|
|
| Message Board |
| CASP9 meeting venue and dates | (2009-11-16) |
|
CASP9 predictors' meeting will take place at the Asilomar Conference Center, Pacific Grove, California on December 5-9, 2010. Details of the future CASP9 experiment are available from the Prediction Center website.
|
|
| CASP9 preliminary timetable | (2009-9-11) |
CASP9 experiment will be run May through July 2010.
Tentative dates are as follows:
March 30, 2010 - registration starts
April 14 - server "dry run" starts
May 3 - first targets will be released on or shortly after this date;
July 17 - last targets will be released not later than this date;
July 31 - prediction season ends;
December 2010 - the predictors meeting takes place at the Asilomar Conference Center in Pacific Grove, CA, USA.
CASP9 organizers
|
|
| CASP8 domain definition and coordinates | (2008-11-21) |
We have released the official domain definitions and coordinates used for CASP8 evaluations. CASP8 Abstract book is also available from our website. Results of the automatic evaluation of the predictions will be available one week before the meeting.
CASP8 organizers
|
|
| Arriving to Sardinia | (2008-11-16) |
A few important information about your travel to Sardinia:
Once you get to the airport of Cagliari, there are two ways to get to the hotel:
By bus: You take the ARST bus to Cagliari. the timetable can be found at http://www.sogaer.it/aeroporto/pullman/ . The cost is 2 Euro and the ticket can be bought at the automatic machines located in the hall of the airport.
The bus leaves you at the bus station in Cagliari. The station is on a square (Piazza Matteotti). You take the bus PF (direction Fiumini) and get out at the Hotel Setar stop (about 40 minutes). The ticket is 1 Euro.
You can take a taxi. The cost is about 40-50 Euro. Please only take official taxis and ask the driver the approximate cost to Hotel Setar.
There will probably be several people coming to CASP in your plane. You might want to share a taxi with them.
Meals included with your hotel room: from dinner on the day of arrival to lunch on day of departure. Any other arrangement should be made directly with the hotel. The cost of an extra lunch or dinner is 22 Euro.
The hotel bill should be settled upon arrival.
The hotel has wireless in all common areas and in most of the rooms.
|
|
| CASP8 job fair | (2008-10-28) |
Dear CASPers,
we would like to take advantage of the CASP8 meeting to help young scientists looking for a position in Computational Biology meeting potential group leaders and vice versa.
We plan to organize an afternoon to get them together for interviews / informal meetings /etc.
If you are looking for a position, could you please send your cv to anna.tramontano@uniroma1.it by the 9th of November?
If you have positions available could you please send a mail with the advert to anna.tramontano@uniroma1.it by the 9th of November?
As soon as we have an idea of how many people are interested in this initiative, we will get back to you with more information.
Thank you very much
The CASP organizers
|
|
| CASP8 junior scientist session | (2008-10-28) |
Dear CASP Participants,
During the CASP8 meeting we will dedicate a special session to topics
suggested by junior scholars. We will also award a poster prize and invite
oral presentations. All students, postdoctoral associates, and others young
at heart are welcome to participate (only junior scholars will be eligible
for awards ;-)).
Our goal is to select areas that are of particular interest to the
community of young scientists. Please send suggestions /issues to be
discussed to Krzysztof Fidelis (kfidelis@ucdavis.edu). We would also
welcome volunteers wishing to help organize this session (contact Krzysztof).
Krzysztof Fidelis
|
|
| CASP8 fellowships | (2008-10-15) |
We have now completed awarding CASP8 registration fee /lodging /travel fellowships and the recipients have been notified. The CASP8 speaker selection will be completed around Oct. 23. CASP8 speakers will be offered registration fee waivers, as well as lodging and travel reimbursements. At the same time we are extending early registration rate deadline to Oct. 27.
CASP8 organizers
|
|
| CASP8 meeting registration; December 3 - 7, 2008; Sardinia, Italy | (2008-9-18) |
Registration for the CASP8 meeting is now open. We expect that this year we will be able to accommodate all the people wishing to participate. The Meeting Registration Form is available at:
http://predictioncenter.org/casp8/meeting_registration.cgi .
Meeting fees consist of a registration fee and a lodging fee for four nights (December 3-7). Rough estimate of total meeting fees (full board) for an academic participant is $880-$1050 depending on the accommodation choice. Details are provided in the registration form.
A limited number of accommodation fellowships and travel fellowships will be available. However, registration should not be made contingent on an accommodation or travel award.
Predictors attending the meeting are also required to ensure that a long abstract and a questionnaire (if requested by assessors) describing their group's method have also been submitted. A web page for submitting your abstract is available at http://predictioncenter.org/casp8/abstracts.cgi .
Please note that meeting registration will not be complete without submitting these materials.
|
|
| Last 5 targets for refinement | (2008-8-2) |
|
Five targets for the refinement experiment have been released yesterday and today. The details of the suggested refinement targets are provided in the pdb files for the starting models and in the "Additional information" field for the targets. All in all, we released 12 targets (14 domains) for the refinement experiment in CASP8 .
|
|
| End of CASP8 target release | (2008-7-18) |
With the two server-only targets today, all CASP8 targets have been made available for prediction. In this round of CASP we have released 128 targets including 57 human/server targets. One target has been canceled so far. We expect the corresponding structures to be gradually released by the PDB. We regularly update our target list to indicate which targets have already appeared in the PDB. Please, check our target list for updates on Wednesdays. At this time we have structures for 34 CASP8 targets available.
Please note, that we will still be releasing targets for the refinement experiment. You may expect new refinement targets within the next two weeks. This week we have released 3 more targets for refinement.
CASP organizers
|
|
| Human/server targets are over | (2008-7-12) |
|
We have finished releasing human/server targets for prediction in CASP8. Last week we released more targets of this type than usual in order to give you full 3 weeks to predict each of them. All in all, we released 57 human/server targets in 11 weeks of the experiment or roughly 1 target per business day. Next week is the last week of CASP8 target release and we will be releasing "server only" targets.
|
|
| T0472 - canceled for human predictions | (2008-7-9) |
|
Target T0472 has been canceled for human predictions as the corresponding structure had been released by the PDB. The target is turned over to the "server only" status and will not be assessed in the human-track part of CASP8.
|
|
| Refinement targets - 3 proteins (4 domains) | (2008-7-8) |
|
Please, pay attention that 3 targets for the refinement experiment have been released today. The details of the suggested refinement targets are provided in the pdb files for the starting models and in the "Additional information" field for the targets.
|
|
| T0465 - switching to human/server target | (2008-6-30) |
|
We are switching T0465 over to human/server target. In order to provide enough time for human-regime modeling, we are adding 10 extra days to the prediction window for this target so that it will expire for human prediction on July 21.
|
|
| No targets on July 4 | (2008-6-27) |
|
Next week we will have no targets released on Friday. Next target release date after the holiday - July 7.
|
|
| Extended timeframe groups | (2008-6-24) |
We are launching an additional service designed to help test methods requiring more time than the usual 3 weeks allowable in CASP8. Registering an additional “extended timeframe” group will provide a time stamp certifying the PRE-diction nature of the submitted models as well as CASP numerical evaluation results in the familiar format. Please note that the predictions sent by an "extended timeframe" group WILL NOT be part of the CASP8 experiment, WILL NOT be included in the final results tables and WILL NOT be assessed by the CASP assessors.
Please, use the appropriate registration form ONLY if you feel that you will need more time than the usual 3 weeks for submitting predictions. Predictions from the "extended timeframe" groups will be accepted for 6 weeks total. If the experimental structure becomes publicly available during the extended time window, the predictions accepted after that date will be discarded. Prediction Center does not fully control the extended deadlines and there is real risk that already submitted predictions will be discarded.
|
|
| CASP8 update. New fold targets appeal. Refinement targets. | (2008-6-10) |
General participation statistics
We are in the middle of the CASP8 prediction season. Interest in the CASP experiments remains high. We have 221 groups including 121 servers actively participating in CASP8. More than 28 thousand predictions have been collected by the Prediction Center in the first 5 weeks of the experiment.
Targets
Fifty nine targets (including 28 human/server targets) have been released during the first part of the CASP8 experiment. As you may have noticed, there have so far been few small ‘new fold’ or very remote fold proteins suitable for testing non-template based modeling methods. This is starting to look like a problem, since, obviously, it's very important the community does find out how those methods are progressing.
So we are writing with an urgent appeal to help find target or targets of this type (typically 150 residues or less). Larger proteins with suitable semi-autonomous domains would also fill this need. For those, we need the relevant domain boundary information to be provided with the target. Please go and pester your friendly experimental colleagues, and see what you can come up with.
Refinement targets
The first target has been released for model refinement (TR389). The experimentalists kindly provided us with the coordinates for this target ahead of time. After the automatic evaluation of the models we want to suggest you one of the best models for refinement. Please, pay attention that the refinement target names start with "TR" instead of "T0" for regular targets.
CASP organizers
|
|
| FORCASP migration | (2008-5-19) |
We are moving FORCASP discussion forum from the forcasp.org website to the predictioncenter.org site (link FORCASP forum is added to the menu). Old posts remain available at the forcasp.org website.
CASP organizers
|
|
| Prediction in non-tertiary structure categories | (2008-5-16) |
Some targets in CASP8 Target List are marked as 'Human/server' and the others as 'Server only'. We have informed you that the human-expert groups should concentrate on predicting 3D structures for the Human/Server targets as the assessors will be comparing human-expert groups on this subset of targets. We want to clarify that this requirement pertains to the tertiary structure predictions only. Human-expert groups are expected to submit predictions for all targets (both "Human/Server" and "Server only") for the categories other than TS.
CASP8 organizers
|
|
| 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
|
|
| 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.
|
|
| 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.
|
|
| 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.
|
|
| 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).
|
|
| 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.
|
|
| CASP 7.5 meeting | (2008-2-1) |
|
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
|
|
|
|
|
