeks! And if we keep accelerating like that...
22) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 18207) Posted 9 Jun 2006 by Tarx Post: About my F@H comment, I referred to the then-current info on F@H in Wikipedia (you can read about it in W's "discussion" page, with some references, which was wiped out). I was curious about the source of that in Wikipedia so I did a history check on the original that was wiped out (and then added in the discussion page). It was written by a user called Kiio. So I checked and noticed that user name doesn't appear anywhere in either Rosetta (neither in a forum nor as a participant) nor in the F@H forum. And also noticed that Kiio didn't respond to a personal request by one of Wikipedia's counter-vandalism unit members to provide source material. And when I checked into that user's Wikipedia's history http://en.wikipedia.org/wiki/Special:Contributions/Kiio, it doesn't look promising that the user is some biochemist or similar expert. So basically it looks like that comment was some entry to Wikipedia by an unknown person and quite possibly an unqualified person. And nobody to back it up, nor any sources/references. Shouldn't have been wiped, but it makes sense that it should have not been in the article, but in discussion. And since unsubstantiated, not worthy to refer to. This thread and some of the R@H and F@H threads that it refers to, seems to have alot more relevant information. Hopefully David Baker will have some further input on what Dr. Pande from F@H has said regarding the two projects. (i.e. the post from Dr. Pande that says "Rosetta and Folding@Home are addressing very different problems.")
23) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 18056) Posted 8 Jun 2006 by Tarx Post: Dimitris Hatzopoulos: My (non-expert outside observer's!) opinion is that the aim of F@H is also fundamental research, on how an why proteins fold. ... Personally I've found helpful to understand what F@H does the info in What are we ACTUALLY work on? ... I just read your very nice "How-To: Join Distributed Computing projects that benefit humanity" page http://www.hyper.net/dc-howto.html. I noticed that it mentioned "Comments about F@H in Wikipedia suggest that due to recent developments, "Folding@Home approach has become somewhat obsolete"(?). My own measure of useful results would be citations (see later)." I saw that Wikipedia was adjusted to correct(?) that statement (that was restated in the discussion page). I'm not sure where that statement originated from (no sources listed) and it seemed to be more of a random opinion (I did a quick google search and didn't find anything like that). As mentioned in this thread (and on the F@H forums) it just looks like two different types of protien related medical research projects with not that much overlap... Do you know any more about that statement (or its source)? (otherwise perhaps it is just someone trolling?) (and what did you mean about "(see later)" )? I want to include a link to your page for one of the large existing folding@home teams (that I'm helping to run) as an alternate project, so I want to careful about info regarding their current project is accurate...
24) Message boards : Cafe Rosetta : Oh Canada? (Message 18052) Posted 8 Jun 2006 by Tarx Post: Just an update: "Canada will overtake: Team Days Ars Technica 8.2 Phoenix Rising 11.6"
25) Message boards : Cafe Rosetta : Oh Canada? (Message 17540) Posted 2 Jun 2006 by Tarx Post: I don't want to get anyones hopes up about the possibilities for this as they will probably say no to the request. But, I could ask the system administrator at Rosetta, if they have the capability to support a forum for teams. At present the this type of thread is all there is. But it might be possible for them to pull an old sever out of the hat that could have a separate forum for each team that wanted to use it. Within each forum you could then create specific threads. My fingers are crossed for this - any news...? And I noticed: "Canada will overtake: Days US-Distributed 3.4 Ars Technica 17.8 Phoenix Rising 36.1 Canada will not be overtaken by anyone!" :)
26) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 17407) Posted 31 May 2006 by Tarx Post: I asked that question to one of the researchers (Dan) at F@H (note: he works with basic research part of the project rather than the specific medical research part of the project) "Just knowing the final, incorrectly folded structure might be enough. But we don't know yet. (Incidentally, it just occurred to me that this is one strong reason for government to fund research. There is no way of knowing what the best solution to a problem will be, and there is no telling which part of a biochemical system is the best one to poke around in to cure a disease, until you give a bunch of geeks around the world rooms full of test tubes, jars of buffer salts, and computers, and a bunch of money ['cause we need beer on the weekends to keep us going]. Only once we understand the problem from a multitude of angles will we know what might be done to fix it." and more... http://forum.folding-community.org/viewtopic.php?t=15286
27) Message boards : Rosetta@home Science : Rosetta AP article! (Message 17406) Posted 31 May 2006 by Tarx Post: [quote]Didn't Google stop sign ups on Google Compute, some time ago? And that was for Folding@Home, not Rosetta. Yes, when Google made major changes to their tool bar, the Google Compute part was no longer compatible with the latest version. The older version is still running on 6,774 computers (active CPUs within 50 days). http://toolbar.google.com/dc/offerdc.html In their FAQ (see link), I laughed when I saw question 9 "I already get enough protein in my diet... why should I care?" For more info about why it stopped check http://forum.folding-community.org/viewtopic.php?t=13539
28) Message boards : Rosetta@home Science : CAN YOU HELP ROSETTA?? (Message 17360) Posted 30 May 2006 by Tarx Post: May I suggest one change on Rosetta website? There is System requirements link on main Rosetta page. And it has headline "Recommended System Requirements". However later in text it is referred as "minimum system requirements". And all requirements asks for 512MB RAM. I'm running Rosetta successfully on computer with 160MB RAM. So I think there should be clearly written what are RECOMMENDED requirements and what are MINIMAL requirements. It also should include minimum capabilities. Is any CPU ok? What about a Pentium 90? Or does it require MMX? Does it need to have SSE? If not does it use 3DNow! (or 3DNow! Enhanced such as K6-2+/III+ have?)? Assuming they have enough free memory (as Aglarond mentioned), perhaps these older systems can help.
29) Message boards : Cafe Rosetta : Oh Canada? (Message 17194) Posted 27 May 2006 by Tarx Post: Unfortunately I didn't get a reply (see 1st post for this thread) from Kenny King (runs the Team Canada site for Climateprediction, Einstein@Home, Predictor@Home, LHC@Home, SETI@Home and Pirates@Home) - in any case it doesn't have a forum either. There are also a few other smaller Rosetta@Home Canadian teams (e.g. BOINC@Canada, CANADA United and umm... CDNgeezer (our second most powerful team member!), what is Curse of 32?) Maybe they would consider joining up under one banner? Hmmm... if we get a team forum it should make it easier... :) (as would trying to encourage other Canadian BOINC members to allocate some project time to Rosetta under our team, plus for new members recruited externally) We want to have a new target in 18 days ;) Once we somehow have a forum, it would be a good time for the moderator to try contact "The Sailor" to add a link to that forum. Sadly, I don't have any ability to setup such a forum. But once it is there, I can help out. Also, I didn't see anything mentioned about the ability to have subteams with BOINC - am I wrong? If not, then that would be a pity as that would be a great way to bring in new groups to our team (instead of them being their own team).
30) Message boards : Cafe Rosetta : Oh Canada? (Message 17105) Posted 26 May 2006 by Tarx Post: Not yet - the last time the US tried "The offensive actions of the United States failed in every attempt to capture Canada." (HistoryCentral.com) Of course that was 1812! Might be a bit different now...
31) Message boards : Cafe Rosetta : Request from a journalist (Message 17011) Posted 24 May 2006 by Tarx Post: Well also probably too late, but still: How did you find out about the project? - Found out about it on the news, although did vaguely know about it as another medical DC. Why did you get involved? - I'm currently heavily involved in Folding at Home (FAH) (Protein misfolding research) DC project. That project has somewhat different goals & approach, but is somewhat of a competitor to Rosetta for volunteered CPU power. With FAH, I've launched two teams and recruited hundreds of people (with about 1000 active cpus currently) (people mostly new to DC) in the last year for that project. But not wanting to have "all the eggs in one basket approach", I decided to learn more about Rosetta DC projet to see if I will also start recruting for it. (So far so good!) Did you buy any new equipment to get into the project or did you just use existing computer hardware? - For this project no. My general recommendation for people is to use what they have, but keep their computers clean, make sure their cooling is adequate, and add more RAM if necessary. And beware energy costs if air conditioning is in use. What have you learned about biomedical research? - Hard to say. Did learn some so far, but only scratching the surface. What have you learned about computers? - Not much. Was already quite advanced. What have you gained from your participation in the project? - Some knowledge but as a fairly new member I'm still learning. And will need to learn a lot more before I could start recruiting for this project. Where do you live? - Canada What do you do for a living? - Computerized systems project engineer/manager How old are you? - in the 30s
32) Message boards : Cafe Rosetta : Oh Canada? (Message 17009) Posted 24 May 2006 by Tarx Post: Has anyone heard from the founder of our team "The Sailor"? Noticed that still contributing (88th in the team) - Rosetta@home member since 27 Sep 2005. (I will venture a guess that this is also the start date of the team). "Canadians doing their bit for the furtherance of science" Noticed that we are close to overtaking 2 teams in the next month (US-Distributed and Ars Technica)! With a bit more crunching we can have Phoenix Rising (currently 6th) and XPC (currently 5th) as a future target. And that will help shake off another team (Hardware Upgrade - Seti@home), that is currently on our threat list (ok, still many months away). Yes a bit of competition is always good! Anything to help the science/research/cure.
33) Message boards : Rosetta@home Science : CAN YOU HELP ROSETTA?? (Message 16916) Posted 23 May 2006 by Tarx Post: ...there are support groups, foundations, hospital areas, etc. for many of these - they usually have newsletters, websites, or even a board to put up flyers... I've had the same thought. But I am uncertain what the most effective way to reach these groups would be. Can you help? Also I'm concerned that since there presently is no direct work on a specific cure per se, I feel such a target audience is going to have a rather different perspective on the acceptable time to see results. I my mind, if we see results in 10 or 20 years I'll be very pleased. But unfortunately the folks in those support groups aren't generally using that size of time window. And so I didn't want to confuse the long term goal with their short term hopes for a cure. Approaching such groups would have to be done very carefully worded contact. Agreed - the long term nature of the work would have to be stressed. At this time, this is only a suggestion for those already affected (directly or in the family) that would often already be in contact with organizations. My help for recruitment for this project will be in another direction.
34) Message boards : Rosetta@home Science : CAN YOU HELP ROSETTA?? (Message 16911) Posted 23 May 2006 by Tarx Post: One area is if you or someone close to you are affected by one of the illnesses mentioned as part of the focus Rosetta (Cancer, HIV, Alzheimer's, Malaria, Anthrax, and "other" viruses), there are support groups, foundations, hospital areas, etc. for many of these - they usually have newsletters, websites, or even a board to put up flyers, etc. They might be interested in providing space for a blurb about this project. And if those running such an organization become involved in this project...
35) Message boards : Rosetta@home Science : Reasons some people avoid BOINC projects (Message 16909) Posted 23 May 2006 by Tarx Post:
36) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 16631) Posted 19 May 2006 by Tarx Post: Hmmm... I'm still wondering about Dr. Pande's post (that was put into the Wikipedia) "Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). ... Some people think FAH is all about structure prediction (which it is not -- that's Rosetta's strength) and some think Rosetta is about misfolding related disease (which it's not, that's Folding@Home's strength)." Is that accurate? And now also the additional concern (as linked to by Dimitris) noting that folding@home seems to be inefficient for its medical goals...?
37) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 16557) Posted 18 May 2006 by Tarx Post: Interesting second link there (not just the snip, but the whole thread as there are comments back & forth with the project leader). Sadly I can't say I understand most of the technical parts. The only thing I could do was a quick check on the comment about the papers and did see that although some of the papers are in physics or chemistry journals, there were also papers in "Journal of Molecular Biology", "Biophysical Journal", "Annual Review of Biophysics & Biomolecular Structure" among others (those sound like the right places?). So much of this discussion I don't really understand (not my field at all!). I did see that on their front page they mention "Your participation can help lead to a cure for these diseases." (such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes.) (I guess these are the "aggregation related diseases" mentioned). But that post makes it almost sounds like their aim is something else and their stated aim is more of a way to obtain sufficient computing power (with the side effect of perhaps some advancement in those diseases). Unfortunately there was no additional reply to that post from the project leader (there was aleady a few) so I can't tell if it was a dark secret, something irrelevant or they just got tired of being baited... And from the Rosetta FAQ "My research group is involved both in fundamental methods development research and in trying to fight disease more directly." - so is the main goal for Rosetta for medical research or to find ways to improve how to do research for future medical research projects? (Is there a smiley icon for confused? because I'd use a few right now!) Yeah, I'd realy like to know more!
38) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 16547) Posted 18 May 2006 by Tarx Post: Hi, I was looking at Wikipedia's entry for Rosetta and Folding @ Home. I noticed that Dr. Pande from the folding @ home project metnioned: "I know Baker and Ranganathan and their work very well and (like the rest of the protein community) find their work very important and impressive. However, Rosetta@home and Folding@Home are addressing very different problems. Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). Thus, those methods are not useful for the questions we're interested in and the diseases we're tackling (Alzheimer's Disease and other aggregation related diseases). Also, one should note that accurate computational protein structure prediction is still very challenging compared to what one can do experimentally, whereas the information obtained from Folding@home on the nature of folding and misfolding pathways matches experiment (eg with quantitative validation in rates, free energy, etc) and then goes beyond what experiment can tell us in that arena. While Rosetta has gone a long way and is a very impressive project, given the choice between a Rosetta predicted structure and a crystal structure, one would always chose the crystal structure. I bet that will be changing due to their great efforts, but that may still be a ways off for that dream to be realized. So, both are valuable projects IMHO, but addressing very different questions. I think there are some misunderstandings out there, though. Some people think FAH is all about structure prediction (which it is not -- that's Rosetta's strength) and some think Rosetta is about misfolding related disease (which it's not, that's Folding@Home's strength). Hopefully this post helps straighten some of that out. " (and a link mentioned "Yes, we've made quite a bit of progress on our methods and can now examine proteins on a considerably larger than we could some time ago") Is Dr. Pande comments correct, or is there more to it e.g. if the latest changes with Rosetta has increased the scope?
39) Message boards : Cafe Rosetta : Oh Canada? (Message 13641) Posted 13 Apr 2006 by Tarx Post: (And we've moved up in that few days to 10th position overall!)
40) Message boards : Cafe Rosetta : Oh Canada? (Message 13333) Posted 9 Apr 2006 by Tarx Post: Can we just create a thread or two for the team in Cafe Rosetta? Or is that frowned upon? We probably won't have enough posts to be worth creating a new forum. Adding to an existing team Canada forum on the other hand (if such exists), would be preferable.

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