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What is validation?

World Community Grid is a volunteer computing grid. This means that work is being sent to computing devices that are outside the control of World Community Grid. Most devices that perform this work are reliable. However, there are a few devices that are not reliable due to things such as users over-clocking their machines, memory errors, disk errors, CPU errors or viruses being present. This means that the results returned need to be validated to make sure that they represent the correct answer.

We perform three different types of validation at World Community Grid:
 

• Redundant Computations: In this type of validation, two copies of the work unit are sent to members devices. Once both results are returned, they are compared to ensure that the results are identical. If they are, then the result is accepted. If they are not identical, then additional copies are sent until several devices agree on what the result should be. This policy establishes a very high level of confidence in the reliability of the results. Mapping Cancer Markers and Uncovering Genome Mysteries are examples of projects that use this technique.
• Single Validation - Type 1: In this type of validation, only one copy of a work unit will be sent to a device if the device is "trusted", that is, if it has been participating long enough and returning good results. If the device is not trusted, then it will still be assigned the work unit, but a second copy will be sent to another device and the rules for redundant computation above apply. As a precaution, the research code computes certain items that allow us to quickly check on the server if the computation is likely to have finished correctly. Additionally, trusted devices are randomly sampled to have their results double-checked. These techniques provide a very high level of confidence in the reliability of the results. FightAIDS@Home and Outsmart Ebola Together are examples of projects that have used this technique.
• Single Validation - Type 2: This is similar to Single Validation - Type 1 except that due to the fact that different results are generated each time the work unit is run (due to the research techniques applied in the application), we send out many copies of each work unit. We currently do not have any research projects utilizing this technique.

Why does this application require zero redundancy, i.e. no comparison of results across devices?

Unlike many of our research projects, FightAIDS@Home – Phase 2 does not require redundancy, where the same research task is sent to two devices and the results are compared for consistency. Instead, this project will be using various processing metrics during the computation of a research task to validate that the task is progressing without errors.

What is DNA?

DNA stands for deoxyribonucleic acid. DNA strands are molecules that act as blueprints for all living things. A single DNA molecule consists of a helical (coil shaped) strand or chain, consisting of four chemical “letters” that make up phrases (“genes”) and the genetic code. These letters are A, C, T and G and stand for the four types of compounds (adenine, cytosine, thymine, and guanine), which are assembled to form the DNA molecule’s gene codes.

What are microorganisms?

Microorganisms are microscopically small life forms, mostly single celled, and include bacteria, archaea, protozoa, yeasts and microscopic algae. Members of these diverse groups are present in almost all environments on earth: in the air, water, earth, rocks, and even where conditions are very harsh, such as the deep ocean and polar environments. They play a crucial role in maintaining all ecological systems and interact closely with one another and with other life forms. They are present in and around other living systems, such as plants, animals and humans.

HPF1 vs. HPF2: Res-res pair score

The pair score in HPF2 is like the pair score in HPF1, but HPF2-pair score takes the position of Rotamers (a way of efficiently representing all side chain atoms) instead of centroid positions (representing the amino acid as a blurred out single point). So think of the HPF2 pair score as a all-atom version of the HPF1 pair score (appropriately re parameterized, of course).

What is unique about how research tasks are managed for FightAIDS@Home – Phase 2? How does this impact how work will be distributed to volunteers?

The simulations researchers need to carry out are typically very long running and complex, each of which would take several months to run on a single device. Instead, researchers split up each simulation for a given drug candidate into shorter running research tasks: much smaller and more manageable pieces. These pieces of work can be run independently and simultaneously on a volunteer devices.

However for FightAIDS@Home – Phase 2, the research tasks within a single drug candidate simulation are dependent on each other where the output of one task is used as the input to the next. This means longer research tasks within each drug candidate simulation which can’t be run simultaneously.

To handle this complexity, we are using two different, but related mechanisms called trickle messaging and intermediate uploads to allow us to track your progress through a research task and manage the handover of that task from one volunteer to the next to get it completed in the shortest time possible. This way, we can track the progress of the long simulations to ensure that computations are not delayed or lost, while the researchers get the valuable results back as quickly as possible. In addition, volunteers acquire their credits sooner too.

What is different about World Community Grid and other BOINC distributed computing projects?

Many of the BOINC projects are oriented toward one single research goal. And for those, the researchers have to set up their own infrastructure and manage the workload themselves. World Community Grid is able to accommodate multiple research projects. We run these projects for researchers from nonprofit organizations so that they do not have to manage the work and thus are able to focus on the science part of the research. For more information about how projects are selected to run on World Community Grid click here

To learn how to register and start participating in World Community Grid click here

How do I limit the number of tasks assigned to one of my devices for a specific project?

Some projects can be very memory intensive, and some devices are not able to handle these memory intensive projects starting up multiple tasks for that project at a single time. Limiting the number of tasks allowed for a project will help to keep that from happening.

To limit the number of tasks for a specific project, please follow these steps:

1. Log in to your member account.
2. Click on Settings and then Device Manager.
3. Select the device profile you would like to make the changes to.
4. On the Device Profiles page, select Custom Profile.
5. Scroll down to the Project Limits section and set the tasks limits to your preferences.
6. Click the Save button.

How much computing power does this project need, and why?

Based on the molecular dynamics simulations that the researchers have done up to now, using a cluster of 20 nodes (160 CPU cores) for a couple of months at a time, they estimate that to extend the simulations to water-flow velocities typical of practical nanotube filters, they will require another factor of 400 or more in compute time. And to simulate a representative range of membrane pore sizes would require a further factor of 10, for a total of order 106 thousand single-core-CPU-years. Add on to this a wide variety of contaminants they would like to add to the water in the simulations, and the sky is the limit!

Of course, the researchers will have to go one step at a time, and a lot of the computing effort will be to verify previous results at each stage and to make sure the results are reliable.

Why are my work units failing with exit code 233 “ERROR: Kernel execution time estimate too high, exiting”?

At the beginning of each work unit run on your graphics card, a small portion of the workload is run to estimate the execution time of a single kernel execution on the graphics card. If this estimate is too high, the application will exit to reduce the risk of Windows restarting the display driver due to the Timeout Detection and Recovery feature of Windows. If this occurs, the above error message will be written to the stderr log. If this occurs multiple times, it is likely the graphics card is not capable of running the project. Please refer to the "What graphics cards are not able to participate in the Help Conquer Cancer research project?"FAQ for a list of graphics cards which are not supported.

If it occurs occasionally but not on every execution, it could be that other graphics intensive work is interfering. We recommend that you set your preferences to not allow World Community Grid to run while you are actively utilizing your computer. This option is available on the Device Profile page under the custom options section. This option is labeled "Do work on my graphics card while computer is in use?". Select "no" and save.

What is Tissue Microarray technology?

Tissue Microarray (TMA) technology is a relatively new investigative tool for harvesting small cylinders of tissue from a range of standard histological sections and arranging them on a on a single microscope glass slide in a grid-like manner. The arrays are subsequently treated with antibodies (proteins which specifically detect and bind to molecular targets of interest) that are complexed with a staining medium to determine the protein and molecular signatures of the underlying pathology of the tissue samples. This technique allows maximization of tissue resources by analysis of small core biopsies of blocks, rather than complete sections. Using this technology, a carefully planned array can be constructed with cases from pathology tissue block archives, such that a 20-year survival analysis can be performed on a cohort of hundreds patients, simultaneously using just a few micro-liters of antibody.

Using TMA technology investigators are beginning to unveil the underlying mechanisms by which healthy tissues are transformed into malignancies and are gaining unparalleled insight as to which patient populations are most likely to respond to a given treatment regimen. TMA’s hold tremendous promise for improved accuracy in prognosis, therapy planning and drug discovery.

How is Protinfo different from other approaches?

Protein structure prediction is an active area of research, and no one method or methodology is "best" for all situations. The public success of projects like Folding@Home, POEM@Home, Human Proteome Folding, and Rosetta@Home are evidence of the interest in solving this computationally challenging problem. We wish to offer another approach that differs in certain subtle but significant ways that can provide complementary and competitive results.

Some approaches (like Folding@Home and POEM@Home) simulate the protein folding process as we believe it occurs in real life, where physical energies are minimized. Protinfo (like Human Proteome Folding and Rosetta@Home) uses a minimization of "statistical energies" to identify likely protein structures, but with a slightly different approach. Rather than relying on a single complex energy function, Protinfo uses a simple, easily evaluated function and chooses the best structures by following up with a set of more sophisticated functions. Another difference is that Protinfo uses a novel continuous sampling methodology that enables us to explore good structures more finely. The continuous sampling methodology incurs little memory overhead and evaluating our compact energy function is very fast. This allows Protinfo to run on almost any computer.

The Protinfo structure predictions have been ranked as some of the best by the Critical Assessment of Structure Prediction (CASP) competition since 1994. You can read more about Protinfo on the researchers' page about this project.