Dear CASP7 participants,

First of all, we apologize for the yesterday's disruption of service
that triggered your worries. It seemed like we could have finished the
prediction season without power outages. But ...

Fortunately, almost all the predictions that were sent to us on
Wednesday night and Thursday morning did reach us and it was mainly an
issue of our server making up for the missed hours (luckily, we managed
to bring our servers back quite fast after the power was restored).

It probably makes no sense to remind you that the prediction season ends
next Monday. Many of you have been waiting for that day to finally get
that deserved rest! But we do want to remind you that there is a
possibility that the refinement experiment will be going on for 3 more
weeks as it was originally scheduled. Just a few hours ago we received
several structures for CASP7 targets, some of which can be suitable for
the refinement. Please check our refinement page on weekend and on
Monday to see whether new targets were released for the refinement. For
various reasons, it was hard to pick targets for the refinement
experiment. As you can see, we had only three so far. And it is very sad
that we had to cancel one of them (TR366) because of the early release.

This is the last of our regular Friday update messages for the season.
>From now on we will be keeping you informed about the CASP post-season
developments through occasional emails and postings at the News section
of our web page. Thank you all for participation and good luck!

--
Andriy Kryshtafovych,
for CASP organizers

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear Predictors,

We are currently opening registration for the CASP7 Asilomar November
26-30 Meeting. The Meeting Registration Request Form is available at:

http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/registration.cgi

The same form allows registering for the Student Addendum Conference
(SAC-CASP7). You will receive a separate letter from the organizers of
SAC-CASP shortly.

Also, there will be a UCSC Bioinformatics Symposium after CASP7.
It will be held on the UCSC campus Sat Dec 2 and Sun Dec 3.
When more details are available, they will appear on

http://www.soe.ucsc.edu/research/compbio/workshop-2006.html

As previous meetings, CASP7 has limited attendance. To expedite the
registration acceptance and to allow earlier completion of the travel
arrangements we will follow the rules outlined below:

1. Early registration is strongly encouraged and preference will be
given to those registering early.
2. Each research group having submitted predictions to CASP7 will
automatically be guaranteed one registration. For the purpose of
meeting registration, a research group is equivalent to an
academic unit, i.e. CASP prediction groups with the same group
leader will be considered as a single academic unit. The first
person in the group does not need to wait for our confirmation
and may proceed with travel arrangements immediately. However,
we reserve the right to deny the registration if more than 1
person from the same academic unit registers as Group
representative #1 or #2 (form).
3. Second registration per group will most likely be available. We
will send confirmations by September 15.
4. People who have not predicted and additional group members will
receive notification by the end of September.

Meeting fees include registration fee and lodging/meals fee. No payments
should be sent at this time. Payment will be expected promptly following
a separate email confirmation from the organizers. Details on how to
submit payment will be provided shortly. There will be absolutely no
refunds.

A limited number of Asilomar accommodation fellowships and travel
fellowships will be available (refunds for American carriers only).
However, registration requests should not be made contingent on
accommodation or travel award. People who register should be prepared to
cover the Registration Fee and the Asilomar Lodging /Meals Fees.

We will very much appreciate your feedback on the organization and
running of the CASP7 experiment this year. Please fill out the form at

http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/polling.cgi


--
Krzysztof Fidelis,
for CASP organizers

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Dear CASP participants,

We are forwarding to you the communication from SAC-CASP7 organizers.
Please contact them directly with your questions.

CASP organizers

------

SAC-CASP7 REGISTRATION OPENED

The third Student Addendum Conference to the Critical Assessment of
Techniques for Protein Structure Prediction, SAC-CASP, will take place
at Asilomar on November 30th and December 1st 2006 (directly after
CASP7).SAC-CASP participation is limited to post-docs, students and
technicians.

Registration:

In order to register for SAC-CASP please fill in the form at
(http://www.pdg.cnb.uam.es/saccasp7/main/registrationForm.html)

Note that payment for the extra SAC-CASP night at Asilomar is through
CASP
(http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/registration.cgi).

When you register for CASP please tick “yes” when asked "Do you plan to
attend SAC-CASP7? (only students and post-docs may register)”.

Call for Papers:

SAC-CASP7 is a great chance for students, post-docs and technicians to
present and discuss their work in an informal and friendly environment.
By reproducing the format introduced at the 2004 meeting in Gaeta, the
2006 student addendum conference to CASP will include talks selected
based on the abstracts submitted by the participants, round table
discussions and a SAC-CASP lecture by a renowned name in the field of
structure prediction to be followed by a red-hot Q&A during which the
lecturer will answer attendees’ questions.

SAC-CASP’s backbone is represented by the participants’ presentations.
These short talks are meant to address the technical aspects of
structure prediction in a more detailed fashion with respect to what is
heard at CASP. Also, presenters are expected to elaborate on
difficulties and perceived bottlenecks, rather than just focusing on
successes. We regard SAC-CASP as an important complement to the main
CASP meeting and hence we encourage all students, post-docs and
technicians participating at CASP to register for the student meeting
and to submit an abstract that will be evaluated for oral presentation
at SAC-CASP7.

We are looking forward to seeing you in Asilomar,

The SAC-CASP7 Organizers
------------------------------------------------------------------------------------------

To find more information about SAC-CASP7 please visit:
http://www.pdg.cnb.uam.es/saccasp7/main/index.html

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear CASP Participants,

This is a Reminder that the Priority Registration for the CASP7 Asilomar
Meeting (November 26 – 30) will end on September 15th (no payments are
due at this time):

http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/registration.cgi

Registration confirmation for a Group Representative # 1 is automatic:
we will not e-mail a notification. Confirmations for Group
Representative # 2 will be mailed promptly after the Priority
Registration closes on Sept. 15th . Space allowing, we will continue to
accept registration requests also after September 15th .

CASP7 will begin with dinner on November 26th and end after lunch on
November 30th . Information regarding how to reach Pacific Grove,
California, Asilomar Conference Grounds can be found at:

http://www.visitasilomar.com/traveltips.aspx

http://www.visitasilomar.com/maps.aspx

Additional travel information is available at:

http://www.pacificgrove.org/mainpages/visitorinfo.htm


We would still very much appreciate your feedback on the organization
and running of the CASP7 experiment this year. A live update is now
available following filling out of the form at:

http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/polling.cgi

--
Krzysztof Fidelis,
for CASP organizers

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear predictors,
(lotsa yadda yadda)
Targets to expire next week:
T0303, T0304 (Mon, July 10)
T0306, T0307 (Tue, July 11)
T0312, T0334 (Wed, July 12)
T0314, T0340 (Thu, July 13)
T0318, T0319 (Fri, July 14)
T0338, T0339 (Sat, July 15)
T0341, T0343 (Sun, July 16)

Soft deadlines:
T0334, T0335 (Mon, July 10)
T0338-340 (Wed, July 12)
T0341-343 (Thu, July 13)

I am confused. At the moment, my computer, which recently joined rosetta@home, is happily working on t304 ... and is, in fact, 90.842% complete.

Should I even have this? It shows a deadline of 9/22 and, at the time of its being pre-empted, had about 18 minutes left to work.

---

1 Thessalonians 4:11.

Bill if your WU is labeled with "CASPR" those are some "rework" (I made that term up) WUs where Baker Lab is trying to refine some of their work. Basically the CASP protein posed some "interesting" properties that they are now studying further to learn more about making accurate predictions for proteins like that one.

[edit] Reviewing your WUs, I see it has "FOLLOWUP" in the name of the WU. Same idea as the "CASPR"s.

---

Rosetta Moderator: Mod.Sense

Bill if your WU is labeled with "CASPR" those are some "rework" (I made that term up) WUs where Baker Lab is trying to refine some of their work. Basically the CASP protein posed some "interesting" properties that they are now studying further to learn more about making accurate predictions for proteins like that one.

[edit] Reviewing your WUs, I see it has "FOLLOWUP" in the name of the WU. Same idea as the "CASPR"s.

Okie dokie ... it just caught my eye and left me perplexed. So, if I understand you correctly, this WU has already been successfully worked once but exhibited some neat stuff so the researchers want to take another look at it. Cool. If it cures the common cold, can I have a bottle of it? ... my wife has a doozey of a cold right now and is sleeping off the whiskey toddy I made up for her. (1T cheap whiskey + 1T lemon juice + 1T honey in a cup of steaming hot tea ... by the time it's finished, it's time for beddy-bye.)

---

1 Thessalonians 4:11.

The work here is similar to building a better microscope. It is a tool that will in the future be used to make curing a virus, as easy (for a scientist) a mixing a hot toddy.

In this case, someone stuck something under the current microscope prototype and for some reason the image was fuzzy. So, let's tweak a couple of things and see if we get a clearer image. (In order to test the image quality of the new design, they send out these "rework" WUs)

If we get a clearer picture, then we've made the tool better for future use. And the tool works for more of the types of things people may want to stick under it in the future.

---

Rosetta Moderator: Mod.Sense

That's quite a nice analogy that, consider it stolen!

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear Predictors,

Following on our earlier announcement, we have now opened an abstract
upload page at

http://www2.predictioncenter.org/casp/casp7/public/cgi-bin/abstracts.cgi

Methods Abstracts are requested from all predictors taking part in
CASP7. The deadline for abstract submission is October 3, 2006 to assure
consideration by CASP7 assessors.

Please submit your abstracts providing a concise and clear description
of the approach tested in CASP7, so that the reader may grasp the most
important points without referring to additional material. If you have
tested more than one approach you may submit a separate abstract for
each. We will accept abstracts from all groups taking part in CASP7,
regardless of their intention to attend the meeting itself. Additional
abstracts in the general area of structure modeling and prediction will
also be considered. The abstracts will be distributed among the meeting
participants and posted at our website after the meeting. If you plan on
bringing a poster to the meeting or on giving a software demonstration
please let us know (below).

We will accept only electronic versions of the abstracts that can be
further formatted - no hard copy materials will be considered. Abstracts
may be submitted in the .rtf or .doc (MSWord) format or as a plain text.
We recommend that the abstract length does not exceed 700 words. If you
have a longer version - please shorten it for us and upload the full
version at the FORCASP website (see below).

Please note, that in addition to the abstracts, you are also invited to
submit Methods Papers at the FORCASP.org website. Papers submitted to
FORCASP will be open to discussion by other predictors. Also, CASP7
assessors will take them into account (in addition to the Methods
Abstracts) when deciding which novel contributions should be presented
at the meeting.


--
Krzysztof Fidelis,
for CASP organizers

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear CASP participants,

It has come to our attention that when registering for the CASP7 meeting
at Asilomar, in some cases the registrations were not fully completed.
In such cases we would not have a record of your submissions. If you
have registered, you should have received a confirmation by *e-mail*
from casp@predictioncenter.org. If this is not the case or you are not
sure, please let us know by sending an e-mail to
casp@predictioncenter.org. Acceptance messages for all registration
requests will be sent out by the end next week.

--
Krzysztof Fidelis,
for CASP organizers

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear CASP7 Participant,

We have received several questions regarding participation of additional group members in the CASP7 Meeting (Asilomar Conference Grounds, November 26-30). So far we have been able to answer them favorably. This year we have reserved enough space to accommodate probably everyone wishing to attend and the registration for the Meeting remains open at least for the next several days.

http://predictioncenter.org

Krzysztof Fidelis
for CASP7 organizers

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear CASP7 Participant

A message from Kevin Karplus:

Third UCSC/QB3 Symposium on Bioinformatics,
Predicting the structure and function of proteins
(Informal post-CASP Workshop)

Engineering Auditorium
University of California, Santa Cruz
2-3 Dec 2006

http://www.soe.ucsc.edu/research/compbio/workshop-2006.html

We particularly need more speakers!

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

We currently have only 6 speakers signed up for the post-CASP
symposium at UCSC. We need at least a dozen---the last workshop in
2002 had about 20.

The symposium is the weekend after CASP:

Engineering Auditorium
University of California, Santa Cruz
2-3 Dec 2006

http://www.soe.ucsc.edu/research/compbio/workshop-2006.html

The talks may be on any aspect of bioinformatics or structural biology
that may be of interest to either CASP attendees or UCSC
bioinformaticians.

Current speaker list is

Silvia Crivelli Graphical Environments for Protein Modeling
Chen Keasar Rare structural features as indicators of catalytic residues
David Bernick New Biology from the Extremes -- comparative genomics of Pyrobaculum
Bernhard Rupp Maps and drugs and rock & roll
Robert Baertsch A model for the proteolipid ring and bafilomycin/concanamycin-binding site in the vacuolar ATPase of Neurospora crassa
Mark Akeson Nanopore analysis of nucleic acids

I have not put together a schedule yet, as there are not enough
speakers---we have barely enough for a one day symposium, not enough
for a 2-day one. [Note: if people are wondering why I'm not signed up
for a talk---I will, though I don't have a new talk prepared.]

Currently the slots are half hour (25 minutes plus 5 minutes for
questions), but I'm thinking of increasing the length to 40 minutes
plus 5 minutes for questions, since we don't have so many speakers to
pack in.

I'd like to get the speaker list together so we can let people know
about the symposium (with a schedule) before Thanksgiving and the
start of CASP.

Thanks,
Kevin Karplus

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Dear CASP participants,

>From our CASP7 web page, the following materials are now available:

1. Classification of targets
2. Short description of CASP7 targets with domain definitions
3. Target difficulty plots
4. Tarballs of CASP7 predictions
5. Abstract book
6. Lists of participated groups (sorted by name and number)
7. List of meeting participants

Detailed program of the meeting will be available within the next two
days.

CASP7 results of automatic evaluation will be released at the
beginning of the meeting (this coming Sunday) through the website
and also distributed to the meeting participants on CDs.

See you in Asilomar soon,
--
Krzysztof Fidelis,
Andriy Kryshtafovych

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.