[World Community Grid] Nieuws updates

[priens]

*** UPDATE 04-APR-2007 *** HDC is klaar!! Nieuw project gericht op kanker komt eraan
*** UPDATE 20-DEC-2006 *** Nieuw project: Help Cure Muscular Dystrophy (Spierdystrofie)
*** UPDATE 17-NOV-2006 *** Nieuw project: Fiocruz Genome Comparison
*** UPDATE 16-NOV-2006 *** WCG bestaat 2 jaar
*** UPDATE 10-NOV-2006 *** Nieuwe projecten, resume HPF2
*** UPDATE 19-OCT-2006 *** WCG verzet 60.000 jaar werk!
*** UPDATE 12-OCT-2006 *** Diverse projecten, toekomst WCG
*** UPDATE 20-SEP-2006 *** Diverse projecten
*** UPDATE 19-SEP-2006 *** Diverse projecten
*** UPDATE 15-SEP-2006 *** FightAIDS@Home
*** UPDATE 12-SEP-2006 *** Help Defeat Cancer
*** UPDATE 21-JUN-2006 *** [rml]"[ World Community Grid] Update topic"[/rml]

-------------------------


Hieronder een quote uit de nieuwsbrief van World Community Grid.
Fase 1 van het Human Proteome Folding project is zo goed als afgerond en de eerste resultaten en gegevens beginnen binnen te komen.

Ook zie je dat Fase 2 op het punt staat om te beginnen, en wel deze maand nog!

Hou die pc's warm mensen. Hopelijk kunnen we weer wat members verwelkomen als de stampede voorbij is!

Voor de volledige nieuwsbrief: klikkie

Human Proteome Folding continues to yield important data
for disease research

By Richard Bonneau, Assistant Professor, Biology and Computer Science Departments,
New York University, Center for Comparative Functional Genomics

Work on the first phase of the Human Proteome Folding project is drawing to a close. Nearly all the calculations on World Community Grid are complete, and a team of researchers at the Institute for Systems Biology (ISB) is now working around the clock (partly due to the fact that the project involves researchers around the globe, and partly due to our drive to publish) to process the results and get them out to other researchers and the volunteer community that contributed so greatly to this project.

Our first publication of results will center on a model-organism -- yeast. Yeast has been a widely studied organism for over a century and due to this and the ease of working with yeast it has become a work-horse in biology. Much of what we know about molecular biology and the function of proteins was first discovered in yeast. For this reason yeast is called a "model-organism."

After we have debugged the process using yeast we will quickly release the remaining 100 organisms folded during the project. These databases will contain sequence-based analysis of the proteins, predictions about how the proteins are organized into domains, and structure and function predictions for the protein domains folded as part of this project.

While all this is going on, IBM is helping us to further model an important subset of the proteins as part of a second phase of the project that also will run on World Community Grid.

Phase Two
The proposed second phase of the Human Proteome Folding project will launch on World Community Grid in April 2006. The two main objectives are to: 1) obtain higher resolution structures for specific human proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta software structure prediction. Thus, the project will address two very important parallel imperatives, one biological and one biophysical.

The project will refine, using Rosetta software in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the project. During the first phase, we aimed to understand protein function. During the second phase, our goal is to increase the resolution of a select subset of human proteins. Better resolution is important for a number of applications, including but not limited to virtual screening of drug targets with docking procedures and protein design. The second phase of the project also will serve to improve our understanding of the physics of protein structure and advance the state of the art in protein structure prediction (helping us to further develop our program, Rosetta).

The project will focus on human-secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the proteins). The simplest example of a human secreted protein turned into a therapeutic is insulin; another example is human growth hormone. Understanding the function of human secreted proteins may help researchers discover the function of proteins of unknown function in the blood.

The project also will focus on key secreted pathogenic proteins. We are still in the early design phases of this part of the project, but we will likely focus on Plasmodium, the pathogenic agent that causes malaria. We hope that higher resolution structure predictions for the proteins that malaria secretes will serve as bioinformatics infrastructure for researchers who are working hard around the world to understand the complex interaction between human hosts and malaria parasites. While there are few silver bullets, and biology is one of the most complicated subjects on earth, we believe that this work will help us understand elements of this host-pathogen interaction or at least its components. This understanding could then be a foundation for intervention.

Lastly, this project dovetails with efforts at the ISB to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future). It is too early to say which proteins will end up being biomarkers, which are substances sometimes found in an increased amount in the blood, other body fluids, or tissues and which can be used to indicate the presence of some types of cancer. However, it is clear that many will end up being secreted proteins. As in the first phase of the project, the power of World Community Grid will be critical in getting results quickly to researchers in the biological and biomedical communities.

http://www.worldcommunity...ter/06Q1/viewHPFUpdate.do

[Voor 4% gewijzigd door priens op 04-04-2007 18:31]

[priens]

Goed bezig mensen! Fase 1a van het FightAIDS@Home project is compleet. Zoals je kan lezen staat 1b al in de startblokken (als het al niet gestart is). En zijn de voorbereidingen voor Fase 2 al in volle gang.
Reden te meer om je te blijven inzetten voor het goede doel!

Voor de volledige nieuwsbrief: klikkie

World Community Grid Completes First Stage of FightAIDS@Home

By Prof. Arthur J. Olson, Ph.D., Dr. Garrett M. Morris, M.A. (Oxon.), D.Phil. (Oxon),
Dr. William M. Lindstrom, Jr., Ph.D., & Alexandre Gillet, The Scripps Research Institute

World Community Grid has already achieved a significant milestone on FightAIDS@Home, completing Stage 1a of the project, which was launched in November, 2005.

The National Cancer Institute (NCI) maintains a database of chemical compounds, many of which are available as actual samples for testing in test tubes. There are some 230,000 compounds in all. Somewhere in this giant haystack of molecules, there might be one or more "lead" molecules for new HIV protease inhibitors. A "lead" molecule is one that is similar to a final drug, but must first be modified by medicinal chemists to make it less toxic or more soluble in water. The NCI constructed a subset of this database that is supposed to represent the chemical variety of all the molecules in the complete database. This subset consists of nearly 2,000 chemical compounds and is called the "Diversity Set".

All life and viruses have a genetic blueprint, or "genome," that consists of a string of DNA letters. In the DNA alphabet, there are only 4 letters, or "bases" as they are known: A, C, G and T. These letters, when written in a particular order create "genes," genetic instructions on how to build "proteins," the molecular machines of life. The genome of the Human Immunodeficiency Virus (HIV) consists of nearly 10,000 bases, which code for just 9 genes. The most commonly-occurring form of HIV is known as the "wild type" form. When HIV infects its target cells, one of its proteins that it uses to replicate its own genetic instructions makes mistakes, and this gives rise to many "mutant" forms of HIV. Some of these mutants happen to be more resistant to the drugs currently used to treat HIV disease. So it is vital that we discover new drugs that are more robust, that can defeat not just the wild type but also the drug-resistant mutant forms of HIV.

One of the 9 genes in the HIV genome codes for a protein called "HIV protease." A protease is a molecular machine that cuts proteins. When HIV replicates, it converts its genetic instructions into one long chain of proteins, but for the virus to mature properly, it must cut the long "polyprotein" into separate proteins. If we block the active site of the protease with a small molecule, a bit like a key fitting into a lock, we can stop the virus from cutting the polyprotein, and thus prevent the virus from maturing into an infectious virus. This is exactly how clinically approved protease inhibitors work.

Stage 1a involved virtual screening of the 2,000 or so compounds in the NCI Diversity Set against 270 wild type and mutant HIV proteases to discover potential new leads and ultimately new drugs. We have analyzed the results for the wild type and have confirmed that our "positive controls" (molecules that we know bind to HIV protease) do, in fact, bind the most tightly to the wild type form of HIV protease, which verifies that the virtual screening is working. These include clinically-approved HIV protease inhibitors such as Indinavir, Saquinavir and Ritonavir, which are currently prescribed to HIV-infected patients. We have ranked the results from our virtual screening and will be presenting the best anti-HIV protease compounds from the NCI Diversity Set to our synthetic chemists so they can incorporate these "lead" molecules into the design of even better inhibitors than the clinically-approved drugs.

The next step is Stage 1b, where we will be screening 230,000 compounds -- the entire NCI database -- against just wild type HIV protease. This will allow us to validate not only the results of Stage 1a, but also the methodology of screening a diverse subset of a larger database against a target. We may discover new compounds against HIV protease, which we could not have found using just the Diversity Set.

We also are preparing Stage 2, which will involve screening virtual libraries of compounds designed in conjunction with our collaborating synthetic chemists against the broad panel of 270 wild type and mutant HIV proteases, again to find new protease inhibitors that work against more than just the most common form of HIV protease. Additionally, the top hits from Stage 1b will be investigated in more detail against this broad panel of 270 targets.

We are very pleased with the insight that we have gained thus far, which could not have been accomplished in the absence of World Community Grid. Thanks to the more than 170,000 volunteers donating their computing time, we have been able to do more than 2 quadrillion calculations, many of which are far more advanced than we have been able to do previously.

http://www.worldcommunity...er/06Q1/viewFAAHUpdate.do

[Anoniem: 98414]

[/offtopic] Je zou haast medelijden krijgen met Alexandre. Geen prof. of dr. Geen tweede initiaal, zelfs niet eens een Oxon of junior......

[Pim.]

Even de draadjes samengevoegd om het overzichtelijk te houden.
Leuk om te horen dat er resultaat wordt geboekt !!

[InSPiRE]

Goed om te horen! Thanks voor de updates. Blijf ze vooral plaatsen in dit topic.

[Jis]

Kijk dat zijn nog eens goede berichten. Dat je met je peeceetje misschien dan ook echt betere medicijnen kunt uitrekenen... je doet het er natuurlijk ook voor, maar als het daadwerkelijk resultaten oplevert is dat toch wel supercool toch

[priens]

http://www.worldcommunity...cg/viewthread?thread=7613


Sometime this afternoon, we will have sent out the last new work units to process for the Human Proteome Folding (HPF1) project. I'm not certain whether the UD or Boinc side of the grid will reach that point first. However, this means that agents looking for more HPF1 work will not get more after this time. Those agents set to only contribute to HPF1 and those which do not meet the minimum hardware requirements for other projects will indicate that they are "Paused" in the lower part of the UD agent window. You should let agents still working on HPF1 finish their current work unit. If for some reason not enough agents return a result for a specific work unit in the next days, a few more copies of those may be issued. But, otherwise new HPF1 work will not be scheduled.

This represents a monumental computing accomplishment and we thank the entire membership for your generous contribution. This has brought valuable data and possibilities into the horizon of the scientist's plans, which would have been ruled out as completely impractical before you all came along to help. The next steps are a lot of post processing of the result data, populating the results database, writing papers, etc. Dr. Rich Bonneau will fill you in on progress with all of this.

Thanks again for all of your crunching. We will be launching HPF2 very soon and several other very exciting projects. In the meantime the FightAIDS@Home project is still processing a mountain of work so keep those machines crunching. Thank you!

[priens]

*** HELP DEFEAT CANCER ***

Update door "djf" Help Defeat Cancer Scientist

Thanks to the outstanding technical team at IBM the Help Defeat Cancer project is unfolding as planned. When the project was first launched in July the biggest challenge for our research team at The Cancer Institute of New Jersey (CINJ) was how to keep generating enough work units to keep up with the rate at which they were being processed. We are constantly performing quality control assessment on the results that are sent back from World Community Grid and have been quite pleased with the results so far. In a few weeks we will be varying some of the experimental conditions used for analyzing the cancer specimens and comparing those results with those obtained using the first set of conditions in order to optimize the sensitivity of the calculations.

Eventjes een kleine samenvatting van de rest: FightAIDS@home loopt ook nog steeds goed. Onlangs heeft het HPF1 ingehaald qua project met het grootste aantal CPU-tijd.
HPF2 is nog steeds in bèta fase. Het schijnt dat de grootste problemen onder controle zijn en we binnenkort weer verder kunnen met dit project.
Ook schijnt er een nieuw project aan te komen. Waar dit project zich op gaat richten is nog onbekend, het zal nog wel even duren voordat het zal starten. Al wel is bekend dat dit project niet zulke enorme systeemeisen stelt als het HDC project (750MB RAM). Dus dit is ook weer voor iedereen (lees: de niet-tweaker ) toegankelijk.


Verder hebben we IEDERS hulp hard nodig: XtremeSystems staat namelijk op het punt ons in te halen!!! Over een week is het zover en kunnen wij in het stof bijten!
Iedereen die nog wat GHz-jes over heeft, deze graag doneren aan WCG en je natuurlijk aanmelden bij het team!
Buiten het feit dat we XtremeSystems zo lang mogelijk moeten voorblijven is WCG een uitstekend project met goede doelen dat goed ondersteund wordt door wetenschappers en moderators op de forums. Give it a try...

[Voor 5% gewijzigd door priens op 12-09-2006 21:12]

[priens]

Update door "mgl1" FightAIDS@Home Scientist

Experiment #1 which was our initial screen of the NCI diversity set against 270 protease variants has been analyzed and the first cut at promising leads was identified. We selected the top 40 of these compounds and ordered them from the National Cancer Institute. They arrived yesterday and they have been delivered to our collaborators here at Scripps for experimental assay. They will first be assayed against wild-type HIV protease. Subsequently they will be tested against a number of HIV protease mutants that are available. We anxiously await the first results from these assays.

Thanks to all of you who have helped bring us to this point.

Art Olson

[priens]

Daar gaan we weer. Er wordt een tipje van de sluier opgelicht wat betreft nieuwe projecten. Het ziet er naar uit dat we een grotere diversiteit aan projecten gaan krijgen!

Door: "Didactylos" - Community Advisor:

There are a number of new projects in the pipeline.

The first will be a relaunch for HPF2.

The projects under consideration include ones like those we are doing now (drug and disease related, heavily focussed on human biology) and completely different projects based in other humanitarian areas of research.

By the end of next year, I fully expect WCG to cover all the main areas of research that so many of us have discussed. And maybe some we haven't even considered.

No details, though. Don't want to raise false expectations. However, if you want a bit of advance warning, why not sign up for the beta program?

[priens]

En alweer één. Zo hoor je een paar maanden niets, zo heb je er 4 te pakken in een week.

Alweer een tipje van de sluier. De 2 eerstvolgende projecten na de re-launch van HPF2 zullen niet uit de US of de UK komen voor de verandering:

Door: "lawrencehardin" - Community Advisor:

Timing for future projects is uncertain. The debug process for HPF2 is an obvious example of why we do not announce future project schedules. Right now, it looks as though the next 2 projects after HPF2 will both be from non-English speaking countries, so next year the World Community Grid should be justifying the World in its title. Translating the web site into Chinese, Japanese and Spanish is slipping into next year while we work on getting new projects ready.

We have a lot coming along!

[priens]

Een tweetal zaken van de WCG-forums. Het blijkt dat één van de twee nieuwe projecten zich gaat richten op spierdystrofie. Maar ze zijn nog maar in de beginfase van de ontwikkeling.

Verder wordt duidelijk gemaakt dat WCG een heel breed platform gaat worden voor heel diverse projecten.
Dus niet alleen medische, maar humanitaire projecten in het algemeen, zoals:
- klimaat modellen
- seismische modellen
- oogst modellen
- medische en moleculaire biologische projecten
- andere projecten die in het voordeel kunnen zijn van de mensheid.


Door: "Didactylos" - Community Advisor:

Okay, then. First, if all goes to plan, Human Proteome Folding Phase 2 will be relaunched. Then, WCG will diversify a little :-D

The pipeline should keep us busy for some time to come, and looking even further ahead there are other projects in the early planning stages that will hopefully be hosted by WCG.

Remember, project areas welcomed by WCG includes climate modelling, seismic modelling, crop modelling, and medical or molecular biology projects. Other types of projects are fine, too - so long as they are demonstrably humanitarian.

Door: "lawrencehardin" - Community Advisor:

...
No time table yet. This refers to a French Muscular Dystrophy project. I mentioned in an earlier post that our next two projects come from non-English speaking countries. This is one of the two. It is a Fortran program, so we will have to develop a library of subroutines for boarding Fortran projects.

By now we are working up a large backlog of things to do: BOINC Simple GUI, BOINC Account Manager, website statistics, website HTML, Spanish, Chinese and Japanese language support, HPF2 debug. Vista is coming. The most recent approved version of BOINC supports compression, but we cannot start compressing everything on the BOINC server until our members upgrade to it. The next version of BOINC is expected to support CPU throttling.

Still, our priorities are plain. Projects are our mission. Everything else is simply a nice frill that we hope our members will find helpful. It is hard to guess just when something will be ready. In the case of the Muscular Dystrophy project, we are barely begun.

Lawrence

[Anoniem: 167389]

(de)Priens is eigenaar van dit draadje, dus hij mag de index in de 1e post updaten.......waarom dus:

Heden 17 oktober 2006, ergens tussen 12:00 UTC en 18:00 UTC heeft WCG 60,000 Computer jaren bijeengegraast. Hier een grafiekje in mekaar geflanst hoe dit tot stand gekomen is...elk kleurtje in het lijntje representeerd een maand....oktober is maar 17 dagen dus dat ziet er nu nog vreemd uit.....eind van de maand staat ie hopelijk recht overeind ;>)

Waar we al weken tegen aan zitten te hikken is 50,000 dagen CPU tijd binnen 24 uur..... vorige week misten we het met elf dagen, en vandaag hangt het wederom om....we zien morgen vroeg of het bewaarheid is.

buonanotte

[Anoniem: 167389]

En hier nog een geflanste grafiek na correctie ref de Gregoriaanse telling der tijden in Anno Domini

[Anoniem: 167389]

En hier de laatste..... hoe de verdeling ligt van de projecten bij de World Community Grid na 60,000 jaar crunchen.......volgende milestones 25 miljoen dagen en 250,000 members (rond Kerst - Epifanie):

[Voor 3% gewijzigd door Anoniem: 167389 op 20-10-2006 09:01]

[priens]

Zo, weer een hoop nieuws van het front. Er zit zeer binnenkort een nieuw project aan te komen waarvan nu de beta-tests zijn begonnen. Dus beta-testers... opgelet. Waarschijnlijk is dit het project voor spierdystrofie zoals in een eerdere post te lezen is.

Verder wordt door een Admin genoemd dat er op dit moment 2 projecten zijn die in de laatste fase zijn voordat ermee gestart wordt en dat er voor volgend jaar nu al 6 (zes ja, je ziet het goed !) andere projecten in de wachtrij staan. Dat belooft dus nog wat!

Ook nog een update over Human Proteome Folding - Phase 2 dat onlangs weer gestart is.

Zie hieronder voor wat quotes van het WCG-forum.

Door: "knreed" - World Community Grid Tech:

We have just started a beta test for an upcoming project. At this time we are not providing any details about the project other then to say that if all goes well with the beta test this project should be launching soon.

If you notice, the graphics do not show anything. This is intended as to not reveal details about the project.

Thank you for your participation. Your willingness to help us beta test these applications helps us have a smooth launch!

Door: "bbover3" - World Community Grid Admin:

(...)
BTW, When comparing World Community Grid to Seti@Home or Folding@Home, don't forget the big difference between the grid..... Other grids only run one research project while we run multiple projects for a variety of research organizations. This keeps the small team we have very busy. We currently have 3 active projects, are close to starting two more, and have 6 in our queue for next year.

We will do our best to provide some of the nice-to-have features that members have been asking for.

Door: "rbonneau" - Human Proteome Folding Scientist:

warning the following has only been edited by sleep deprived people ... my wife and I just had a kid ... so that's areason for my lapse in the forum ... but not an excuse ...

Please take a look at our collaberators websites, and see for yourself what they are doing, for those of you who don't want to read all this below, tha basic idea is that the higher res structure predictions will be part of how we provide bioinformatics support (along with other bonneau-lab activities) to these labs.

Disease relevant areas of focus for HPF and HPF2: Three Specific Collaborations Centered on Annotating Disease Related Proteins enabled by HPF2.
Here we detail three of our main efforts to get the information resulting from the grid into the hands of groups working on disease. In each case the our lab has begun to put together tools and databases to suit the specific needs of these three research efforts. In general HPF and HPF2 are providing vital bioinformatic support, helping these groups to understand the structure and function of proteins central to their research efforts. We encourage you to explore the websites of each of these three groups to learn for yourself more about their efforts.
These collaborations will inform our development of tools for integration of organism-specific information with our structure-prediction-derived information. We describe the efforts ongoing in these three labs and then go on, in each case, to describe how this project will interface with these efforts in terms of anticipated development of tools and prioritization of aims and development required by each specific effort. This work is being carried out in collaboration with Lars Malmstrom, in the Goodlett lab (Medicinal Chemistry Dept., University of Washington). In each case we describe a collaboration that explains why we have asked you to fold these proteins. Each collaboration corresponds to a set of proteins in the HPF2 queue.

Protein Set #1: Malaria proteins.
Collaborator: Patrick Duffy, Paul Shannon, Seattle Biomedical Research Institute, Seattle, http://www.sbri.org/research/duffy.asp
The Duffy lab aims to create a pregnancy malaria vaccine. In 2003, Dr. Duffy and a consortium of laboratories launched the Pregnancy Malaria Initiative to identify the necessary antigens for a malaria vaccine to protect women during pregnancy. They are using bioinformatics, microarray and proteomics tools to characterize the distinct features of these parasites and evaluate parasite surface proteins that may be developed as pregnancy malaria vaccines. The proteins identified by the consortium are now being assessed by the Human Proteome Folding project (HPF2), in order to understand their function and structure so that vaccine designs can be improved. Using the paradigm established in their studies of pregnancy malaria, the Duffy lab has also launched a program to develop vaccines against severe childhood malaria. With support from the Grand Challenges in Global Health (GCGH) Program, an international consortium led by the Duffy lab is now trying studying the immune responses that protect African children from severe malaria. African children may only suffer one or two episodes of severe malaria before developing resistance, and earlier studies showed that antibody purified from the serum of immune adult Africans could cure young children with malaria. The consortium is thus identifying parasite proteins that may be targeted by protective antibody, as a key step in developing vaccines for children. As part of the Human Proteome Folding project we are working with the Duffy Lab to dramatically improve their ability to annotate many of proteins they have recently found to be important to Plasmodium and its specific interactions with its host.

Protein Set #2: human cancer biomarkers of unknown structure and function.
Collaborator: Leroy Hood, Nathan Price, Institute for Systems Biology, Seattle, http://www.systemsbiology.org/
Multiple groups involved at the Institute for Systems Biology are currently involved in a coordinated effort to characterize biomarkers that can be used for early diagnosis and sub-classification of Human cancers. In particular specific efforts are underway in the Laboratory of Leroy Hood to find prostrate, bladder and ovarian cancer biomarkers. This effort coordinates proteomic, microarray, pathology, and bioinformatics efforts into a overall effort to determine reliable and readily assayable predictors that can be used as markers for diagnosis and selection between alternate therapeutic/intervention regimes. The Bonneau and the worldcommunity grid lab are involved in the functional annotation of putative proteins and proteins of unknown function found in these studies. To date several hundred putative biomarkers of unknown function have been prioritized, and are being processed along with the other sets of proteins described above, on the world community grid. Along with Nathan Price, at the ISB in Seattle, the Bonneau lab has been applying structure based annotaiton to elucidate the structure/function of putative biomarkers discovered using these genome-wide screens.

Protein Set #3: Gram-negative pathogens.
Collaborator: David Goodlett; University of Washington, Seattle: http://goodlab.mchem.washington.edu/
: Dave Goodlett’s laboratory has used Francisella tularensis subspecies novicida (strain U112), a murine pathogen, as a model to study virulence in Francisella tularensis, a human pathogen. Both organisms are extremely virulent to their respective hosts causing high morbidity/mortality if left untreated by antibiotics. Like familiar Gram-negative bacteria, such as Yersinia pestis, F. tularensis is a class A agent. Our (Bonneau lab) primary roll, so far, has been to carry out genome annotation for the most difficult proteins in these gram-negative pathogens using our structure-inclusive pipeline.
The Goodlett lab was able to verify that many proteins in these genomes with no homology to other genomes are actively expressed at different conditions, increasing our interest in applying the described methods to these genomes. U112 strain genome consists of a single circular chromosome of 1,910,031 bp (32.48% GC) compared to previously sequenced F. tularensis SchuS4 strain with 1,892,819 bp; ~ 350 Kb of genome is unique to U112. Among other findings U112 has a single copy of the pathogenicity island sequences versus two in SchuS4 and significantly more complete metabolic pathways. Database search of tandem mass spectra detected 65.4% of predicted genes as expressed proteins with false discovery rate of < 0.01% using a mock database. In combination with genome annotation ~ 80% of genes are predicted to be expressed. Of predicted genes ~ 30% had no homology to genes encoding proteins of known function preventing corroboration of their authenticity. However, observation of gene products validated authenticity of > 50% of these hypothetical genes representing 23.2% of all expressed genes; no pseudogenes observed. Finally, we are using Rosetta de novo, fold recognition and homology-modeling to predict structure and infer function for many genes of unknown function.

more in a few weeks,
Rich

[Anoniem: 167389]

WCG is 2 jaar op de kop af en hier de projecten in beeld:


PS het "Upcoming Project Beta" wordt spoedig hernoemd en overeenskomstig, de graph automatisch aangepast. Voor "full view", dubbel klikken.

[priens]

*** NIEUW PROJECT: Fiocruz Genome Comparison ***

Jaja, het zat er alweer een tijdje aan te komen. WCG heeft er weer een nieuw project bij: Fiocruz Genome Comparison
Wil je een exacte uitleg over dit project, ga dan naar de bovenstaande link of naar deze site.

Dit project is ook zeer geschikt voor oudere pc's, want de systeemeisen zijn erg interessant:

* At least a 160MHz Intel Pentium™ processor or equivalent
* At least 60 MB RAM (with virtual memory enabled)
* At least 25 MB free disk space available for use by the project (in the agent install directory)
* The ability to display 8-bit graphics at 800x600 resolution
* An Internet connection with minimum 40 kbps speed
* Operating System: Windows 98, ME, 2000 or XP

Da's een welkome afwisseling nadat HDC kwam en 200MHz, maar wel 750MB RAM vereiste!

Op dit moment zijn er dus vier actieve projecten:
- FightAIDS@Home
- Help Defeat Cancer
- Human Proteome Folding, Phase 2
- Fiocruz Genome Comparison

Door: "Viktors" - World Community Grid Tech:

World Community Grid is pleased to launch the Genome Comparison project by Fiocruz in Brazil. This project will perform a pairwise comparison between all predicted proteins in complete genomes available in the public DNA databases. When scientists study a new protein, they look for similar, better-understood proteins as a guide to their function. This in combination with other information will help annotate these genomes leading to faster and better understanding of cellular function and infectious agent relationships. For more detailed information and frequently asked questions (FAQs) about the project, please press the Research button in the upper navigation bar or click here.

In addition to providing information about this project, we have created a forum for discussions about the Genome Comparison project. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title "Fiocruz Genome Comparison Scientist" are authorized to comment as representatives of the research organization: Fundacao Oswaldo Cruz (Fiocruz).

The Genome Comparison project is one of four projects running on World Community Grid. In addition there is FightAIDS@Home, which has been running on since November of 2005, Help Defeat Cancer, which has been running since July of 2006, and Human Proteome Folding Phase 2, which was recently restarted on World Community Grid. For more detailed information and FAQs about each of these projects, please press the Research button in the upper navigation bar or click here. We thank all of our members for all of their valuable contributions to the projects to date and hope you will continue to help us process those as well as this latest project.

Because there are four research projects running on World Community Grid, your grid agent could receive work units from any of the projects. You may elect to focus your computer's time on only particular projects, if you have a preference. To do so, press the My Grid button in the upper navigation bar and select My Projects or click here.

If you are already a member of World Community Grid, there's nothing that you have to do to prepare for the Genome Comparison project. The next time your grid agent communicates with the servers, it will send you a work unit from one of the projects at random for which your machine meets the minimum requirements and according to your project participation elections. To know which project you are running, please double-click on World Community Grid icon (or BOINC Manager icon if you are running BOINC) in the system tray, and you will see the title of the project in the display.

If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the Help section of the website, (2) Review the forums to see if anyone has asked/answered the question that you have, (3) Ask the question in an appropriate World Community Grid forum found here and a Community Advisor or a more experienced member will provide an answer, and (4) Send an email to the support desk from the Contact Us link found at the bottom of every page of the website.

We thank you for running the Fiocruz Genomic Comparison project.

En een warm welkom door een nieuwe project scientist:
Door: "wdegrave" - Genome Comparison Scientist:

elcome to the “Genome Comparison” project. Your contribution will provide valuable information to researchers around the world, studying proteins function and their roles in disease processes while also contributing to discoveries in medicine and biology. The project is finding, in a consistent and comprehensive manner, all possible similarities between predicted proteins from all of the known genome sequences decoded to date. We thank all of the members of World Community Grid for their valuable contribution to this exciting project form Brasil.

[priens]

*** NIEUW PROJECT: Help Cure Muscular Dystrophy *** Een project voor Spierdystrofie.

En het vijfde actieve project bij WCG is een feit. Op dit moment is er dus meer dan genoeg te kiezen, namelijk:
- FightAIDS@Home
- Help Defeat Cancer
- Human Proteome Folding, Phase 2
- Fiocruz Genome Comparison
- Help Cure Muscular Dystrophy

Helaas voor ons (want de meesten hier gebruiken BOINC) draait dit project alleen op de oude UD client. En wel omdat Phase 1 van dit project waarschijnlijk maar 2 maanden duurt. Hierna worden de resultaten geevalueerd en wordt Phase 2 gestart die uiteraard gewoon op BOINC draait en ook veel langer duurt.

De minimum systeemeisen zijn ook weer lekker licht:
- 550MHz Pentium of gelijkwaardig
- 60MB RAM
- 25MB Harddisk ruimte

Hieronder een korte introductie. Meer is hier te lezen.

World Community Grid and researchers supported by Decrypthon, a partnership between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research) and IBM are investigating protein-protein interactions for 40,000 proteins whose structures are known, with particular focus on those proteins that play a role in neuromuscular diseases. The database of information produced will help researchers design molecules to inhibit or enhance binding of particular macromolecules, hopefully leading to better treatments for muscular dystrophy and other neuromuscular diseases.

What is neuromuscular disease and muscular dystrophy?
Neuromuscular disease is a generic term for a group of disorders (more than 200 in all) that impair muscle functioning either directly through muscle pathology (muscular dystrophy) or indirectly through nerve pathology. Most of them are rare (affecting less than one person in 2,000), have a genetic origin (80%) and affect both children and adults. These chronic diseases lead to a decrease in muscle strength, causing serious disabilities in motor functions (moving, breathing etc.). Disease expression is variable; some disorders are progressive, while others remain stable for several years, and the same disease can cause different symptoms from one person to the next.

Despite advances in therapeutic techniques, there is currently no curative treatment available for persons affected by neuromuscular diseases.

Door: "Viktors" - World Community Grid Tech:

World Community Grid is pleased to launch the Help Cure Muscular Dystrophy project for Association Francaise contre les Myopathies (AFM) in Paris, France. In order to understand how proteins perform their necessary functions in living cells, a better and more detailed understanding of function and protein-protein interactions is required, to ultimately help researchers to design therapeutic strategies. Your contribution will provide valuable information to the research that is part of the Decrypthon Program. Eventually your contribution will benefit all researchers working on many genetic diseases, particularly neuromuscular diseases. The ultimate hope is that this will help scientists develop innovative therapies that will lead to treatment for the vast majority of neuromuscular diseases, including Muscular Dystrophy. For more detailed information and frequently asked questions (FAQs) about the project, please press the Research button in the upper navigation bar or click here.

This project is slightly different than most of our other projects in that what we are launching is only Phase 1 of a larger project. We anticipate that Phase 1 will run for approximately 2 months. Then the researchers will examine the results in preparation for running Phase 2, which will run for a significantly longer period of time. Early estimates are that Phase 2 may start around August of 2007. Because Phase 1 runs for such a short time, we did not expend the resources required to run the project on both the UD and BOINC platforms. Thus, we are running Phase 1 using only the UD agent and will run Phase 2 on UD and BOINC. We know that this may disappoint some members who run BOINC but we hope that you can understand that preparing the software for a project takes two to three months and when the project (Phase 1) is only 2 months long, it doesn’t make sense to run the project on all platforms.

In addition to providing information about this project, we have created a forum for discussions about the Help Cure Muscular Dystrophy project. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title "Help Cure Muscular Dystrophy Scientist" are authorized to comment as representatives of the research organizations for this project.

The Help Cure Muscular Dystrophy project is one of five projects running on World Community Grid at this time. The other projects include FightAIDS@Home, which has been running since November of 2005, Help Defeat Cancer, which has been running since July of 2006, Human Proteome Folding Phase 2, which has been running since October of 2006, and Fiocruz Genome Comparison, which has been running since November 17, 2006. For more detailed information and FAQs about each of these projects, please press the Research button in the upper navigation bar or click here. We thank all of our members for their valuable contributions to these projects and hope you will continue to help process all five projects.

Because there are five research projects running on World Community Grid, your grid agent could receive work units from any of the projects. You may elect to focus your computer's time on only particular projects, if you have a preference. To do so, sign into the site and press the My Grid button in the upper navigation bar and select My Projects or click here.

If you are already a member of World Community Grid, there's nothing that you have to do to prepare for the Help Cure Muscular Dystrophy project. The next time your grid agent communicates with the servers, it will send you a work unit from one of the projects at random for which your machine meets the minimum requirements and according to your project participation elections. To know which project you are running, please double-click on the World Community Grid icon (or BOINC Manager icon if you are running BOINC) in the system tray, and you will see the title of the project in the display.

If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the Help section of the website, (2) Review the forums to see if anyone has asked/answered the question that you have, (3) Ask the question in an appropriate World Community Grid forum found and a Community Advisor or a more experienced member will provide an answer, and (4) Send an email to the support desk from the Contact Us link found at the bottom of every page on the website.

We thank you for your run time contribution to the Help Cure Muscular Dystrophy project as well as all of our other projects.

En natuurlijk zijn nieuwe members altijd welkom!
[World Community Grid] hitparade van week 51

[priens]

Eindelijk weer wat nieuws van het front:

Help Defeat Cancer zit erop!!

World Community Grid is pleased to announce that the Help Defeat Cancer (HDC) project is finished. The last work units have been sent out and when the final results are returned, the project will come to an end. This project, which launched on July 20, 2006, will have run for just over 9 months by the time the last results are returned. During this time 88,000 members will have donated 2,900 years of computer time on 138,000 different computers. This is a significant contribution to cancer research.

But the end of this project is really only a beginning. Based on the results, the researchers who are working on this project have a very aggressive plan to make Tissue Microarray technology an integral part of early cancer detection. World Community Grid's team will keep in close touch with the research team and will post updates on the website in the Research pages. The researchers will also continue to update their HDC website with exciting updates about this project and the inroads it is making on cancer research.

On behalf of the research staff at the University of Medicine and Dentistry of New Jersey, World Community Grid's team wish to express our thanks to you for contributing your PC power to this project. With your contribution, this project was completed in a fraction of the time it would otherwise have taken.

Maar er is meer nieuws... Een nieuw project dat zich op kanker gaat richten is alweer in aantocht:

We also want to inform you that World Community Grid has started work on a new cancer project to discover ways to accelerate the crystallization process used in studying cancer protein structure using X-ray Crystallography, which will help researchers identify proteins involved in cancers and lead to new drug therapies and cures. We plan to launch this new cancer project in the May/June 2007 time frame. You will receive more information on this project prior to the official launch date.

Bron: WCG Mail


Er gebeurt dus nog vanalles. Uiteraard zijn de andere projecten ook nog actief, dus werk genoeg voorlopig.
Kom eens langs in onze hitparade en join als je nog wat CPU-power over hebt!

[Anoniem: 167389]

17-aug-'07 WCG annonceert BOINC migratie / uit-fasering van de oude en niet onderhouden UD agent

25-sep-'07 WCG verlengt de duur van individuele taken (meer stappen/pogingen per opdracht)

03-okt-'07 Website update en Circulatie van WCG Volume 5 Newsletter per email

10-okt-'07 Nieuwe versies van FightAIDS@Home en Discovering Dengue Drugs - Together projecten

[Mobster]

D'r was dus al wel een topic! Had ik zelf ook even naar kunnen zoeken natuurlijk

Goed bezig Sekerob! Nu eens kijken of we de boel een beetje centraal kunnen houden!

[Anoniem: 167389]

Zet maar in je agenda:

• Help XXXXXX Cancer, +/- Nov 1 technische lancering (This project does not have any excessive resource requirements.) http://www.pmhf.ca/ (de project naam staat hier voluit op de voorpagina, eventjes.... een database 86 miljoen kanker samples in X-Ray.Chrystallography voorbewerkt op IBM's Blue Gene). 5 November is de PR launch.
• Discovering Dengue Drugs - Together phase 2, ergens H1-08 (parallel met DDDT-phase 1). Gebruikt CHARMM ipv AutoDock.
• Help Cure Muscular Dystrophy phase 2, ergens laat H1-08

Geen datums,

• gericht Malaria,
• Cholera(?),
• Rijst Modelling,
• Kanker Spectrometry (net als het goed afgesloten Genome Comparison uit Fiocruz),
• AfricanClimate@Home phase 2, een misschien en hangt of van de eerste 27 14 dagen simulatie die thans in voortgang is.
en
• nog een rits *proposals* die verwacht worden, op basis van info aanvragen *inclusief* nog een voor Kanker.

• Het Help Defeat Cancer, midden dit jaar afgesloten, heeft een zeer grote funding gekregen op basis van resultaat om nog meer in die richting te onderzoeken....potentieel dus nog een project.

• FA@H en HPF2 beiden zeker tot eind 2008 en mogelijk met nog meer experimenten, 2009

LET OP: ALLE NIEUWE PROJECTEN ALLEEN OP BOINC!!!!!

De kalender in overvol, dus laat die quads maar komen.

[Voor 30% gewijzigd door Anoniem: 167389 op 24-10-2007 09:57]

[scorpionv]

Kijk eens, november 1st een nieuw Cancer project, daar doe ik het een beetje voor als oud UD-er

[Wolfje666]

Idd, datwas de reden van overstap naar WCG na het stoppen van UD.

[Anoniem: 167389]

Beta te verwachten voor het komende HCC project op donderdag/vrijdag Oct.25/26, als er geen spaak in het wiel gestoken wordt.

[Anoniem: 167389]

Waarom ze dat altijd laat op vrijdag moten doen weet ik niet, maar hier is de verwachte Beta annoncering:

Beta Testing starting for a new project

We have just started a beta test for an upcoming project. At this time we are not providing any details about the project other then to say that if all goes well with the beta test this project should be launching soon.

If you notice, the graphics do not show anything. This is intended as to not reveal details about the project.

The validators and assimilators will be added over the next few days as they are fully tested.

Thank you for your participation. Your willingness to help us beta test these applications helps us have a smooth launch!
----------------------------------------
[Edit 1 times, last edit by nelsoc at Oct 26, 2007 10:31:15 PM]

De WCG website was vandaag diverse malen uit de lucht wat altijd een teken is dat er aanpassingen worden gemaakt om het nieuwe project in te passen.

[Anoniem: 167389]

Voor wie een beetje gheil is op veel resultaten per dag of gewoon kort gras fijn vind, het Discovering Dengue Drugs - Together project is naar 1 uur batches geSwitched (gemiddelde target). Rapporten komen binnen dat snelle machines ongeveer in 30-35 minuten door een werk-plag grazen.

Faster New Batches of Work

We have loaded in some new batches of work for Discovering Dengue Drugs - Together (DDD-T). We released 100 of them to start out with and those have an average runtime of 54 minutes with about half of the work units validated. We estimate the work units will run about an hour on the average machine. These shorter work units start with the numbering sequence 0201. Also, with these new work units the target molecule is different then the previous target for 0101 batches.

-Uplinger
[Oct 25, 2007 4:39:25 PM]

[Anoniem: 167389]

Heard it thru the grapevine

Re: Help Conquer Cancer Project Launch

Everything is ready for the Help Conquer Cancer (HCC) project launch. We're scheduled to start the launch at 10am eastern time (USA) tomorrow, November 1, 2007.

Unfortunately it will not launch with Mac. There seems to be an issue with the new Mac operating sytem (Leopard). Viktors will post something in the Known Issues forum later today.

Dat zal wel rond de 14-15 uur CET worden voordat het website geupdate wordt en het werk de feeders in gaat... je zal hier dus geen woord over op WCG vinden (vette ) Als 'All Projects' niet aanstaat, zal de Device Profiles en of My Projects bezocht dienen te worden ingeval het niet automatisch toegevoegd wordt.

Let op dat Leopard ook voor AC@H verkeerde resultaten aflevert en daarom op Mac is stilgelegd.

Re: AfricanClimate@Home Intel Mac Comparison Problem
There appear to be very slight differences in the computation results on Mac's running the new Leopard operating system compared to the older versions. Thus our result validation check is failing. We are working on a way to fix this and will then resume running this project on the Mac platform. Sorry for any inconvenience.

Het probleem in het quorum is dus Mac OS X 10.4 en eerder versus 10.5. Heeft het iets van doen met 32 bit en 64 bit mix?

Tenslotte: Een nieuwsbericht van Human Proteome Folding Phase II. Het gaat erg goed met het project!

http://homepages.nyu.edu/~rb133/wcg/thread_2007_10_31.html

De laatste paragraaf

The last dataset that is of great interest and you will be crunching soon is the Global Oceanic Sequencing dataset or GOS. The story behind this dataset begins with a man and his boat. Well really it's a team of researchers and one of the researcher's yacht. (We don't all have yachts by the way ) Anyway, they took this boat out into the sea, stuck a bucket a foot below the surface and started sequencing what was in the bucket and did it across a few thousand miles of ocean. What they found was an absolutely incredible diversity of organisms. They almost doubled the number of known protein sequences and discovered over 1700 new protein families. Very exciting stuff. Besides just the general fundamental questions that can be answered with knowing the diversity of organisms, the organisms may have some pretty awesome applications. They hope to find new antibiotics, new industrial enzymes, new organisms that bind toxic metals and who knows what else. We're going to fold some of the new protein families to begin a somewhat daunting task of annotating this massive dataset and clue researchers into where to look for interesting things. Hopefully you're on board with us. (I couldn't help putting a cheesy rally call )

[Voor 41% gewijzigd door Anoniem: 167389 op 01-11-2007 13:04]

[Anoniem: 167389]

Update iz Help Conquer Cancer

1, Het My Projects zowel als de Device Profiles hebben nu automatisch HCC als nieuw project aangevinkt gekregen. Er is dus geen actie nodig om aan dit Kanker onderzoeksproject deel te nemen.

De conditie voor automatische toevoeging voor deel selecties in Device Profiles is, dat My Projects wel "All Projects" is.

De Research Project pagina isgeupdate evenals de de voorpagina. Dit is de directe link: http://www.worldcommunity...case/hcc1/viewHcc1Main.do

[Voor 36% gewijzigd door Anoniem: 167389 op 01-11-2007 16:44]

[Suicyder]

Anoniem: 167389 schreef op donderdag 01 november 2007 @ 15:57:
Update iz Help Conquer Cancer

1, Het My Projects zowel als de Device Profiles hebben nu automatisch HCC als nieuw project aangevinkt gekregen. Er is dus geen actie nodig om aan dit Kanker onderzoeksproject hier ook aan deel te nemen.

De Research Project pagina is nog niet geupdate.

Bij mij niet automatisch aangevinkt, dus als je het project wil laten meewerken zoals ik, controleer het dan even!

[Anoniem: 167389]

Zie update in mn vorige post voor conditie van automatische toevoeging!

De annoncering is zojuist geplaatst:

Launch of the Help Conquer Cancer Project

World Community Grid is pleased to launch the Help Conquer Cancer project by the Ontario Cancer Institute (OCI), Princess Margaret Hospital and University Health Network of Toronto, Canada. The mission of Help Conquer Cancer is to improve the results of protein X-ray crystallography, which helps researchers not only annotate unknown parts of the human proteome, but importantly improves their understanding of cancer initiation, progression and treatment. For additional information on this project, please press the Research button in the upper navigation bar or click here.

Forums
In addition to providing information about this project, we have created a forum for discussions about the Help Conquer Cancer project. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title "Help Conquer Cancer Scientist" are authorized to comment as representatives of the research organization: University Health Network (Toronto, Canada).

Project Participation
Help Conquer Cancer is the ninth research project to be launched on World Community Grid and one of five projects currently active. The other four active research projects are: AfricanClimate@Home, (launched August, 2007), Discover Dengue Drugs – Together (launched August, 2007), Human Proteome Folding - Phase 2 (launched July, 2006) and FightAIDS@Home, (launched November, 2005). For more detailed information and FAQs about each of these projects, please click on the Research button in the upper navigation bar or click here. We thank all of our members for all of their valuable contributions to the projects to date and hope you will continue to help us process those, as well as this latest project.

Because there are five research projects running on World Community Grid, your grid agent could receive work units from any of the projects. You may elect to focus your computer's time on only particular projects, if you have a preference. To do so, press the My Grid button in the upper navigation bar and select My Projects or click here. Please note, that members were not automatically opted in to the AfricanClimate@Home project due to the computationally intensive code. To read more specifics on the system requirements for Help Conquer Cancer and the other projects, click here.

If you are already a member of World Community Grid, running the BOINC version of our software, there's nothing that you have to do to prepare for the Help Cure Cancer project. The next time your grid agent communicates with the servers, it will send you a work unit from one of the projects at random for which your machine meets the minimum requirements and according to your project participation election preference. To know which project you are running, please double-click on World Community Grid icon in the system tray, and you will see the title of the project in the display. To contribute to the Help Conquer Cancer project, you will need to be using the BOINC software rather than the United Devices software. If you are running the United Devices version of our software, you should use this occasion to migrate to the BOINC software so that you may participate in all current and future research projects. You may migrate to BOINC by following the instructions here. Migrating is easy and takes less than 5 minutes. The install process even uninstalls the UD software for you automatically.

Questions?
If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the Help section of the website; (2) Review the forums to see if anyone has asked/answered the question that you have; (3) Ask the question in an appropriate World Community Grid forum found here, and a Community Advisor or a more experienced member will provide an answer; and (4) Send an email to the support desk from the Contact Us link found at the bottom of every page of the website (except in the forums).

Thank you!
[Nov 1, 2007 3:44:27 PM]

[Anoniem: 167389]

Nog meer nieuws: Was er al een Minimal Impact, Maximum Output en een Custom Profile is er nu ook een Standard Profile en een Power Savings profile bijgekomen. De laatste heeft een optie, evenals Custom natuurlijk, om de computer na X tijd ongebruikt te zijn geweest in slaap te laten glijden. De default na wat heen en weer flippen blijkt 20 minuten te zijn. De Crunch While in Use is wel aan anders wordt het wel erg kort

[Voor 18% gewijzigd door Anoniem: 167389 op 01-11-2007 17:52]

[Anoniem: 167389]

Het houdt niet op. De HCC project scientist heeft ook een post gemaakt. Gegeven het feit dat de database door IBM op BlueGene voorbewerkt, 86 miljoen samples heeft, zal de hier onder aangegeven 1-2 jaar wel zeker zijn beslag nemen. Gelukkig kunnen ze de resultaten gebruiken en er verdere ontwikkeling mee doen terwijl het werk in stukjes terug komt.

Jurisica
Help Conquer Cancer Scientist (WCG member since Feb.01, 2007 !! )

Welcome to the Help Conquer Cancer Project, and thank you for participating in this important research. The mission of our project is to improve the results of protein X-Ray crystallography, which helps researchers not only annotate unknown parts of the human proteome, but importantly, improves their understanding of cancer initiation, progression and treatment. Although our focus is cancer, results from this project will help other diseases as well.
Analyzing the results from this experiment will also lead to better understanding the underlying principles of protein crystallography. For the first time, a comprehensive crystallography image analysis will be done, which was impossible before due to computational complexity. In turn, CrystalVision will be improved to provide faster and more accurate image classification. This will lead to more protein structures being determined. In addition, determining more 3D structures of proteins will also lead to improved in silico structure prediction.
Thank you again for making vital contribution to the project. It is highly appreciated, as it would take us over 162 years on the largest computer available to us to finish this computation. Although, we expect to finish the project in about 1-2 years on the World Community Grid, we will start analyzing the data incrementally. We will keep you informed about our results at http://www.cs.toronto.edu/~juris/WCG/wcg-hcc.html.
Thank you
Help Conquer Cancer Project Team

[Anoniem: 167389]

Bezoek WCG Forum and My Grid Member profiel voor nieuwe features zoals project badges ** en een widget, naar smaak in te delen met info van jouw keuze om op je persoonlijke website/pages te plaatsen.... bijv:


De widgets zijn dynamisch.

Member News January 14, 2008.
http://www.worldcommunity...g/viewthread?thread=17862

Er is nu ook een soort van XML RSS feed link op alle forum website paginas.
Hierin staan alle courante draadjes van de WCG fora.

http://www.worldcommunitygrid.org/forums/wcg/rss

** De te verdienen badges voor elk project waar 14 dagen op gegraasd is met uitzondering van AC@H waar 1 dag CPU tijd genoeg is:

Beta Testing
AC@H (1) African Climate

HPF (1) Human Proteome Folding
FA@H FightAIDS@Home
HPF2 Human Proteome Folding, phase 2
HDC Help Defeat Cancer
FGC Fiocruz Genomic Comparison
HCMD (1) Help Cure Muscular Dystrophy
DDDT (1) Discover Dengue Drugs Together
HCC

Haakjes (1) betekend dat het de eerste fase is.

[Voor 80% gewijzigd door Anoniem: 167389 op 20-03-2008 17:30]

[Noordvogel]

Sekerob, bedankt voor het immer doorgeven van interessant WCG-nieuws! Vooral de RRS feeds spreken mij aan.

[xahmol]

Leuk die widgets, maar wie maakt die dingen nu in iframes ipv dynamisch gegenereerde JPEGs of zo? Die iframes kun je bijna nergens gebruiken (iig niet in signatures) en zijn ook nog eens niet in mijn eigen homepage te gebruiken omdat ik nu net zoveel moeite heb gedaan om die XHTML 1.1 Strict te krijgen en XHTML Strict de iframe tag niet ondersteund.

Maar goed leuk idee, alleen de uitvoering had van mij iets beter gemogen (of op zijn minst de optie te geven of je een JPEG, iframe of Flash als output wil).

En als je dan toch badges introduceert, waarom die dan niet in de widget? I want to show of my badges ;-)

[Anoniem: 167389]

Zie draadjes op WCG v.v. de discussies hierover.... ontwikkelingen van features worden op 'positive feedback' gebaseerd en de badges in de widget is ook al door een paar anderen genoemd.

En als er al DPC discussie is over stats, er is nu veel meer en veel uitgebreidere Stats XML beschikbaar. Misschien als al onze vereerde statsbakkers den hoofden bijeen steken

<iframes> is web 2.0 was een commentaar en iemand was bezig een plug in te maken voor op zn wordpress page. De keuze was bewust om het op de toekomst te richten zo begrijp ik.

[xahmol]

OK, zal eens op de WCG fora kijken (was ook zeker niet bedoeld als kritiek richting jou als brenger van het nieuws overigens, dit was alleen mijn eerste reactie toen ik het zag).

En: <iframes> is Web 2.0 en toekomstgericht? Wie heeft dat nu weer verzonnen? Het is niet voor niets niet meer opgenomen in de nieuwste HTML specs, iframes zijn een onding waar veel betere alternatieven voor zijn. Enige probleem is dat natuurlijk IE weer eens de offciele alternatieven (de object tag) niet ondersteund.

Ja, ik weet, moet dat niet hier zeggen maar op het WCG forum, een wordpress plugin is leuk, maar dan hebben we nog Myspace, Hyves, internetfora en andere blogsoftware (gebruik zelf Nucleus).

EDIT: Daad maar bij het woord gevoegd en mijn opmerking hier gepost. Nu alleen maar hopen dat ik daar niet meteen wordt afgebrand als newbie die zonodig alles beter moet weten (weinig ervaring nog op het WCG forum, maar de fora van DC projecten zelf hebben nogal eens de neiging nogal vijandig te zijn naar post die niet alleen maar hallelujah ja amen zeggen).

[Voor 24% gewijzigd door xahmol op 16-01-2008 12:46]

[Anoniem: 167389]

Enig nieuws:

Help Defeat Cancer, het vorig jaar afgesloten Kanker project heeft de eerste resultaten bekendgemaakt. In samenwerking met IBM wordt een database nu geprepareerd die voor de wereldwijde medische en in het bijzonder voor oncologie wordt opgezet voor versnelde diagnostiek.

Tapping into the Cancer-Fighter Collective for Treatment
http://www.sciam.com/arti...ancer-software-technology
IBM, Cancer Institute of NJ, and Rutgers Ally to Advance Cancer Prognosis
http://www.genengnews.com...e=29432791&source=genwire
IBM and University Researchers to Develop Research Tools to Improve Cancer Patient Outcomes
http://money.cnn.com/news...es/marketwire/0352785.htm

Help Conquer Cancer, het huidige project waar rond 180 miljoen plaatjes voor moeten worden doorgewerkt (86 en 84 miljoen wordt genoemd, in quorum 2 + fallout door fouten) heeft zn eerste voortgangsverslag. De toegang dient doorgeklikt te worden door naar Progress te gaan en het January 2008 Update verslag te kiezen (of latere als die er zijn).

http://www.cs.utoronto.ca/~juris/WCG/

Goed nieuws.

Voor wat betreft de traagheid op bepaalde machines hier een kleine analyse mijnerzijds genomen vanaf een quad die bulkt van L2, het geheim om HCC snel te draaien:

- 22% van de partners doet er zodanig lang over dat de claim 'over' is waardoor de credit aan de lagere van de 2 in het quorum wordt aangepast (de Q6600 dus)
- 24% doet er zodanig lang over dat de claim 'net niet over' is waardoor toch nog een gemiddelde berekend wordt met groot voordeel voor de laagste claimer (de Q6600), maar niet dramatisch voor de hogere.
- 54% is normale variatie waar het gemiddelde berekend wordt.

Overall wordt bij 78 procent dus bij mij de 'doorsnee' waarde toegewezen. Heb hier niet de onderclaimers meegenomen. Een paar procent claimt veel te laag en krijgt dus volgens de regels de 'normale' credit.... een paar vreemde excepties daargelaten. Let wel we hebben het dus over HCC. De andere lange termijn projecten hebben weinig last van quirks.

De benchmark claims voor 64bits cliënten zijn geinflateerd daar we 32bit science draaien. Als je toch alleen maar 32 bits projecten draait is het beter ook die cliënt te gebruiken waardoor 'outlier' situaties minder snel ontstaan op 64bits OS en de claims meer naar die 24% groep tenderen.

WCG techs zijn bezig met een verdere analyse en met de eerste tussen resultaten die beter doen begrijpen wat in het product van belang is zal een revisie van de science niet onwaarschijnlijk zijn. Statistisch doet het HCC project nog steeds gemiddeld het meeste met 69 credit per uur (de mix dus van langzame en snelle machines). Dengue doet 66 per uur en AfricanClimate doet 70. Over Human Proteome en FightAIDS is moeilijk wat te zeggen omdat de oude en langzamere UD clienten hier nog in meedraaien. In doorsnee krijgt mn quad minder als claim voor HPF2 en gelijk voor FAAH. Daar HPF2 evenals AfricanClimate ook nog al data intensief zijn speelt ook hier veel L2 cache in het voordeel.

Sommige dual core machines doen het ook goed als ze maar 1 HCC job draaien met een andere klus op de 2e core. Als je 'All Projects' kiest minus AC@H wordt de kans ruim ingeperkt dat er 2 tegelijk draaien.

We houden je op de hoogte.

[Voor 6% gewijzigd door Anoniem: 167389 op 31-01-2008 09:03]

[scorpionv]

Kijk eens aan, dat is goed nieuws! Kankeronderzoek is leuk, maar de toepassing er van gaat waarschijnlijk mensenlevens redden

[Anoniem: 167389]

De Widgets zijn weer terug met toegevoegde waarde (te bereiken via de My Grid pagina) Zet het op je personal Webpage, Myspace, overal waar het werkt met verschillende achtergronden en formaten:

The Create Widget feature has been re-enabled, with new options including: displaying Global Statistics, removing member name from the Widget, and opting to display special announcements such as project launches and milestones. The World Community Grid Software License agreement has been updated to govern the use of the World Community Grid Widget, and a checkbox related to the updated agreement was added to Create Widget page.

Ook zijn de meeste web pagina's, forum draadjes en statistieken nu in XML te vangen. Alle frequent bezochte forums heb ik nu in RSS links staan op mn LiveFeed balk.

Do you have an XML interface for the statistics?
XML is a standard used on the internet that allows data to be shared in a standardized, but flexible method. In the past, members have extracted information from the public statistics pages by parsing the HTML on those pages and storing it in a database for uses such as display stats for their team on their Team website. This will be easier to do now that an XML interface is available for most of the public statistics pages.

You can obtain an XML version for most of the public statistics pages by simply adding either "?xml=true" if there are no other parameters in the URL or "&xml=true" if there already are parameters on the URL for the page.

Alternatively, you can view the XML page and follow the references provided on that XML document to go to locate pages that are in XML format.

De stats tijd teller zou nu ook werken. Voorheen begon het bij maximaal 59:59 minuten. Als het langer duurde begon het weer opnieuw. De laatste metingen geven een middag onderbreking aan van 40 minuten en nacht van 100 minuten. De begintijd is variabel omdat het ophalen van de data nogal in volume kan schelen.

[Anoniem: 167389]

Een eerste update van Discovering Dengue Drugs - Together.

http://www.utmb.edu/disco...ther/Project%20Status.htm

Als het goed gelezen wordt, dan gaat hier de huidige quorum 2 op de helling. Dit vormt een interessante horde voor het bepalen van de credits. Vast of gegroepeerd zoals by HPF2? we zullen zien.

January 22, 2008 update

· An initial optimization of docking parameters was completed in early Fall, 2007. This allowed us to reduce computation time ~20-fold without impacting the accuracy of pose predications.

· Dengue virus NS3 protease (Protein Data Bank entry 2FOM) was used as a target to screen a combined drug and lead-like library containing 2.2 million compounds. These calculations (termed workgroup 0201) were completed in ~2 months. Grid resources for these calculations were limited to <10% of World Community Grid to minimize file transfer bottlenecks resulting from packing only a single ligand into each workunit.

· Predicted inhibitors obtained from screening our ligand library against dengue virus NS3 protease are being analyzed in our laboratory using a protease inhibition assay. Compounds with promising inhibition constants will be further evaluated in cell culture and animal models.

· West Nile virus NS3 protease (Protein Data Bank entry 2FP7) was used as a target to screen a combined drug and lead-like library containing 2.2 million compounds. These calculations (termed workgroup 0301) were completed in ~2 months and ended in early January ‘08. Grid resources for these calculations were also limited to <10% of World Community Grid to minimize file transfer bottlenecks resulting from packing only a single ligand into each workunit.

· Predicted inhibitors obtained from screening our ligand library against West Nile virus NS3 protease are being analyzed in our laboratory using a protease inhibition assay. Compounds with promising inhibition constants will be further evaluated in cell culture and animal models.

· Additional docking calculation optimizations are entering beta testing. These optimizations will enable us to reach our goal of screening our ligand library against a single protein in less than 2 weeks. This involves packaging multiple ligands (~10) into a single workunit, thereby minimizing file transfer bottlenecks. In addition, checksum error checking will be embedded within each workunit, eliminating the use of redundant calculations to validate each workunit.

· Trypsin protease (Protein Data Bank entry 1EB2) is being screened against our ligand library to provide a negative control for inhibitor discovery (termed workgroup 0401).

· Hepatitis C virus protease is being readied for computational screening.

· Our Discovering Dengue Drugs – Together project has currently benefited from 3,626 years of computer processing time on World Community Grid. We are grateful to those individuals who have unselfishly volunteered their computers to help us find cures for dengue, West Nile, and Hepatitis C diseases.

[Anoniem: 167389]

Hier een linkje voor verspreiding aan mensen die DPC op World Community Grid willen joinen. Het is het WCG registratie formulier met team DPC informatie reeds ingevuld

http://www.worldcommunity...ter.do?teamID=025RSMBR9N1

edit:
nav latere reactie hier maar daden bij andermans woorden gevoegd en tevens de onderhoudstijden van het WCG website gevoetnote wanneer registratie niet mogelijk is.

[Voor 27% gewijzigd door Anoniem: 167389 op 15-02-2008 14:36]

[Troetelbiertje]

Misschien iets voor in de Wiki?

[Noordvogel]

Of voor in het Stampede-draadje...

[Anoniem: 167389]

Er is een nieuwe versie 5.20 van Help Conquer Cancer uit die het Page Faulten met een factor 10000 gereduceerd heeft voor bep.OS/CPU combinaties. ihb WXP had er last van. Voor die koetjes worden de run-tijden drastisch korter voor gem. betere punten per uur. Een Linux beta is in de maak daar ook die er last van hebben even als MACs.

Door de perikelen van 'te' korte werkstukken en het trechter effect is de gehele productie licht ingezakt.... vandaag of morgen zal dat weer bijtrekken. De HPF2 jobs v.a. batch lo200 worden 50% langer en krijgen dan 18 dagen de tijd om afgemaakt te worden. Dat zal de megaflushers wel aanspreken. Dit is ook gedaan om de UD converters met zeer trage koetjes die gewend zijn aan 2 maanden een beetje tegemoet te komen als ook om de stress van de BOINC work-generators en feeders en scheduler (shared memory functies) te reduceren wat de groeicapaciteit naar boven radicaal verbeterd.

[Anoniem: 167389]

Een update van Human Proteome Folding, Phase 2 is op 21 februari gepubliceerd.

http://homepages.nyu.edu/~rb133/wcg/thread_2008_02_21.html

Extract:

Much has happened since the last status report and the most exciting thing to report is how fast the grid is running. We are barely keeping up with you as your machines are folding proteins faster than we could provide new proteins. Coming up though, we have a few tough nuts to crack so we shouldn't have a problem. First off we've tackled many disease causing organisms including ones that cause malaria and anthrax. Another set of proteins which are from multiple organisms is the GOS data set which came from "sequencing the sea". These are all the finished organisms.
gaat hier door:

Added: Ook een courant productie grafiekje voor dit project zoals hierna voor HCC. Zie draadje op WCG voor wat meer uitleg bij de fluctuaties: http://www.worldcommunity...g/viewthread?thread=18690

[Voor 13% gewijzigd door Anoniem: 167389 op 16-04-2009 09:42]

[Anoniem: 167389]

Een productie grafiekje voor Help Defeat Cancer. Duidelijk is te zien hoe vanaf 18 feb de output een sprongetje maakt met de beta en het loslaten van science versie 5.20. De dip 22/23 feb is een typische weekend beweging als veel bedrijven hun crunchers stil leggen. Ook IBM is op het 'Power Savings' plan. Te begrijpen als je 300,000 PCs beheerd en de stroom daarvoor moet betalen. De punten per uur liggen nu tegen de 72 waar het op 1 januari nog net 68 was. Verwacht komende dagen verdere sterke stijging daar m'n quad 110 per uur doet.

[Anoniem: 167389]

Vandaag Discovering Dengue Drugs Together produktie update:

Overall is het aantal dagelijkse CPU jaren laag wat met scheduler, feeder en work generator capaciteit te maken heeft. Deze week werd een nieuwe DDDT beta getest en als succesvol zal een volgende beta rond 5x meer rekenen in een werkstuk stoppen. Dan kunnen de trossen los en het doel doorgezet worden om het aandeel DDDT op WCG een groter percentage toe te wijzen. Als in eerdere post aangegeven gaat het quorum principe bij DDDT op de schop hetgeen de efficiency effectief zal verdubbelen. Statistisch interessante dockings worden sws nader bekeken en herrekend op juistheid.

qua credits per uur ligt dit project net een fractie hoger als Help Conquer Cancer (vorige post), dat nu na de nieuwe versie steeds meer stabiliseert met lagere gemiddelde run-tijden.

M.i.v. 4 maart gaat versie 5.15 in produktie met nieuwe multi-job tasks die 3-4 in een Work Unit verpakken en 4 maal langer gaan duren. Vanwege langzamere crunchers wordt de deadline ook tegelijk aangepast een verhoogd van 7 naar 12 dagen.

[Voor 12% gewijzigd door Anoniem: 167389 op 16-04-2009 09:41]

[Anoniem: 167389]

Update: WCG staat op 99.23% RAU (Recent Average Uptime). Zijnde het 1 na grootste project, een prestatie (maar je mag dat ook wel verwachten met het hi redundancy server park waar IBM 'onze' WCG op laat draaien. De Grootste zit in het onderste kwart van de lijst:

http://boincprojectstatus.ath.cx/

Rond Mei '08 als AfricanClimate@Home, Phase I klaar is komt er een Nieuw project ipv. Dan rond Augustus krijgen we Help Cure Muscular Dystrophy Phase II als 6e project, parallel dus. Ergens daartussen of erna maar zeker in 2008 ook nog Discovering Dengue Drugs - Together, Phase II. als 7e project (nog steeds zijnde geluiden dat het begint voor Phase I eindigt). Het gebruik van de CHARMM software (onder BOINC) om de data van fase 1 verder te verwerken is goedgekeurd. Eerste interne alpha testen worden in de komende tijd verricht, dan moet het naar de security groep voor auditing.

Geen nieuwe badge voor de laatste, maar velen die geen UD agent draaiden, alleen BOINC krijgen nu alsnog een kans. We zijn bezig de admin en web-developer te pushen om de badges brons, zilver, goud randje te geven als er hogere sub-project bijdragen zijn gedaan. Geen voor 14 dagen. maand voor brons, 3 maand voor silver en 6 maand voor goud, of iets dergelijks.... das nog ver weg, maar een aanstaande web-update rond midden maart voegt weer wat meer zichtbare en minder zichtbare bellen toe.

[Voor 11% gewijzigd door Anoniem: 167389 op 06-03-2008 11:21]

[Anoniem: 167389]

Een update van het AfricanClimate@Home project met een news flash. De wetenschappers hebben tot nu toe 8 cycles van 14 dagen terug ontvangen die het climaat proberen te voorspellen voor 2003. Tot nu toe loopt het netjes in de pas met de werkelijke gemeten gegevens over dat jaar hetgeen de juistheid van het model onderschrijft. Het project is inmiddels cycle 24 aan het afmaken, dus April-Mei moet het wel gebeurd zijn, maar er is wel op geduid dat mogelijk bepaalde blokken herrekend moeten worden v.a. een moment waar het niet meer overeenkomt met de omliggende blokken. Lees het verhaal ook in pdf of:

/me op moment van posten werkte de pdf wel, maar de newsflash link niet... er staat meer preamble op de website

[Anoniem: 167389]

Ter gelegenheid van de verlenging van taken deadlines een nieuwe project matrix. FightAIDS@Home en Help Conquer Cancer zijn van 9 naar 10 dagen gegaan evenals AfricanClimate@Home dat van 5 naar ook 10 dagen is verlengd.

[Anoniem: 167389]

Let Op, Aankomende Announcement: De FightAIDS@Home & Discovering Dengue Drugs - Together die de AutoDock motor gebruiken gaan de komende dagen opdrogen om ruimte te maken voor een spoedig te BETA-testen versie die ook klaar is voor BOINC 6, backward compatible blijft naar 5, een verbeterde 'quarternions' calculatie heeft, EN op single distro gaan draaien. Dat maakt dat deze 2 projecten 2 maal zo hard gaan lopen.

Wees dus zo goed als je een van deze projecten als exclusieve keuze hebt, tijdelijk (of aanbevolen, altijd) het 'alternatief' werk vakje in je device profiel aan te vinken en te saven op de WCG website.

Added:

FAAH Announcement: http://www.worldcommunity...g/viewthread?thread=19662
DDDT Announcement: http://www.worldcommunity...g/viewthread?thread=19661

[Voor 11% gewijzigd door Anoniem: 167389 op 10-04-2008 20:29]

[priens]

Goed nieuws dus!

[Anoniem: 167389]

De 1e (werkende) Help Conquer Cancer release voor Linux versie 6.03 is heden ook in productie gegaan:

http://www.worldcommunity...g/viewthread?thread=19665

Het feit dat deze versie met 6 begint betekend dat ze ook klaar is voor de toekomstige BOINC 6 releases. De in vorige post genoemde FightAIDS@Home en Discovering Dengue Drugs - Together versies zullen ook die 6 in de versie nummers dragen ter indicatie.

[Anoniem: 167389]

Uit het WCG-DPCH dagdraagje van 11 mei, de lancering van het nieuwe crunch doel

Nutritious Rice for the World project:

I'm going to give you an early peek at an animated version of the Rice screen saver:


FAQs about the screen saver.
=========================================

Screensaver/Graphics: What is the rotating shape in the center?
It is a representation of the latest structure predicted by your computer.

Screensavers/Graphics: What is the red graph titled RAPDF?
This is the score of the best structure over time. The score comes from the Residue-specific All-atom conditional Probability Discriminatory Function (RAPDF), which measures how similar a predicted protein structure is to real structures. Good structures have a low score. You can read more on the researchers' page about this project.

Screensavers/Graphics: What is in the background?
The background is a photo of a rice field in Asia.

Screensaver/Graphics: Can I look at the information in a different way?
When you are viewing the graphics, there are keyboard controls that will change the way the information is displayed. These keys only work in the standalone graphics mode, they won't do anything when viewing the screensaver.
Workunit:
M toggle member info (show/hide)
I toggle progress graph size and position (large/small)
Protein visualization:
B toggle backbone shape (show/hide)
S toggle structure atoms (show/hide)
C carbon (C and Cα)
A carbon (Cα)
N nitrogen
O oxygen

Zij die de betas hebben gedaan herkennen de 2 progress bars onder aan. De lancering is rond 11:00 Eastern Time tijd dus reken op wat web interrupties als de site geüpdate wordt. Per WCG policy wordt het project automatisch toegevoegd en dien je via het Device Profile of My Projects het uit te vinken ALS je niet mee wilt helpen bij het toekomstig verminderen van het wereld honger probleem (een beetje emo chantage mag toch ;>).

EN mbt de bijna onmiddelijke vraag:

Is this genetically engineering new rice strains?

"No this project is not about genetic engineering - which is done in the laboratory and exchanges genes from different species. This research examines the structure of the proteins that make up rice at a level of detail that has not been possible before. Once we know the structure, we can identify the function and thus identify the plants to select for cross-breeding. Cross breeding is a technique that farmers have used since the human race began to cultivate crops rather than just collect whatever grew around them.".

Als altijd gaan alle resultaten van dit project in de 'public domain' ter algemene beschikbaarheid aan de wereldwijde wetenschappelijke gemeenschap.

Tenslotte, een link naar het officiele project website: http://protinfo.compbio.washington.edu/rice/

Op naar de 11e badge (moet eerst die 10e nog zien te krijgen:D

[Anoniem: 167389]

World Community Grid in het Nieuws.... New York Times Blog:

http://bits.blogs.nytimes...for-super-rice/index.html

Project Nieuws Draadje voor Nutritious Rice for the World:

http://www.worldcommunity...g/viewthread?thread=20269

[Anoniem: 167389]

Heads up koeien voor wat 'insider' info van de chief WCG tech, knreed (in matrix verder terug in dit draadje bijgewerkt):

We have added some more filesystem storage. As a result we have increased some of the deadlines. The deadlines are now 12 days for all projects except Human Proteome Folding Phase 2 which is set to 20 days.

The average runtime per project for results validated yesterday is:

AfricanClimate@Home: 7.8 hours
Discovering Dengue Drugs - Together: 7.0 hours
FightAIDS@Home: 7.8 hours
Help Conquer Cancer: 7.0 hours
Human Proteome Folding - Phase 2: 11.6 hours
Nutritious Rice for the World: 8.0 hours

Dit betekend dat DDD-T terug is gegaan van 14 naar 12 dagen deadline en HPF2 op het zelfde is gebleven, spreek 20 dagen.

Na de laatste wijziging geldt Rijst met app.versie 6.15 als het project met veruit de laagste fout index en hoogste gemiddelde punten: Per heden middag, naar voldags stats geextrapoleerd

[Anoniem: 167389]

Help Cure Muscular Dystrophy lead wetenschapper heeft net een update geplaats over de voortgang der ontwikkelingen en stappen die nodig zijn voordat de fase 2 gelanceerd kan worden. WCG hanteerd intern 4e kwartaal als doel, maar dat hangt natuurlijk van de goede werking en porting af naar het BOINC platform.

Zoals ieder zich herinnerd, of niet, draaide fase 1 alleen op de UD agent waardoor velen niet de gelegenheid kregen om de badge ermee te verdienen, deze dus . Of het de zelfde wordt is nog niet hard besloten.

Dacht afgelopen dagen iets gelezen te hebben over een nieuwe gemanipuleerd gen behandeling, eenmalig, wat tot verbetering zou leiden.

Nu dan het woord aan Alessandra Carbone "Help Cure Muscular Dystrophy" Scientist (vanuit Frankrijk)

Help Cure Muscular Dystrophy Update on June 5, 2008

Dear All,

Here is a short update on the HCMD project:

- We improved the MAXDO code (this is the program running on the grid). The MAXDO code has been improved so that the receptor and ligand proteins are now treated symmetrically during the energy minimization process. As a consequence, the docking of two proteins is about 4 to 5 times faster than in the previous version of the program.

- We finished the implementation and optimization of JET (this is the program which will predict the positions of the protein interfaces) for interfacing it with MAXDO. Running JET predictions before MAXDO is crucial because of the large computational time that docking is taking. By predicting in advance the protein interfaces, we are able to reduce greatly the surface region to be investigated with MAXDO on your machines.

- Right now, we are working on the interface between the two programs, JET and MAXDO. There are two problems that we are dealing with right now: 1) We want to estimate the surface of a protein that we need to dock, based on JET predition, to be sure to have enough information to discriminate correct partners. 2) We want to develop a numerical criteria that, based on JET predictions and MAXDO analysis, discriminates correct partners. This criteria will follow the one that we have developed during phase 1 and that was based on real interface information.

- As soon as the interface problems are done, we shall make the last refinements to the MAXDO code. This will take about a week of testing and then we will deliver the code to World Community Grid.

- Last but not least, we are collecting from French scientists interested in the project a set of proteins important for muscular dystrophy which will be tested on phase 2. In phase 2 we shall look for protein partners for our target proteins within a very large dataset of potential candidates.

Looking forward to working with you very soon on the project.

Very best regards to All,

Alessandra
[Jun 5, 2008 2:40:39 PM]

[Anoniem: 167389]

Nieuws van het Help Cure Cancer front. Het project is momenteel op rond 8.2%. The techs en wetenschappers zoeken nog steeds naar manieren om het harder te laten lopen zonder inboeting op kwaliteit van de image analyse.

May 2008 Research Update

Hello World Community Grid members,

The HCC project is coming long nicely. We have posted an update on the state of the research here:

http://www.cs.utoronto.ca/~juris/WCG/UPDATE-MAY2008.pdf

Your donated CPU cycles make this research possible. Thank you very much for your contributions.

Christian A. Cumbaa
Research Associate
Ontario Cancer Institute
[Jun 12, 2008 3:29:57 PM]

[Anoniem: 167389]

Voor die het niet gezien heeft in zijn junk mail folder of WCG vergeten heeft, er is net Nieuws Brief Volume 6 aan alle leden gezonden die ooit een werkstuk hebben ingeleverd. Ging uiteraard naar het laatst bekende post adres. Hier een link:

http://www.worldcommunity...er/08Q2/viewNewsletter.do

Samengevat:

-AfricanClimate@Home fase 1 is klaar
-UD Agent is heengezonden en er wordt nu alleen gegraasd met BOINC
-Nutritious Rice for the World heeft meer als 10% compleet.
-Server upgrades en migratie naar laatste MySQL en DB2-9.5 voor betere prestatie van alle website and BOINC-daemon elementen

en meer

[Anoniem: 167389]

Nieuw sub-project... zoeken wat plantjes in staat stelt om zonlicht in energy om te zetten of wel organic photovoltaics:

The Clean Energy Project website: http://cleanenergy.harvard.edu/

De WCG Research info pagina: http://www.worldcommunity...case/cep1/viewCep1Main.do

Werkstukken: komen in 3 types A, B, C. A/B is quorum 2, C is Quorum 5 van 10, deadline 20 dagen. De werkstukken van type C zijn allen uniek!

WCG/Wiki: tba

De badge, met gouden, silveren of bronzen rand:

Graphics:



Productie:

[Voor 5% gewijzigd door Anoniem: 167389 op 16-04-2009 09:46]

[Noordvogel]

Bedankt voor alle nieuws-updates, Sekerob!

offtopic:
Ik kreeg geen WCG-WU's meer binnen, maar een reset heeft het verholpen. Helaas nog geen CEP-stukjes gehad...

[Voor 8% gewijzigd door Noordvogel op 06-12-2008 12:15]

[Anoniem: 167389]

Update van Help Conquer Cancer - in het kort is 25% van het werk compleet en zijn 11 interessante doelen gevonden.

new HCC status report

Hello World Community Grid Members,

The Help Conquer Cancer status report for April 2009 is ready. The full report is here (pdf).

This month marks a milestone in Help Conquer Cancer: 25% of our work units have been processed on the Grid, representing 3 million crystallization trials on over 2,000 proteins. Analysis of these results is proceeding on multiple fronts. Our latest crystal-finding classifier, generated from HCC results, can identify 4 out of 5 images containing protein crystals, greatly reducing the effort of manually searching through images for crystals, and thereby increasing the rate of protein structure solution. Using this classifier on a set of 5.7 million images, we recently identified 11 proteins with favourable crystallization conditions, all of which are homologous to human proteins on our cancer target list (spanning lung, ovarian, prostate and head & neck cancers). Finding crystallization conditions clears one hurdle on the path to determining the structure, and ultimately the function, of these cancer targets.

Thank you all for your contributions to HCC and to the World Community Grid -- they make this research possible.

Christian

---
Christian A. Cumbaa, Research Associate
Ontario Cancer Institute
[Apr 8, 2009 3:09:22 PM]

[Voor 1% gewijzigd door Anoniem: 167389 op 08-04-2009 16:54. Reden: grafiekje toegevoegd]

[Witlof]

Daar doen we het toch tenslotte voor

[priens]

Top!

[Anoniem: 167389]

FightAID@Home heeft zojuist Newsletter 7 uitgegeven. Het project is inmiddels tot experiment 29 gevorderd en 'wet tests''zijn in voorbereiding gebaseerd op laatste resultaten.

[Voor 9% gewijzigd door Anoniem: 167389 op 15-04-2009 10:39]

[Mobster]

Feedback is wat wij als crunchers willen hebben. Top van WCG en ook van Sekerob natuurlijk dat ie het hier weer post

[Anoniem: 92171]

Dit is, gelukkig, wel wat anders dan bij TSC/D2OL.

[Cow_tipping]

Ik ben ook erg blij dat ik de uitleg daadwerkelijk snap. (dat is ook bij andere projecten ondanks de uitleg niet altijd het geval)

[Anoniem: 167389]

Discovering Dengue Drugs - Together update

Ik denk dat de hoofd onderzoeker een beetje te vroeg is met zn 'fase 1 is klaar' commentaar. WCG denkt dat deze nog minstens doorloopt tot na de start van fase 2 op CHARMM (Zelfde analysis software als voor Clean Energy). Mooi is dat er nog een andere tropische ziekte, leishmaniasis (berglepra) toegevoegd is aan de 4 die al deel uitmaakten van het project t.w. West Nile, Dengue (Knokkelkoorts), Hepatitis C en Gele Koorts.

What's the latest news from Galveston?

Hello again from Galveston! Below is a status update that will be posted on our web site update board. However, I thought I would get it out via the forums as well.

Thanks again for all your help!

- Stan
______
April 13, 2009

We are back on track with our DiscoveringDengueDrugs-Together project, and life is returning to some semblance of normalcy in Galveston and at UTMB. We thank World Community Grid members for their support and patience during the past 6 months following Hurricane Ike.

The Autodock phase (Phase 1) of our dengue project is now complete! We have screened (i.e., computationally tested) more than 3 million potential drug candidates against each of 10 different proteases from dengue, West Nile, and hepatitis C viruses. Inhibiting these target proteases prevents virus replication. We continue to analyze the 30 million Phase 1 results. We are using biochemical, cell-based, and small animal assays to characterize some of the inhibitors identified during our recently completed Phase 1 calculations.

The CHARMM phase (Phase 2) of our project is being optimized at Texas Advanced Computer Center (TACC; www.tacc.utexas.edu) in Austin, Texas and ported by IBM to the grid for testing. This phase will perform extensive molecular dynamics calculations to accurately calculate binding free energies for the best potential drug candidates predicted in Phase 1. These calculations will significantly reduce the number of false positive predictions produced in Phase 1, thereby increasing our success rate for identifying experimentally active compounds from ~10% to >80%. Launch of Phase 2 is anticipated for early summer, 2009.

As we prepare to launch Phase 2 of our project to discover drugs for dengue, West Nile, and hepatitis C infections, we will also begin Autodock calculations in support of a collaborative drug discovery effort against leishmaniasis disease. This work is done in partnership with researchers from Universidad de Antioquia, Colombia (http://www.pecet-colombia.org). Leishmania affects ~12 million people throughout the tropics, subtropics, and southern Europe, with ~2 million new cases each year. The disease is spread by the bite of sand flies infected the Leishmania parasite. Although a handful of antimicrobials exist to treat some forms of leishmaniasis, concerns about their modes of delivery, effectiveness, resistance, and cost spur our drug discovery efforts into novel anti-Leishmania drugs. For this project, scientists in Colombia identified a set of enzymes critical for survival of the Leishmania parasite. Atomic structures exist for each of these enzymes, this allowing us to computationally examine our drug candidate library for compounds that prevent the Leishmania enzymes from functioning.

As reported earlier, this project is now running better than ever before. We have moved our main computational tasks (those required to prepare workunits for World Community Grid and analyze results returned from the grid) to the supercomputers housed at TACC. This establishes a nice synergy between one of the world’s most powerful supercomputers and the world’s largest computer grid. Our storage capabilities have increased in size and robustness with redundant storage occurring at TACC and locally on our 12 TByte IBM DS3200 disk system.

As stated before, we greatly appreciate the computer time that has been unselfishly provided by the members of the World Community Grid!

- Stan
[Apr 22, 2009 11:47:50 AM]

[Anoniem: 167389]

We kunnen nu voor het gehele team zien hoeveel er op elke science bijgedragen is:

Website Updates for May 1, 2009: Team Stats By Projects and Project Team Challenges
World Community Grid is happy to announce that you are now able to see your team's statistics by project! The statistics are also available in XML format so team statisticians can create all kinds of new graphs and charts! Read more about the XML interface in this FAQ.

In addition to monitoring your team's statistics by project, your team's captain is now able to challenge other teams to compete for contributions to a specific project! See if you can recruit new members to your team to contribute to your favorite cause!

In the News & Media section, there is a new video to watch about the Nutritious Rice for the World project featuring Dr. Ram Samudrala and Michal Guerquin.

The Research Proposal submission schedule on the Submit a Proposal page has been updated for dates in 2009 and 2010.

There is now a link to the System Requirements FAQ on the research project pages (in the right sidebar) so that people looking at projects can more easily determine if they can run a project in which they have an interest. We have also added an FAQ containing the download sizes for the various components of each of the active research projects.

Finally, the following items have been corrected:
- The checkbox for automatically opting-in to new projects was not staying checked after saving My Projects. It will now be saved and displayed correctly.
- Challenges that compete based upon the increase in contribution were calculating the increase incorrectly. They will now have the baseline stats properly computed [edit: for all new challenges].
[May 2, 2009 1:39:36 AM]

[Anoniem: 167389]

Nieuw Project Annoncering: Influenza Antiviral Drug Search

Launch of Influenza Antiviral Drug Search Project

World Community Grid is pleased to announce the launch of the Influenza Antiviral Drug Search project by Dr. Stan Watowich and his research team at The University of Texas Medical Branch (Galveston, Texas, USA). They are collaborating with researchers from the Galveston National Laboratory at UTMB (Galveston, Texas, USA) for testing of drug candidates. The mission of the Influenza Antiviral Drug Search project is to find new drugs that can stop the spread of an influenza infection in the body. The research will specifically address the influenza strains that have become drug resistant as well as new strains that are appearing. Identifying the chemical compounds that are the best candidates will accelerate the efforts to develop treatments that would be useful in managing seasonal influenza outbreaks, and future influenza epidemics and even pandemics. For more information click here.

Project Badge
If a member contributes a minimum of 14 days of CPU Run Time to this project, they will receive an Influenza Antiviral Drug Search project badge on their member statistics page and next to their member name when they post in the forums. There is a different badge for each research project and beta testing. To read more about badges, click here.

Forums
In addition to providing information about this project, we have created a forum for discussions about the Influenza Antiviral Drug Search project. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title " Influenza Antiviral Drug Search and Discovering Dengue Drugs - Together Scientist" are authorized to comment as representatives of the research organization: The University of Texas Medical Branch (Galveston, Texas, USA).

Project Participation
Influenza Antiviral Drug Search is the thirteenth research project to be launched on World Community Grid and one of eight projects currently active. The other seven active research projects are: Help Conquer Cancer (launched November, 2007), Discover Dengue Drugs – Together (launched August, 2007), Human Proteome Folding - Phase 2 (launched July, 2006), FightAIDS@Home Phase 2 (launched November, 2005), Nutritious Rice for the World (Launched May, 2008), The Clean Energy Project (launched December, 2008) and Help Fight Childhood Cancer (launched March, 2009) . For more detailed information and FAQs about each of these projects, please click on the Research button in the upper navigation bar or click here. We thank all of our members for their valuable contributions to the projects to date and hope you will continue to help us process those, as well as this latest project.

Because there are eight research projects running on World Community Grid, your grid software could receive workunits from any of the projects depending on your Project profile. If you prefer, you may elect to focus your computer's time only on particular projects. To do so, press the My Grid button in the upper navigation bar and select My Projects or click here. Work is sent only to machines which meet minimum system requirements set for a particular project. To read more specifics on the system requirements for the Influenza Antiviral Drug Search project and the other projects, click here.

Questions?
If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the HELP section of the website; (2) Review the forums to see if anyone has asked/answered the question that you have; (3) Ask the question in World Community Grid's Influenza Antiviral Drug Search project forum found here and a Community Advisor or a more experienced member will provide an answer; or (4) Send an email to the support desk from the Contact Us link found at the bottom of every page of the website (except in the forums).

We thank you for contributing to the Influenza Antiviral Drug Search project
[May 5, 2009 2:42:09 PM]

[priens]

Mooi! Weer een nieuw project, en nog wel eentje die erg toepasselijk is op het moment!
Eens kijken of we hier nog wat zinnigs aan kunnen bijdragen aan het onderzoek.

Sekerob, enig idee hoe lang dit project ongeveer zal gaan draaien?

[scorpionv]

Kijk nou, ik heb de eerste flu workunits al binnen gehad

[Anoniem: 167389]

depriens, er werd al langer over gepraat met UTMB toen er een telefoontje van Uni California, San Diego binnenkwam afgelopen week. Daarna is het gefastracked. Met de ervaring, de bekende compound libraries en het al in detail bekende H1N1 http://www.rcsb.org/pdb/explore/explore.do?structureId=3B7E was het een bijna routineklus. De graphics zijn een derivaat van FA@H en zullen waarschijnlijk nog wat polijstwerk krijgen evenals wat project pagina's. De gebruikelijke About the Project ontbreekt nog en wat volgordes op diverse plaatsen moet nog recht gezet worden. Duur ? 1-2 jaar denk ik, of niet want er zijn meer targets. Eerste lab tests willen ze al over 14 dagen beginnen op basis van eerste resultaten. Dit project is gelijk Normal Weight gegeven om het wat momentum te geven.

[Anoniem: 167389]

Het Help Cure Muscular Dystrophy - Phase 2 project is gelanceerd. Het heeft naar schatting, gebaseerd op de rekenkracht die phase 1 nodig had, ongeveer 92,000 oude CPU jaren valuta nodig. Dat is op alleen maar quads van deze tijd, ongeveer 17,500 quad jaren denk ik zo. (70,000 CPU jaren naar WCG tijdrekening). Met CPU progressie dus 2 jaar of korter, overwegende groei van WCG.

Technische achtergrond informatie van decryphton: http://www.ihes.fr/~carbone/HCMDproject.htm

De Announcement (links in de text staan in het origineel. Weer een nieuwe Badge!

Launch of the Help Cure Muscular Dystrophy – Phase 2 Project Reply to this Post
Reply with Quote
World Community Grid is pleased to launch the Help Cure Muscular Dystrophy – Phase 2 project by researchers supported by Decrypthon, a partnership between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research) , and Unversite Pierre et Marie Curie. The mission of the Help Cure Muscular Dystrophy – Phase 2 project is to investigate protein-protein interactions for more than 2,200 proteins whose structures are known, with particular focus on those proteins that play a role in neuromuscular diseases. The database of information produced will help researchers design molecules to inhibit or enhance binding of particular macromolecules, hopefully leading to better treatments for muscular dystrophy and other neuromuscular diseases. For additional information on this project, please press the Research button in the upper navigation bar or click here.

Project Badge
If a member contributes a minimum of 14 days of CPU Run Time to this project, they will receive a Help Cure Muscular Dystrophy – Phase 2 project badge on their member statistics page and next to their member name when they post in the forums. There is a different badge for each research project and beta testing. To read more about badges, click here.

Forums
In addition to providing information about this project, we have created a forum for discussions about the Help Cure Muscular Dystrophy – Phase 2 project. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title "Help Cure Muscular Dystrophy Scientist" are authorized to comment as representatives of the research organizations: Unversite Pierre et Marie Curie (Paris, France) and CNRS (Lyon, France).

Project Participation
The Help Cure Muscular Dystrophy – Phase 2 project is the fourteenth research project to be launched on World Community Grid and one of nine projects currently active. The other eight active research projects are: Influenza Antiviral Drug Search (launched May, 2009), Help Fight Childhood Cancer (launched March, 2009), The Clean Energy Project (launched December, 2008), Nutritious Rice for the World (launched May, 2008), Help Conquer Cancer (launched November, 2007), Discover Dengue Drugs – Together (launched August, 2007), Human Proteome Folding - Phase 2 (launched July, 2006) and FightAIDS@Home Phase 2 (launched November, 2005). For more detailed information and FAQs about each of these projects, please click on the Research button in the upper navigation bar or click here. We thank all of our members for their valuable contributions to the projects to date and hope you will continue to help us process those, as well as this latest project.

Because there are nine research projects running on World Community Grid, your grid agent could receive work units from any of the projects depending on your Project profile. If you prefer, you may elect to focus your computer's time only on particular projects. To do so, press the My Grid button in the upper navigation bar and select My Projects or click here. Work is sent only to machines which meet minimum system requirements set for a particular project. To read more specifics on the system requirements for the Help Cure Muscular Dystrophy – Phase 2 project and the other projects, click here.

Questions?
If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the HELP section of the website; (2) Review the forums to see if anyone has asked/answered the question that you have; (3) Ask the question in World Community Grid's Help Cure Muscular Dystrophy – Phase 2 project forum found here and a Community Advisor or a more experienced member will provide an answer; or (4) Send an email to the support desk from the Contact Us link found at the bottom of every page of the website (except in the forums).

We thank you for contributing to the Help Cure Muscular Dystrophy – Phase 2 project.
[May 12, 2009 2:21:09 PM]

[Anoniem: 167389]

En de project chart, die dynamisch bijgewerkt zal worden, voor zolang het duurt:

[Anoniem: 167389]

WCG in de wetenschaps-sectie van de online Volkskrant:

http://www.volkskrant.nl/..._ingezet_tegen_griepvirus

[Noordvogel]

Interessant artikel. Jammer dat DPC niet wordt genoemd

[priens]

Mooi artikel en vrij actueel nu!

[DukeBox]

Ik las gisteren toevallig ook een heel stuk over WCG in het IBM business blad, zeh ebben er best een leuk stuk van gemaakt maar verder het 'standaard' verhaal.

Wat ik wel opmerkelijk vond is dat ze aangaven dat de bij hun de meeste systemen maar voor 20% gebruikt werden en de overige 80% gebruikt wordt door de client... vervolgens staat er een bladzijde verder een stuk over hun 'green' status en dat ze software hebben ontwikkeld om het gemiddelde energie gebruik van systemen tot 80% te verminderen op o.a. energie gebruik van de CPU.... hoezo tegenstrijdig.

[Anoniem: 167389]

Deze draad is bedoeld als WCG nieuws draadje, 'green' crunching iets voor een apart topic, maar IBM intern heeft hun klanten met de 'muis/keyboard' inactive optie draaien... the Power Saving preset die je op de My Grid > Device Manager > Device Profile kan aankiezen, dus.

[Omied]

Noordvogel schreef op zondag 24 mei 2009 @ 10:52:
Interessant artikel. Jammer dat DPC niet wordt genoemd

Idee voor DPC-crew om een brief in te sturen met verwijzing?

[Anoniem: 167389]

Laat antwoord, 1-2 jaar. De code is FLU1, met een eerste indicatie hoe het project loopt:



Het Discovering Dengue Drugs Together, Phase 2 project loopt nu zeer goed nadat ze de hurricane Ike hebben doorgemaakt, daardoor maanden stillagen en nu samenwerken met TACC voor werk voorbereiding en nabewerking op hun 'normale super-computer.

Dr. Stan Watowich van de UTMB gaf net een link door naar een eerste 'paper' zoals het in het jargon heet in pdf.

New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors. For members wishing more detailed information about this project's underlying research and computational approaches, we have recently published a review article that discusses efforts to find small molecule drug-like leads that disable the dengue virus NS3 protease. These structure-based grid-centric approaches can be applied to most disease targets (such as influenza virus proteins). A copy of this article can be found here.

I hope you enjoy!

Stan
[Jun 26, 2009 3:09:09 AM]

WCG en het grid gebaseerde zoeken krijgen behoorlijke benoeming. Fase 1, zal wegwns begin Q4-09 ten einde zijn, maar voor die tijd zal DDDT- Phase 2 al opgestart zijn, met vooraf een Beta natuurlijk.

[Anoniem: 167389]

World Community Grid heeft op 07/07/09 een prijs gewonnen:

IBM awarded for innovative solution to tackling world’s most critical social and environmental problems

IBM was awarded the prestigious Coffey International Award for its application of technical expertise in innovative ways to address the greatest societal challenges of our time at the annual Business in the Community (BITC) Awards for Excellence last night.

lees hier verder: http://www.bitc.org.uk/me.../international_award.html

[Anoniem: 167389]

Nieuws over badge uitbreiding (die nu ook de min.periode aangeven) en wat verbeteringen daar waar de projecten uitgelijst worden. Het is een beetje WIP... heb veel te veel Saffieren exemplaren (2 jaar minimum bijdrage).

World Community Grid is pleased to announce several new updates to the web site.

Additional Badge Levels: Three new levels of Project Badges have been added. The new badges are for run time contributed to each research project:
- Ruby: 180 days
- Emerald: 1 year
- Sapphire: 2 years

We hope that these new levels of attainment will continue to highlight the accomplishments of our members and provide members who already have obtained Gold badges for any of the active projects something new to shoot for!

In addition to the new Project Badges, the web site now sorts lists of research projects by status (active projects are first, followed by completed projects) and then by project launch date. This may be seen on your My Grid page, as well the My Projects and Statistics by Project (http://wcg.chicago.ibm.com/stat/viewProjects.do) pages.

The next 3 enhancements are to the Results Status page and will help Members gather information to aid the Tech Team and Community Advisors in resolving issues:
- The result name now appears on the Result Log pop-up page
- The Application Version Number is now shown on the Workunit Stats pop-up page
- The more specific statuses: "Server Aborted" and "User Aborted" were added Results Status page

nelsoc
[Jul 14, 2009 4:51:13 PM]

[scorpionv]

Holy crap, inderdaad nieuwe badges. Ik schrok me een hoedje toen ik op WCG keek

[Anoniem: 167389]

Fase 1 bijna klaar:

Final Batches of DDD-T Phase 1 have been loaded.

Greetings everyone,

Discovering Dengue Drugs - Together Phase 1 is almost complete!!!! biggrin

I have loaded in the last new work from the researchers last night. I am estimating that new work for DDD-T will last for about 12 days. This means that after all of the new work has been sent out, members with DDD-T selected as their only project may start seeing "No new work available for the projects selected". It will take about 10-14 days after that last new work unit has been sent to actually return all of the results to the researchers. This is due to make up work units being sent out to additional hosts for calculations.

Thank you for contributing towards this project as of this posting over 11261 years of CPU time have been completed!

-Uplinger

(Note: these numbers are just estimates and may be off by a day or so).

http://www.worldcommunity...g/viewthread?thread=26235
----------------------------------------
uplinger
Jul 15, 2009 3:38:15 PM]

[Anoniem: 167389]

Op het thema van badges, is de Help FAQ nu ook up to date. De huidige stand:

What is a Project Badge?

A Project Badge is an acknowledgment of the contribution that a member has made to one of the research projects running at World Community Grid. All available badges may be viewed here.

A badge appears as a image for a member on their My Grid page, the Member Information page and next to their name in the forums. A badge is awarded to a member based upon how much computer processing time they have contributed to the project.

There are 6 levels of badges for run time donated to each research project and each is denoted by a different color background:

* Bronze - 14 days
* Silver - 45 days
* Gold - 90 days
* Ruby - 180 days
* Emerald - 1 year
* Sapphire - 2 years

No badge will appear until members contribute a minimum 14 days of run time to a research project. World Community Grid may occasionally change these rules for certain projects. This was done for the AfricanClimate@Home project, which required only 1 days worth of run time for a Bronze badge, 7 days for a Silver badge, and 30 days for a Gold badge, 45 days for Ruby, 60 days for Emerald, and 75 days for Sapphire.

[Voor 3% gewijzigd door Anoniem: 167389 op 16-07-2009 16:54]

[MAB The Frisian]

De forumpage wordt hier al enige tijd niet geopend. Iemand enig idee wat daarvoor de reden zou kunnen zijn ? Heb met de andere pages geen problemen.

[batsma]

kijk maar op het grutte pier forum, daar heb ik de vraag ook al eens gesteld. ik krijg ook alleen een witte pagina te zien als ik het SCG forum probeer te openen

[Anoniem: 167389]

SCG? Was de dagdraad niet een betere plek geweest voor deze vraag? Zie het WCG Forum index overigens prima... geen minuut interruptie in dagen. Cookie/Cache clean doet wonderen, vaak.

bvd.

[batsma]

Anoniem: 167389 schreef op vrijdag 17 juli 2009 @ 12:21:
SCG? Was de dagdraad niet een betere plek geweest voor deze vraag? Zie het WCG Forum index overigens prima... geen minuut interruptie in dagen. Cookie/Cache clean doet wonderen, vaak.

bvd.

was een tiepvout ik bedoelde natuurlijk het WCG forum.

[Anoniem: 167389]

Van de Discovering Dengue Drugs - Together, hoofd wetenschapper Dr. Stan Watowich, met een belangrijk regeltje onderstreept:

Final Batches of DDD-T Phase 1 have been loaded.

Many, many thanks to World Community Grid members for successfully completing Phase 1 of "Discovering Dengue Drugs-Together". The "together" part is most appropriate since we truly need your computational expertise and resources to get through this project!

We are validating the final workunits, analyzing all results, and developing drug insights from the Phase 1 data you produced. Do not be surprised if new DDDT-1 workunits show up in your cache from time to time since we will likely need to test an additional target or two to help refine our evolving drug predictions. Thus, although completed, DDDT-1 will remain officially active on the grid.

Now, on to launching Phase 2 - so very very soon!

All my best,
Stan

[Jis]

Op het forum van WCG is onderstaande berichtgeving en dankwoord van het einde van het Clean Energy Project te lezen:

The Clean Energy Project (Phase 1) Completion

World Community Grid is pleased to announce that as a result of the generous contribution of computing power from our members, Phase 1 of The Clean Energy Project finished on October 13, 2009.

The project launched on December 5, 2008 and ran for less than a year. During that time over 57,000 members processed almost 2 million results which required over 2,000 years of computing power from over 121,000 computers.

With the completion of this project, our members have significantly contributed to the research of discovering new materials that efficiently harvest solar radiation for the next generation of solar cells. This research information has helped determine which materials are most promising for developing affordable solar energy technology. This same research would have taken 22 years to complete on a regular scientific cluster.

Phase 1 was designed to perform molecular mechanics calculations: Some of the computers contributing to the Clean Energy Project are carrying out molecular mechanics calculations of molecular crystals, thin films and molecular and polymer blends to study the packing arrangements and for predicting charge and excitation energy transport properties of the candidate materials. These calculations will be carried out using the CHARMM molecular mechanics package developed by the Karplus group at Harvard University.

Phase 2 of the project will perform electronic structure calculations: To obtain the relevant optical and electronic transport properties, some of the computers connected to the Clean Energy Project will be computing calculations using wave function methods (such as Hartree-Fock or second-order perturbation theory) and density functional theory. These calculations will help researchers build a database of molecular properties that together with the results of the molecular mechanics calculations will help us identify potential candidate materials. The electronic structure calculations will be performed with the Q-Chem quantum chemistry code, developed by Q-Chem, Inc.

At this time, the researchers are busy performing post-processing on the results from Phase 1 and are preparing for Phase 2. You may read about these plans and get the latest update from The Clean Energy Project Scientists in this forum thread .

On behalf of The Clean Energy Project research staff at Harvard University, USA, we wish to express our sincere gratitude to you for contributing your computer power to this project. With your contribution, this phase of the project was completed in a fraction of the time it would otherwise have taken.

[gp500]

Op naar fase 2 dus. ik heb 1 of 2 wu's gedaan voor CEP.

[Xaverius]

Damn, nog geen goud binnen...

[priens]

Het is zover, Discovering Dengue Drugs - Together - Phase 2 is gestart.

In het kort de doelstelling van het project (Engels):

Mission
The mission of Discovering Dengue Drugs - Together - Phase 2 is to identify promising drug candidates to combat the Dengue, Hepatitis C, West Nile, Yellow Fever, and other related viruses. The extensive computing power of World Community Grid will be used to complete the structure-based drug discovery calculations required to identify these drug candidates.