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| Message Board |
| Request for CASP8 targets | (2008-5-7) |
Dear CASP8 participants,
The CASP8 prediction experiment has just begun, and as always, it will only work if we have the help of the experimental community in providing targets.
Many targets have been provided by structural genomics centers in the last two CASPs, and expect to that will be the case again this time. However, we still very much need targets from the broader structural community. We need all sorts of targets but in particular, there are several sorts of targets we expect to be short of.
1. We expect the number of ‘new fold’ provided by the SG centers will be smaller this time, and we really really need these to test ‘ab iniito’ target prediction methods. So if you have one, we would be very very grateful if we could use it as target.
2. We want to improve our test set for assessing disorder prediction methods, so if you have structure that contains significant disorder, we would very much appreciate using it as a target.
3. In all the CASPs to date we have only ever had one membrane structure target, so if you have you could make available, that would be great.
CASP only succeeds because of the support and co-operation of the members of this community, and we very much need your help.
The time table is similar to other CASPs: The prediction season opened at the beginning of May, and will run until the end of July. We will release targets continuously throughout that period, as evenly spaced as possible, and hope to have about 100 targets altogether. Each target will be available for prediction for a period of three weeks, although in some cases we request a longer period to allow it to be used to test refinement methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed.
It’s fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the beginning of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December.
So, if you have any thing suitable, we would be most grateful if you would enter the data on the web form: http://www.predictioncenter.org/casp8/targets_submission.cgi
OK, that's about it. Please get in touch if you have any questions or concerns. Hoping for lots of targets....
CASP8 organizers
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| CASP8 started | (2008-5-5) |
We have released the first two CASP8 targets. Good luck everyone in predicting these and all the subsequent CASP8 targets.
Please, pay special attention to the column "Type" in the Target List. In the current CASP experiment we are planning on releasing between 50 and 60 targets to be evaluated in the human and server track and many more targets (depending on target availability) to be evaluated in the server-only track. Assessors will be comparing all participating predictor groups on the subset of Human/Server targets and, additionally, the server groups on all released targets. The human-expert groups should concentrate on predicting structures for the Human/Server targets. Those, wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation emphasis will be placed on the "Human/Server" targets. Subject to availability, we will give priority to releasing targets containing low homology domains in the Human/Server track.
Server predictions for all targets will be made publicly available immediately after acceptance by the CASP verification system. Receiving status of server predictions can be checked from the main CASP8 web page by following the link "Server Predictions." Please note that tarballs of all 3D models (with AL predictions already converted into coordinates) will be posted at the same place usually with one-day later. The electronic address of these tarballs will be sent to the quality assessment (QA) servers 4 days after the original target release. QA servers will have an extra 3 days to submit QA predictions.
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| CASP8 server dry run - April 28 | (2008-4-28) |
On April 28 we will have the last round of dry runs for the servers. Please get your servers ready.
The first CASP8 targets will be released on May 5.
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| CASP8 server rules | (2008-4-2) |
CHANGES relative to CASP7
There will be just minor changes to the rules for server participation in CASP.
According to the suggestions of CASP7 predictor meeting, in CASP8 we are extending the window for accepting server predictions. Servers will now have full three days to return the prediction. No additional time for corrections will be allotted but corrections will be accepted within the original 72 hour window.
Also, according to another recommendation of the CASP7 predictor meeting, we will have two different sets of targets for evaluation in the human-and-server track and in the server-only track. We plan to release as many targets as possible for evaluation in the server-only track and a subset of around 50 targets from among these for the human-and-server track.
For the servers participating in the model quality assessment category, we will be sending a link to the tarball of accepted server structure predictions on a particular target in 1 business day after closing the window for server 3D predictions. The quality assessment servers will have another 3 days to generate the model quality assessment prediction.
DRY RUN
We will be testing connectivity with registered CASP8 servers starting on April 14, 2008. To test your server, we will send you an old CASP7 target (T0283). Please respond as you would for CASP8 targets. Of course, these predictions will not be part of the CASP8 experiment.
If your server participated in CASP7, we expect the test to be just a formal recheck. For new servers: we will be sending 3 variables to your server's submission URL: the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results). For the quality assessment servers we will be sending the TARBALL-LOCATION variable instead of (or in addition to, if you specify so) the SEQUENCE. Please, make sure you provide the required parameters in your CASP8 server registration.
IMPORTANT THINGS TO REMEMBER
1. Target distribution procedure for servers.
You will be receiving CASP8 queries from the distribution server in Davis and the results will be collected directly by the Prediction Center. At the end of each week we will notify you about how many targets we plan to release the following week. Targets are planned to be released on business days only. We plan not to exceed a load of 3 targets per day for servers. Targets will be made available and requests to all servers will be sent around 9am PST. The submission engine will resend the query if it encounters obvious connecting problems (network timeouts, 'no response' etc.). Failures that go beyond that require special attention, but we'll make every effort to notify server curators ASAP if we suspect something is not working. The facility that allows checking data flow status by server predictors will also be available.
2. Server submission format.
Please submit your predictions in the standard CASP format. Your submissions will be immediately verified at time of submission. CASP warning and error messages will return directly and immediately to you, and will refer to the material you submitted, allowing you to respond in close to a server time frame, if necessary. Please note that, as in previous experiments, no prediction will be finally accepted by CASP until it passes CASP format verification.
Below we summarize differences in format of server submissions from that of human groups.
2.1 Header AUTHOR should contain your group name instead of the 12-digit predictor code, e.g.
AUTHOR 3D-JIGSAW
or
REMARK AUTHOR 3D-JIGSAW
2.2. Header SCORE in your prediction is allowable and optional (a real number reflecting self-estimation of the prediction quality).
2.3. For servers, it is allowed to have several models for the same target in one file. If your server returns only one file with several models, we will preprocess such an entry. You may add only one set of required header fields (PFRMAT, TARGET and AUTHOR) at the beginning of the file. Our script will split a multiple model file into separate files (one model per file) and only then we will send each model separately to our verification software (models numbered 6 and higher will be ignored). Error messages (if any) will be sent for each model separately. So you will be able to correct models (if needed) separately.
3. The timeframe for server prediction acceptance is the following. All server groups have 72 hours since target distribution to return the prediction. Error notifications will be sent to the server contact person's email address. If your prediction doesn't pass the CASP verification system, you will need to correct your format manually and resubmit the rejected prediction within the original 72-hour window. To do this, you will need to include the following line in your revised prediction:
REMARK Corrected server submission
and send it by email to: servers@predictioncenter.org .
After 72 hours no server predictions will be accepted or altered in any way. If you expect your server to work on prediction generation more than 72 hours, then we would advise you to register a regular (not server) prediction group for CASP8 instead.
You will be able to check the submission status of your prediction through the Server Submission Status Page or through the Model Viewer facility.
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| CASP8 registration | (2008-3-22) |
The registration for CASP8 experiment is now open.
To register for the experiment, you will need to register with the Prediction Center (PC) first (if you haven't done this yet). At this step we will collect the basic registration information to be used for your participation in CASP8, all subsequent CASP experiments, between-CASP initiatives, and local services. The information provided by you will not be shared with anyone outside of the CASP system.
After you register with PC and login to our website, you will be able to register for the CASP8 experiment (a separate registration form under the CASP8 menu). You will find five separate registration forms there. Please, read the registration instructions and use the appropriate form.
We ask that you register with the Prediction Center at your earliest opportunity as we plan to release future CASP8-related news mainly through our website. We recommend that you select an option "Subscribe for Prediction Center newsletters" as in this case you will be receiving emails every time the news are posted on our website. This functionality was just recently added to our registration form. So, if you have registered earlier, please go to "My personal Data" link and select this option.
Also, we ask server group leaders to register as soon as possible as we are planning on testing the connectivity with the registered CASP8 servers starting April 14, 2008. Server participation rules and the details of the dry run will be posted in the Message Board section of our website shortly (this section is available from both the Prediction Center home page and the CASP8 home page).
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| CASP8 preliminary timetable | (2008-2-1) |
Registration for the experiment will start in the last week of March 2008.
Prediction season will run from early May through early August 2008. The first prediction targets will be released not earlier than May 5, 2008; the last prediction targets will be released not later than July 18, 2008; prediction season will end not later than August 1, 2008.
According to the recommendations of the CASP7 predictors meeting, we will be releasing about 50 targets for evaluation in the human and server track and as many targets as we can for evaluation in the server-only track (including "human and server" targets). The human-expert groups wishing to take the challenge and predict all of the released targets (including the "server-only" ones) are welcome to do so but the evaluation accent will be placed on the selected targets. Subject to the availability, we will give priority to targets containing low homology domains for inclusion in the human-expert modeling experiment.
The meeting to discuss results of the experiment will be held on the island of Sardinia, Italy, December 3-7, 2008. The meeting will take place at Hotel Setar , near Cagliari. The hotel is located in Quartu S. Elena, 10 kilometers from Cagliari and 15 from the Cagliari airport.
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| CASP 7.5 meeting | (2008-2-1) |
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Together with CNIO, Madrid, we are organizing the next between-CASP meeting (CASP7.5). It is going to take place in Madrid, Spain in April 2008. The idea of the between CASP meetings is to update the progress of structure prediction as measured by the CASP experiments. In contrast to the full CASP meetings that are exclusively for participants and developers, this meeting will be open to all interested scientists. All interested please check the meeting web page: http://ubio.bioinfo.cnio.es/casp/index.html
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