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Search Results for:  Verification Code

What is the Verification Code and what is it used for?

The Verification Code is a private, personal code that you can use to verify your team membership and team stats. There are teams that provide incentives and/or rewards to members for being a part of their team. World Community Grid is providing the Verification Code as a way for these teams to verify their members' statistics and team membership without requiring members to give the team their password.

Note that your Verification Code will change if you change your member name and/or password. If your team is relying on your verification code to verify your membership and statistics, be sure they have your current Verification Code.

To verify the team membership and statistics for a member, use the API:
http://www.worldcommunitygrid.org/verifyMember.do?name=MEMBERNAME&code=VERIFICATIONCODE

You will get a response in XML containing the membership information for that member. If there is an error, it will be reported back in the XML response.


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Is there an API to get a list of in-progress and recently returned results for a member?

Yes. The URL for the API to access a members results is:

https://www.worldcommunitygrid.org/api/members/{member name}/results?code={verification code}

member name is the member name of the member whose results data you wish to access
verification code is found on the My Profile page of the member whose results data you wish to access

The default format is JSON.

Optional parameters are (can be combined):

  • Limit: Defines the number of results returned. Default is 25.
  • Offset: Defines how many results are skipped before the API returns any data. Default is 0.
  • SortBy: Defines the sorting order of the results. Options are: DeviceId, SentTime, ReportDeadline, ReceivedTime or CpuTime. Default is SentTime.
  • Format: The format of the data. Options are XML or JSON. Default is JSON.
  • ModTime: Return results which were last modified on or after this time. This value is a Unixtimestamp (number of seconds since midnight Jan 1 1970).
  • ServerState: Return results based on whether they are currently in progress or have already been reported back to World Community Grid. 4 would return in-progress results, 5 would return results which have already been reported back to the server.
  • Outcome: Return results based on the outcome of their processing. 1 means success, 3 means error, 4 means no reply, 6 means validation error, 7 means abandoned./
  • ValidateState: Return results based on the validation status. 0 means pending validation, 1 means valid, 2 means invalid, 4 means pending verification, 5 means results failed to validate within given deadline.
  • FileDeleteState: Return results based on their file delete state.  0 means not deleted.  1 means ready to delete.  2 means deleted.

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I have a platform that isn't supported by World Community Grid. Could I get a copy of the research application code and compile it myself?
No. The code has to remain in the control of the World Community Grid support team. Even the slightest change in the code, including using a different compiler, could render the research results useless. In addition, the license agreement that we have with the researchers for their code stipulate that only the World Community Grid support team can touch the source code. The source code usually differs slightly from potential public versions of the same code due to changes made for use with the specific grid project. Furthermore, we typically run many tests to make certain there are no problems on a given platform.
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What about other mobile platforms?
At this time, World Community Grid can only support Android mobile devices, but we are investigating options to expand to other platforms in the future. Apple's App Store Review Guidelines does not currently allow apps that download code in any form, apps that install or launch other executable code, or multitasking apps. This is likely to prevent World Community Grid from being accepted as an iOS app.
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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.
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What is the difference between a genome and a metagenome?
A genome consists of all the genetic code for an individual organism, while a metagenome describes all genes and elements encoded in a group or community of organisms, for example, all of the microorganisms within a sample of soil or ocean.
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How do I change my email address?

To change your email address, take the following steps:

  1. Log in to your World Community Grid member account.
  2. Select Settings from the top right of any webpage.
  3. Click on the My Profile tab on the left hand side of the page.
  4. Change your email address.
  5. Enter your current password and press Save.
  6. Verify your new email address via the verification email sent to the new email address.

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What is the World Community Grid widget?
The World Community Grid widget is a way for you to promote World Community Grid and show your team or personal contribution on your website or blog. It consists of a small piece of HTML code that you place on your website. This HTML code will display your custom widget with the most the current statistics for your or your team.

Here is an example:


To get your custom widget, just log in to World Community Grid, go to the Settings page, and click on the Create a Widget link in the left hand navigation. This will take you to a form where you can customize a widget with the World Community Grid logo, and your personal (or your team's) statistics. When you're happy with your widget, just copy the code at the bottom of the form, and paste it into your website!


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What proteins do these viruses make?
While the flaviviruses and the hepaciviruses have some differences in their genome and coding strategies, the proteins they encode are very similar. They all encode the structural proteins that surround the nucleic acids. These include the envelope glycoproteins, the capsid protein, and the membrane protein. In addition, they encode non-structural proteins. These include a helicase, polymerase, methyl transferase, and the protease. It is the highly conserved protease that is the target of inhibition for this study.
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Why are my work units failing with exit code 234 “Error: cl_khr_local_int32_base_atomics extension required by this program is not supported”?
The Help Conquer Cancer graphics card application requires the OpenCL extension cl_khr_local_int32_base_atomics and will not run on cards that do not support this extension. If you see the error above it is because your graphics card does not support the extension.
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What proteins do these viruses make?
While the flaviviruses and the hepaciviruses have some differences in their genome and coding strategies, the proteins they encode are very similar. They all encode the structural proteins that surround the nucleic acids. These include the envelope glycoproteins, the capsid protein, and the membrane protein. In addition, they encode non-structural proteins. These include a helicase, polymerase, methyl transferase, and the protease. It is the highly conserved protease that is the target of inhibition for this study.
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Why do I get the error: exit code -1073741510 (0xc000013a) (On Windows Vista)?

The message exit code -1073741510 (0xc000013a) means that when you log off of Windows the application gets terminated quite abruptly. Vista can shut down very quickly and not allow BOINC enough time to stop properly. This problem was corrected in the 5.10.45 version of BOINC. Please ensure that you are running the latest recommended version of the World Community Grid software.

To determine what version you are currently running on your computer, right click on the World Community Grid, or BOINC, icon in the bottom right corner of your display (by the date and time). Click on “About World Community Grid – BOINC Client” or “About BOINC” and the current version of the software will be displayed.

You may check if you have the latest supported version of the World Community Grid software by visiting this page: https://www.worldcommunitygrid.org/ms/viewDownloadAgain.do . The version number is displayed below the name of the agent for each operating system. If this number is the same as the version number that you have installed then you have the latest supported version.


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Higher resolution is important for other methods as well
Progress in high-resolution structure prediction will invariably be carried out in parallel with methods including but not limited to: predicting protein-protein interactions, designing proteins and distilling structures from partially assigned experimental data sets. Indeed many of the scoring and search strategies that high-resolution de novo structure refinement methods employ were initially developed in the context of homology modeling and protein design (Kuhlman et al. 2002) (Rohl 2004a). The Rosetta commons is currently developing Rosetta for all these methods and more. The part of Rosetta we use for HPF2 is less than half the code.
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Do you have a startup script for the BOINC client on Linux?
There are two common ways to have BOINC automatically start on a Linux system. The first will start BOINC when you log in to your Linux system. This involves placing code into your shell resource file (such as .bashrc). The second will start BOINC when the system is started. You can read more about this at the following sites: http://www.spy-hill.net/~myers/help/boinc/unix.html#start and http://boinc.berkeley.edu/autostart_dennett.txt
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What are proteins?
A Protein is a chain of amino acids that folds in a particular structure necessary for the function of that protein. The chain can be composed of up to 20 different kinds of amino acids, and the types and order of those amino acids are encoded in the gene sequence (the genetic code). The amino acid sequence is also known as the “protein sequence” because there are multiple gene sequences that can specify the same protein sequence. A cell is made of thousands of proteins (in addition to fatty molecules called lipids, sugars and other chemicals) that can have either a structural function or an enzymatic activity. Enzymes are proteins that help break down other molecules or build new ones. Several enzymes can work in concert to convert molecules into other chemical building blocks for the cell (for example, sugar into lipids), or to extract energy from sugar.
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What does the Uncovering Genome Mysteries project screensaver show?

The graphics show a portion of a pair of protein sequences, which have been compared on your computer or device in the form of “letter codes”. The letters (A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V) represent the twenty types of amino acid molecules that are assembled in a chain to form the protein molecule. The matching letters in the two protein sequences are highlighted.

When sequences match, it means that the unknown organism produces a protein that is similar to a more well-known protein. This can indicate that the two proteins have similar functions, and give scientists a head start in understanding the unknown organism.


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Why are my work units failing with exit code 232 “ERROR: .\VerifyGPU.cpp:65 Unknown”?
This failure occurs for work units running on the graphics card during a test of the ability of your graphics card to run the work unit. If you see this error, make sure you are using the latest video driver for your graphics card. Also, remote desktop connections can have an effect on graphic card applications and it is recommended not to have an active remote desktop connection while the Help Conquer Cancer graphics card application is running.

You may learn more about updating your video drivers at the website of your graphics card manufacturer: Nvidia or AMD
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Why did the Genome Comparison project compare protein sequences?
Only a fraction of the predicted protein content encoded in completely sequenced genomes has actually had their biological function and expression confirmed through laboratory analysis. The assignment of predicted biological functions and structural features to raw sequence data is called annotation, and is accomplished mostly by comparing them to predicted proteins or protein coding genes with information stored in different public domain databases around the world. However, annotation is often incomplete, uses non-standardized nomenclature or can be incorrect when inferred from previous incorrectly annotated sequences. Thus, an all against all controlled comparative database would be of great use as a reference.
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What are proteins?

Proteins are the fundamental building blocks for many components within living organisms. More specifically, they are a long sequence of subunits called amino acids, of which there are 20 kinds. Each gene specifies the specific order of the amino acids assembled to make a particular kind of protein. When this sequence of amino acids is constructed by the organism, it tangles or folds into a very particular shape. The shape (structure) of the protein determines its function.

Proteins can be small or large, sometimes containing thousands of atoms. When you eat food containing proteins, your digestive system breaks them down into their constituent amino acids so they are available for your cells to make new proteins according to your genetic codes.

Learn more about proteins at https://www.worldcommunitygrid.org/research/proteome/details.do


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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.

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Who are the scientists involved in this study?

The Microbiome Immunity Project brings together researchers at the Broad Institute of MIT and Harvard, Massachusetts General Hospital, University of California San Diego and the Simons Foundation’s Flatiron Institute.

The Broad Institute brings expertise on the role of the human microbiome in health and disease to the project. By coupling microbiome analysis with the clinical knowledge at Massachusetts General Hospital, they analyze data generated from individuals with these diseases to prioritize genes from bacteria that are relevant in autoimmune diseases such as Inflammatory Bowel Disease and Type 1 Diabetes.

The Knight Lab at the University of California San Diego brings knowledge on and expertise in microbial genomes. They prepare input data for World Community Grid based on information from the Broad Institute. After obtaining results from World Community Grid, with the help of the Flatiron Institute, they annotate protein functions inferred from structures. The Knight Lab will also coordinate efforts to predict protein-protein interactions and design small molecules. They will also build a resource to collect all of the Microbiome Immunity Project predictions and share them with researchers from around the world.

The Flatiron Institute provides the expertise in predicting protein structure and function. They will work with the Knight Lab to further develop these codes to predict large microbial protein families, about which little is currently known.


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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.

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