Grid.org Project News: New Cancer Data and more

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Grid.org Project News: New Cancer Data and more

Postby Jwb52z » Mon Jan 09, 2006 1:56 am

UD - Robby Brewer
UD Employee

21 Dec 2005 18:31 Post subject: New Cancer Data

Dear Members,

We have made some great progress on getting the new cancer job ready. There was an issue with the format of the data we received from Oxford and we believe that we have resolved this. I have been able to get successful cancer runs using the new data on an internal system. Hopefully we will be able to get some of the data loaded onto grid.org today or tomorrow.

In the past we have utilized the beta server and the beta tester team to help verify that things are working correctly before moving to grid.org. Due to hardware issues this is not going to be possible this time. If you are one of the beta tester members please do not be offended at this. We plan to reinstate the beta tester group when we migrate to the new system. I know everyone is anxious about the cancer data so we will not wait.

What this means is that it is possible that there may be a problem with the job when we submit it. I will be keeping an eye on the system and will be able to flip back to the current job quickly if necessary. Since the current job is basically stale data anyway this should not upset anyone. I will post again once the new job is submitted.
_________________
Robby Brewer
Senior Support Engineer
United Devices

UD - Robby Brewer
UD Employee

21 Dec 2005 22:19

I have submitted (one of) the new cancer jobs. I am currently processing ligand 29 of 600 and it appears to be working correctly. We will keep a close eye on it for any problems. The old cancer job has been set to not dispatch any more workunits, but is still active so that any outstanding results can be returned. As I mentioned, there may be a need to do some additional tweaking on the new job, but as of now it looks good.
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Robby Brewer
Senior Support Engineer
United Devices
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Postby Jwb52z » Mon Jan 09, 2006 2:04 am

UD - Robby Brewer
UD Employee

04 Jan 2006 15:16 Post subject: Unable to connect for Cancer job

Dear Members,

There was a small issue with the cancer job that caused devices to not be able to download a new cancer WU. This was an unforseen side affect of trying to retreive results so that we can have them verified with our Oxford contact. The process consists of running a script that verifies minimum successful results, retreives them from the grid server, and aggregates them into a known format. Apparently the script marks a WU as complete during the final stages of processing. I have since reset the WUs so they will dispatch again.

To try to prevent this from happening again, I am going to submit another cancer job (a duplicate of the current one) that I can experiment with
hopefully without affecting the current one.

Note that until I can successfully get the retrieval script to work and get the results to our Oxford contact for validation, I will not be able to upload the bulk of the new data. Please have a little patience during this phase of the project. As I mentioned, in the past we had the luxury of a beta test system to work these issues out, but unfortunately that is no longer the case. This requires us to do some testing on the production system which we really do not like to do.

Thank you for your contribution.
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Robby Brewer
Senior Support Engineer
United Devices
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Postby Jwb52z » Sat Mar 11, 2006 1:03 am

UD - Robby Brewer
UD Employee

08 Mar 2006 16:25 Post subject: Comment On Cancer Data

Dear Members,

I have received a response from our Oxford contact regarding some of the issues we have seen with the new cancer data.

High number of hits - It was stated that a determination could not be made at this stage as to whether the data was generating too many hits or not. After we process all of the data and send it back, they will apply a cutoff criteria in order to isolate the best hits. It may be that once the data is analyzed, they will suggest a change to the Ligandfit input parameters and a rerun of the data. Remember, research implies trial and error.

Aborts - While nothing specific was identified yet, they stated that is was possible for the data to cause Ligandfit to error out. It was mentioned that some of the datas are not discrete organic molecules which may be different that data that was processed in the past. It may be that under certain circumstances this data causes Ligandfit to abort, although we have seen that a replay of the data usually produces a good result so we are not talking about a bad WU per se. They also stated that in the future they will filter out anything that they think may cause an issue. Bottom line is this issue remains elusive and we do not have the answer yet.
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Robby Brewer
Senior Support Engineer
United Devices
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Postby Jwb52z » Sat Mar 18, 2006 4:09 am

UD - Robby Brewer
UD Employee

15 Mar 2006 21:05 Post subject: Cancer Job

Dear Members,

As per our new process described on Monday, I have uploaded a new cancer job and rolled up results from the previous one. On Friday I will deactivate the previous job afterwhich no more credit will be given.

Hopefully this process will keep results at a minimum to conserve disk space, but still allow everyone to participate and receive credit for their work.

Thank you for your contribution.
_________________
Robby Brewer
Senior Support Engineer
United Devices
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Posts: 997
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Postby Jwb52z » Sat Apr 22, 2006 8:21 pm

UD - Robby Brewer
UD Employee

19 Apr 2006 19:12 Post subject: Cancer Job

Dear Members,

I have rolled up the results for the previous cancer job and have submitted a new one. Results will be credited until Monday for the previous job.
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Robby Brewer
Senior Support Engineer
United Devices
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Posts: 997
Joined: Tue Aug 30, 2005 10:56 pm

Postby Jwb52z » Wed Dec 20, 2006 11:43 am

UD - Mary Bass
UD Employee

11 Dec 2006 23:07 Post subject: Upcoming plans for and changes to Grid.org

Greetings and Happy Holidays!

First of all, on behalf of United Devices I’d like to thank each and every one of you for your steadfast support of this unique, invaluable resource. For the last several years, Grid.org has played an important role in some tremendously important research and it is the largest and most respected volunteer-based grid of its kind in existence. None of that would be possible without all of you!

We have some exciting information to convey concerning Grid.org status and plans – but before I do that, please allow me to express our sincere regret for the frustrations that some of you have been experiencing lately. During the past year we have had technical difficulties with Grid.org that have contributed to your frustrations, but we have changes planned that should significantly improve your experience.

These are some of the plan highlights we have for Grid.org in the coming months:

We will migrate the Grid.org software to the latest version. Planning for this is well underway, and the migration will begin in the first quarter of 2007! In the first quarter (Jan-Mar) of 2007, we’ll begin a Beta Program (see below) in preparation for the final upgrade to the new release. We will perform the entire upgrade to the new version by end of Q2 of 2007.

The following new features will be introduced with the latest version.

- Support for multi-processor and multi-core machines
- Support for cache ahead so that users can request multiple work units
- Enhanced non-intrusiveness options
- The possibility for members to generate their own tools, GUIs, and reports using a new Grid MP Agent API
- New look and feel for the Grid MP Agent GUI
- Improved support for Microsoft XP operating system – enhances support for multi-users and allows fast user switching
- Support for Microsoft Vista operating system (both 32-bit and 64-bit)
- Support for Microsoft Internet Explorer 7
- Overall performance improvements to the grid
- General defect repairs

Right now our outreach committee is actively working on reviewing and selecting new projects to run on the updated Grid.org software. The initial conversations we’ve been having look very promising and we should be ready to make an announcement about the selected project by end of Q1 2007, to launch in the May-June timeframe. Your active co-operation in the Beta program will be key toward expediting this process!

As mentioned above, we will implement a Beta program and ask for volunteers to help with Beta testing of the new system. This program will initially be implemented with a target of 100 volunteers as the first phase of the upgrade to the new version of Grid.org. The Beta program will run for several weeks and is intended to identify any deployment issues that might be lingering in the new version so we can resolve them prior to the upgrade of the entire member community. We will provide you with additional details and initiate a call for Beta volunteers shortly before we begin the program.

Thank you once again for your continued support of Grid.org. We’re looking forward to keeping you informed on status of the initiatives outlined above – visit this site regularly for more information.

Sincerely,

Mary Bass
Directory of Marketing
United Devices, Inc.
Austin, Texas 78759
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Postby Jwb52z » Thu Mar 15, 2007 1:34 am

UD - Mary Bass
UD Employee

12 Mar 2007 22:20 Post subject: Grid.org Upgrade Update

Greetings from UD!

My apologies for not posting an update sooner -- in case you aren't aware of this, UD had our yearly conference last week in Boston (see http://www.ud07.com/index.php ). Check out the agenda and speakers -- it was our best conference yet!

So, it's time for an update on the Grid.org migration and beta program I wrote about last quarter. The good news is that the new release of Grid MP is complete and we are still targeting Q2 for the upgrade of Grid.org (as previously announced).

We are still planning to implement a beta program for testing of this version prior to final upgrade. Several new requirements (including something exciting we'll be announcing by the end of Q2) have necessitated a slight delay in scheduling the beta program, so the target timeline to begin beta has slipped to early Q2 -- though we still intend to complete the full upgrade by end of Q2 as originally planned.

If you've already volunteered for the beta program, thanks! If you would like to, please let us know as there is still time. We will reach out to all volunteers with beta program info in the next few weeks.

So, to summarize, here's what you can expect from UD regarding grid.org in the next 3-4 months:

> By early Q2: Beta program initiated
> Mid Q2: Announcement about the next big Grid.org project
> By end of Q2: Grid.org migration to the latest release complete

Thanks once again for your support of Grid.org!

--Mary
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Mary Bass
Director of Marketing
United Devices
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