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DB changes, new hardware, thanks | November 19th 2008 |
I have just moved the entire Phyre system to a much larger computing farm which should speed things up considerably for users. In addition, there have been some fold library changes and sequence database changes. If you have any problems with the new system please let me know as soon as possible. There are bound to be some teething problems at the beginning. Also I would like to offer my sincere thanks for the large number
of glowing letters of support we received for our grant proposal to
continue to develop the Phyre server. The grant is now in the hands of
the funding body and it will be quite some time (possbly 6 months)
before we hear whether we have been successful or not. Once again I
would like to express my gratitude to those who took the time to write
a letter.
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Delays | March 27th 2007 |
Repeated hardware problems have delayed the intended updates to Phyre. However, I have decided to list some of the most common requests I have had from users, so at least I can remember what they were.
That's all I can remember right now. If anyone has more things they'd like to see please e-mail me so I can add it to the list Lawrence Kelley | |
Database Updates soon - Phyre downtime | February 20th 2007 |
Some news at last! I finally have the time to do a bit of work on the server. Over the next few days I intend to install a new fold library and get the fully automated fold library updates in place. Because this will involve some code alterations, I will have to take Phyre down for a few days. After that *hopefully* we will have fully automated updates. After that, I will hopefully get a few variants of Phyre in an advanced options page, one of them mimicking very closely the behaviour of 3D-PSSM. So those of you who still like the old school methods will be able to use them. Finally I hope to get the multiple sequence alignment input in place in the advanced options.Thanks for using Phyre! Lawrence Kelley | |
Database problems - Apologies | September 12th 2005 |
Apologies for the recent downtime of the server. We experienced some
major database crashes. As for good news, the new server has been
updated to SCOP 1.69, all PSSMs have been recalculated, and a new
supplemental PDB database created. There are many improvements on the way, but at the moment I'm in the process of writing a paper on the enhanced version of Phyre. Many thanks for your continued patience and support. Lawrence Kelley | |
User-feedback | July 13th 2005 |
Many thanks to those of you who have e-mailed me with
problems/suggestions/praise. As a result a variety of small changes
have taken place, which I think warrants a small version
change. Several people have contacted me regarding two issues: I would also be interested in anyone's experience of the server compared to 3d-pssm. Has Phyre found things 3d-pssm didn't? Or vice versa? Do you find the rather crude functional site prediction useful? Is anyone having problems using Jmol? I have also finally fixed the prosite matching. Little blobs appear where prosite hits are found along your sequence and hovering over them will reveal prosite info. Once again, many thanks for the feedback and please keep the e-mails coming. Lawrence Kelley | |
Beta-testing | June 22nd 2005 |
The system is now live. A lot of changes are going to happen in the
near future. Current improvements over 3d-pssm include: What to expect in the future: I am currently amusing myself fixing sundry bugs and getting the thing as bomb-proof as possible. Your feedback is particularly useful. If you have any problems/suggestions please let me know. Lawrence Kelley |
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Phyre - Completely new protein structure prediction system | April 5th 2004 |
A brand new fold recognition system is on its way. The new system is
nearing completion. Benchmarking suggests it is far superior to
3D-PSSM. However, it requires substantially more CPU power. As a
result I will probably have to shut down 3D-PSSM once the new system
is up and running. More details to follow.
Lawrence Kelley |
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Lawrence Kelley, Riccardo Bennett-Lovsey & Alex Herbert |