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Michael H.W. Weber
Cruncher Germany Joined: May 22, 2005 Post Count: 11 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Well, as far as I understand, this project is aiming at improving protein crystallography techniques - although the information given here on how this shall be ultimately achieved seems rather scarce.
----------------------------------------It is clear that proteins involved in cancer have to be analyzed using crystallographic techniques, too. Hence, any method improving this technique will - among many other topics - also contribute to cancer research. But what is the direct relevance to cancer? I mean shouldn't this project better be re-labeled such that its name more accurately indicates what its major goal is? Or have I missed some important information? Michael.
President of Rechenkraft.net - This planet's first & largest distributed computing NGO. We make those things possible that supercomputers don't. Twitter contact.
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Is that not a little bit splitting hairs? If you visit the Princess Margaret Hospital website and everything around it, it breaths nothing but cancer involvement. The "Help Conquer Cancer" credo has long long existed. The HCC product is primarily aimed at better / faster cancer diagnosis, crucial, but the good thing is that the knowledge gained will benefit many other medical research. Any medical research project brings x-disciplinary information to surface, so think, with Cancer research funding behind, it's A Okay "Total Irre" with me.
----------------------------------------Ah ja, the main researches link states what he does and the owners are determining factor of a project name, not WCG! http://www.cs.toronto.edu/~juris/ cheers
WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 2 times, last edit by Sekerob at Nov 2, 2007 12:37:31 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello Michael H.W. Weber,
'Help Conquer Cancer' is a phrase that the Canadians have been using for years in their anti-cancer projects. It is not just this one computer project - - it is a whole theme. I suppose that we could accurately label this project 'Help Conquer Cancer - Protein Crystallography' . . . . but that is an unwieldy long title. Lawrence |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Well, as far as I understand, this project is aiming at improving protein crystallography techniques - ... Michael. Michael, Since I am motivated as much by a desire to understand the "nuts and bolts," of scientific research as by some abstract desire to increase scientific knowledge, I am also annoyed by these promotional gimmicks. They tend to confuse this retired lab tech. Heck, I only have a technical degree. When I studied biochemistry, back in the 70's, I was told that proteins were freeze dried into crystals, and then x-rayed. This liquid crystal stuff is new to me. Not that I understood anything about x-raying freeze dried protein crystals either! I would like to know what they mean by wanting to "improve the CrystalVision system to enable automated, accurate and fast crystallography image classification." I googled CrystalVision AND crystallography, and Google returned, among other things, a trademarked protein analysis system. Since the University Health Network does not indicate that CrystalVision is trademarked, it probably is not the same thing. ============ Does anyone know of a distributed computing team that consists of people with only one average computer that they turn off at night? That's about the only type of distributed computing team that I would join. I like to talk about WHAT I am crunching more than HOW FAST I am crunching. =========== Jack |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello stewjack,
----------------------------------------My introductory-level understanding of this project is that crystallizing proteins so that they can be analysed with X-rays is an art, or at best a craft. Grad students can spend a large part of their lab time in years of study trying to crystallize proteins. With luck, they will have crystallized several new proteins by the time they earn their degree. HWI ( Hauptman-Woodward Medical Research Institute in Buffalo, NY ) has established a high-throughput system that runs 1536 different experiments on a single protein. After gathering image data from these 1536 experiments over a period of a month, we are trying to analyse the images to classify the results in a way that will help a lab technician / graduate student decide whether or not to try to crystallize that protein and give hints on how to proceed with the lengthy and arduous task of developing a method to crystallize that protein. OCI ( Ontario Cancer Institute ) has picked out 9400+ proteins involved in cancer research that they would like to crystallize for further study. They have already been run through the HWI system and Blue Gene has reduced the data to a format that our application program can handle. Since these are early days for this type of research, we also get to help develop and verify the application program, which will help other scientists with their protein crystallization problems. Lawrence [Edit 1 times, last edit by Former Member at Nov 3, 2007 2:05:22 AM] |
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JmBoullier
Former Community Advisor Normandy - France Joined: Jan 26, 2007 Post Count: 3715 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Does anyone know of a distributed computing team that consists of people with only one average computer that they turn off at night? That's about the only type of distributed computing team that I would join. I like to talk about WHAT I am crunching more than HOW FAST I am crunching. Jack, that could be the start of an interesting discussion but in this thread that would be typically off topic. Therefore if you actually like to share views on this subject you should post your question in a new thread in the Chat Room section. See you there?. Jean. |
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Michael H.W. Weber
Cruncher Germany Joined: May 22, 2005 Post Count: 11 Status: Offline Project Badges: ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
Could someone please explain to me, how image analyses of (apparently non-optimally crystallized) protein crystals may help to improve crystallization techniques?
----------------------------------------Michael.
President of Rechenkraft.net - This planet's first & largest distributed computing NGO. We make those things possible that supercomputers don't. Twitter contact.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Michael,
Proteins consist of hundreds to thousands of atoms. Incompletley cryatalized proteins can give you parts of the structure. Enough partial images can give you a hint as to what conditions (Ph, solvent, vibration isolation, etc.) will give a better crystal. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Oops!
Sorry, geopsychic, but that is not so. The 1536 different experiments on each protein cover a wide range of pH and other factors. Knowing which ranges cause precipitates to form, especially micro-crystals, is a useful hint that could save weeks of lab time. Remember, each experiment runs for about a month because some crystals form slowly. Doing this all manually could take weeks of work spread out over an 18 month period. The idea is to speed up the processing, replacing lab time with cheaper CPU time. Lawrence |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
The project applies multiple image analysis algorithms to a set of over 100K images of crystallization experiments. Each of these experiments has been scored visually by multiple researchers and provides a gold standard training set including all the typical outcomes. The aim is to identify which or which combination of image analysis algorithms provide best agreement with the human classified images. Those algorithms will then be used to automatically classify >9 million other previous experiments and new experiments as they are conducted in realtime. With something like 9000 different macromolecules, many related to cancer, automated scoring of all the results along with the incomplete factorial sampling of chemical space may provide predictive techniques to crystallize samples. It may for example, be possible to identify subgroups of macromolecues that respond better to crystallization from crowding, e.g. with PEGs, or those that like conditions with salt in. Invariably the more important the sample, then the harder it is to get. A little predictive knowledge can go a long way in optimizing the techniques applied to the sample. Crystallization is still an empirical process as it is very difficult to predict how a biological macromolecule will crystallize without knowing it's three-dimensional structure (obtained from X-raying the crystal). Even knowing the structure it's hard to predict other crystallization conditions.
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