Df News!

[JJc]

Protein Update

09/25/2003

- The next protein update is *tentatviely* scheduled for Thursday, October 2, 2003, at 11:00 am EST. More details to come on Monday.

[JJc]

10/01/2003

- Some users have reported long waits for uploading their data. We are currently looking into the problem and will post more iformation shortly.

[JJc]

We have changed the protein change day to Friday, 11:00 EST so we have time to ensure everything is working OK again and to give people enough time to upload buffered work that got stuck.

Thanks for your continued patience (those of you who are still here, anyways)


__________________
Howard Feldman

This from here.

[SitFlyer]

Grace period extended this weekend

Update will proceed Friday as scheduled. Servers seem to be working fine now. Please note the web server died on Tues night here, any earlier problems are/were caused by other factors and are still present in all likelihood. We are working on a new backend to hopefully improve this.

We apologize to our European friends for any inconvenience but remind you that updates are automatic and do not require your attention (except if we mess up ). We will extend the upload grace period an extra 48 hrs, i.e. 72 hrs for full credit and 96 hrs for half credit so you can upload old stuff on Monday still for full credit if you have to.

From here

[JJc]

10/07/2003

- We are now on the last protein of our folding 'mini-experiment', protein L with a 14-residue floppy tail removed. Both this protein and protein G (two proteins back) have been folded essentially to completion (well under 3A RMSD) and so the folding pathways we have obtained can be compared to experimental observations of folding pathways, as well as simulated unfolding pathways, to learn a bit more about how proteins fold. As we analyze the data over the next few months we will post results here. For the next protein, we will switch back to an energy-only scoring function (not RMSD-based), so that we will be doing true blind prediction. Thus expect higher RMSDs to native than we have been seeing recently. Our hope, of course, is that we are still able to completely fold proteins using the current approach without using the explicit knowledge of the native structure that we have been using for the last few proteins.

[Guru]

10/09/2003

- Complete Windows packages for the new protein (client and screensaver) are now available for download.

10/08/2003

- The system will be down briefly for maintenance today, at 4PM EST. It should not be down for more than 30 minutes.

[Guru]

10/16/2003

- We are currently in the transition process to a new and improved website. If you find that some things are temporarily missing, or part of the website is temporarily unavailable, do not be alarmed and please be patient, we will switching over quite soon.

[JJc]

dfGUI v3.2 for Win available (Multi-Language)

Here is another big update to dfGUI with multi-language support and a bunch of new features and bug fixes.

You can get it in the regular location:
http://gilchrist.ca/jeff/dfGUI/
v3.2 (Oct. 18, 2003)
- Modified client running status message from "Client appears to be running" to be "Foldtrajlite.lock found. Client might be running" since dfGUI doesn't know for sure if the client is in fact running when the .lock file is present. Always check your Task Manager to be sure.

- The tray icon for dfGUI will try to "refresh" itself every Refresh period in case the Explorer crashes and the dfGUI icon disappears.

- Added "Reset" buttons to the Energy Graph and Time Graph tabs.

- Added "Install Service" and "Remove Service" buttons to the Config tab to allow users to easily set up the DF client as a service on their machine. It supports installing up to 8 service clients.

- Can now handle new 8 service client support

- Modified service manager to use CONNECT instead of ALL_ACCESS which should not limit start/stopping the DF client as a service to just users with Admin access. (Thanks Frank M.)

- Added Total Time display to Energy and Time graphs which will display the total time (Days:HH:MM:SS) the completed generations in that set have taken so far (including gen 0). There is also the option to disable this time dispaly in the Graph Config tab.

- Added dfGUI.stop file support. If you create a file named dfGUI.stop in the dfGUI directory, the next time dfGUI does a Refresh and finds the file, it will close (and delete the .stop file). If you would also like the DF Client itself to stop when this event occurs, go to the Config tab and select the "AutoStop on Close" check box.

- Modified timing in code after click on "Upload" button to make sure dfGUI waits long enough before launching DF Client again.

- Modified Time Graph code to hopefully reduce the number of holes in the graph from missing generations. If a generation finishes in less time than your dfGUI refresh rate, then dfGUI will miss the generation data and you will have holes in your graph.

- Added support to dfGUI for multiple languages. The config tab now allows the user to select a language other than English if the supporting language files are available. The languages are not hard-coded into dfGUI so new languages can be added without having to re-compile the software, just provide new language files to the user. The initial languages available are English, Dutch, German, Italian, and Norwegian. You will notice that labels and buttons have been resized and moved around slightly to accomodate the different amount of space other languages take. A very special thanks to Gras, Federico, Nofinger, and HansArne for the hard work they did at doing all the translations for dfGUI. There was a lot of text to translate!

[Guru]

10/24/2003

- We have been having some hardware trouble with the stats server. As a result, you may notice periodically that the stats have not updated for some time. Rest assured all data is still being collected normally, only the stats are affected, and these can be regenerated at any time once the machine is repaired, reset or replaced.

10/21/2003

- We will be switching to a new protein on Tuesday, October 28, at 9 AM EST. The main difference for this protein will be scoring purely based on energy, and not RMSD - i.e., we won't be "cheating" in scoring the structures. Note that this update will include an update to the client as well as a new protein to work on.

[Guru]

11/01/2003

- We have identified a bug in the screensaver version released on Tuesday, which causes the program to appear to stop working after completing a generation. No harm is done, but the user must exit and restart the screensaver to continue working. We will post a corrected package on the Download page on Monday morning, and apologize for any inconvenience. In the mean time you should be able to avoid this problem by setting it to 'not connect to the internet' in the screensaver settings, until you get the new version.

10/28/2003

- The new protein is called cytochrome C (code 1YCC) and comes from baker's yeast. It has 108 residues. We have worked on this protein in the past, and now would like to get results for it with the new algorithm.

[Guru]

11/03/2003

- The fixed screensaver and client versions have been posted on the Downloads page.

[High_Jumbllama]

Hmm. Debating to see if this is what was causing my widespread folding problems or to wait for BOINC.

Edit:
Seems to be fine on my work machine. It will spread again when I get some free moments first on the 256MB workstations.

Edit2:
Boss kept me busy like crazy for a change. It could have also been a latency problem with the internet on the network we were having. Cleared out the DNS cache for good measure. I had just recently replaced the LNE100tx 5.1 card with a 3com 905c and forgot to uninstall first. I ripped as many registry entries as I could find out primarilly the one that seems to start as a service. Latency cleared up within minutes though nobody was happy that they had to stay off the server for 12 minutes during my reboot. Most everyone was in early anyway.

Edit3:
8 more of the 2ghz 256MB machines are folding again.

[Guru]

14/03/2003
New look for website
We have changed our website. We are now a part of the Blueprint Initiative, a non-profit research organization in Mount Sinai Hospital working to aid and further scientfic research by providing publicly available data and tools. Blueprint is actively researching protein folding and molecular structure, location, dynamics, sequence, interaction and evolution as they relate to systems biology in an effort towards simulating a living cell. We hope you enjoy the new look and added functionality. Please report any errors that you may find.

[High_Jumbllama]

Now 11 2ghz 256MB machines and one 1ghz 256MB machine.

Hey, who woulda thunk I'd be the top producer for a day!

[Guru]

11/24/2003
Points returned to normal
Over the weekend there was a statistics glitch which evaluated uploaded results at about 1/25th their worth. All users that had uploaded any results over that time period have been awarded the missing points based on the amount of work they contributed. Users who were working offlie were not affected.

11/20/2003
Memory leak fixed
A small memory leak has been fixed - new executables are available for download. The changes to the client will be included in the next protein auto-update

11/19/2003
New client executables availabe
New client executables are available for download. The changes in the client are:
- fixed "cannot set co-ordinates" error
- added recovery behaviour when running out of disk space