What happened to the biweekly science updates announced here: https://boinc.bakerlab.org/rosetta/rah_science_news.php ?

January 25, 2006

I will use this space to give biweekly updates on recent results and the work units planned for upcoming weeks.

Please don't let this project follow down the same road as others have with the falloff of communication.

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What happened to the biweekly science updates announced here: https://boinc.bakerlab.org/rosetta/rah_science_news.php ?

January 25, 2006

I will use this space to give biweekly updates on recent results and the work units planned for upcoming weeks.

Please don't let this project follow down the same road as others have with the falloff of communication.

thanks for the reminder; the update will be coming soon. recent results are very exciting!

we are focusing this week on trying to find the sources of the errors that some of you are experiencing

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thanks for the information

yes please keep us informed ... we love information.

there are discussions on other boards about the lack of information given by the project managment and i am glad to see that we still have frequent updates.

please keep these going

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thanks for the information

yes please keep us informed ... we love information.

there are discussions on other boards about the lack of information given by the project managment and i am glad to see that we still have frequent updates.

please keep these going

will do my best. please tell me what info people want, and I'll try to answer it here, and maybe you could post it on the other boards. results on the science side have been fantastic, and it looks like we have made a major advance with your help, but we still need more cpu power and i'm concerned about the fall off in new and old users. other than fixing the bugs, which we think we have a general solution to, what can we do? any and all adverising help greatly appreciated! thanks, David

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<snipped> ... but we still need more cpu power and i'm concerned about the fall off in new and old users. other than fixing the bugs, which we think we have a general solution to, what can we do? thanks, David

Number 1 thing after the software bugs (which BTW is a really big deal)?

Fix the credit problem so credit awards are fair. No redundancy means no control over inflated credit claims. Once a project gets a bad reputation for unfair credit awarding, it takes a LOT of work to get people to come back. For every cruncher in it "for the science", there's a pack of us in it for the competition.

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Proudly Banned from Predictator@Home and now Cosmology@home as well. Added SETI to the list today. Temporary ban only - so need to work harder :)



"You can't fix stupid" (Ron White)

The information about what the different science runs are computing and the Rosettas team goals for each individual run make for some very interesting news. This type of feedback is very important to alot of crunchers and crunching farms. This has been a very big issue for along time. Thier can never be to much feedback and the more the better.

Even though it put a strain on the Rosseta@home resources the results of each science run with the individual crunchers contribution highlighed was really fantastic.

And lastly, this is just strictly my own opion, but if you really want to bring the computers in, couple tons of feedback with a Cancer Biomarker crunch or some type of Cancer calculation.

Just a basic Cancer crunch brought over a million signups to grid.org a few years back. This was using THINK to screen molecules for thier interaction ability to cancer protiens.

Have a great day all.....Ciao....

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Let's not forget that Rosetta is one of the most demanding (in terms of hardware and until the very recent "run-for-x-hours" fix, also in terms of network bandwidth) projects. The demands of the other projects (except new BBC/CPDN) are minimal compared to Rosetta. High turnover of new/old users may be partially due to this, they join only to find out their PC can't cope.

I think Bruce is correct:

And lastly, this is just strictly my own opion, but if you really want to bring the computers in, couple tons of feedback with a Cancer Biomarker crunch or some type of Cancer calculation. Just a basic Cancer crunch brought over a million signups to grid.org a few years back. This was using THINK to screen molecules for thier interaction ability to cancer protiens.

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Best UFO Resources
Wikipedia R@h
How-To: Join Distributed Computing projects that benefit humanity

Let's not forget that Rosetta is one of the most demanding (in terms of hardware and until the very recent "run-for-x-hours" fix, also in terms of network bandwidth) projects. The demands of the other projects (except new BBC/CPDN) are minimal compared to Rosetta. High turnover of new/old users may be partially due to this, they join only to find out their PC can't cope.

I agree, you've put off a good few of our dial-up participants, me (almost) included. This should change now that you've fixed up that particular problem (80 meg is just not feasable per day on dial up, even on 128K ISDN like mine).

I've noticed that we're sort of stuck on about 20TeraFLOPS for some time now, I'm not sure this would work but how about stealing the university linguists (I assume that you have some) and turning R@H into a multiple language board. The sort of thing I'm talking about is (country)flags across the screen pick the one that you want to read R@H in and ta-da it's in you native language, all done by people that actualy know the grammer and so on.

forgive the spelling OpenOffice died on me :(

Edit: to get rid of some blank space at the bottom and a bit of formatting

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Some suggestions:
* screensaver should be updated to show the rmsd and the lowest energy found so far during the WU, in addition to the latest accepted ones.

* Regular updates and feedback from the team is important, both on the science part and the tech part is important

* I think it also would help retain users if you could get the Top predictions to be more or less automated each month, and that users on their result page could access their current top prediction at any time. Maybe even have a Java-applet where you can navigate inside your protein structure(s) and have various options for display.

* More information about the various proteins we run WU on. Provide link to various databases on proteins for example. It looks like several of your users like to learn about the science, so it would be nice to know in what biological processes the proteins participate in, what class/family of protein do they belong to and so on. I am sure some of this could be automated with lookups to current protein databases.

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One thing that returns every time is feedback of:
* Which jobs are we crunching? What are you doing with our CPU-power? (So a bit info on the queries we're running)
* What are the results?

In my point of view, this is a very important point for many crunchers.
Is our CPU-power spent well. This also encourages people to put more and more power to a project.

As already mentioned before:
Can't you make a webpage, or a read-only forum where you post (if possible) at a regular basis this info? This would gather all information together at 1 place without other slack. At this and the other forums, we can discuss about it afterwards.

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Member of Dutch Power Cows

Just thought I'd clarify and add some thoughts.

I agree with most of what's below, it's the cancer stuff I'm not sure about, if your not actively working on it, I'd probably leave it out of your advertisment. I know that proteins can and will help cancer sufferers in the future but...

Have Jack look at seti technical news a lot of us are computer geeks, tell him to treat it like kind of a blog or diary.

We had a planned outage today to remove a couple more items from the server closet (the Classic SETI@home data server and several large, heavy disk arrays which contained the old science database). In order to safely do so, we wanted to power down several important machines so they wouldn't accidentally get bumped and go down ungracefully.

The Bay Area is having a rough winter, and a storm today brought lightning which knocked out power to the entire campus, including our lab, around 8am. Most of the servers went down without a hitch. And with the power off anyway we went ahead and cleaned up the closet as planned. We can now get behind the racks again without painful contortion.

Powering up the entire network is painful, as servers need to revive in a set order, and many hidden mounting issues come to light (that only get tickled by a reboot). Plus some drives needed some fsck'ing. Everything eventually booted up just fine, except for the master science database.

One of the fibre channel loops disappeared on this particular server. Bad cable? Bad GBIC? Not sure just yet, as the terminal wasn't working well enough to give us all the boot diagnostics. We hooked up a laptop and fought with hyperterm to see these messages, but by the time we got that working the machine booted just fine for no explicable reason... but all the metadevices needed to be resynced. This resync could take up to 24 hours, during which the master science database will be down. That means no splitting and no assimilating, and we'll probably run out of work to send before too long. Oh well.

Also to Dr DB I would suggest you also post a sort of blog or online diary, frustrations, annoyances, wins and set backs (I don't mean human relationships you understand, just the problem(s) at hand).

* I think it also would help retain users if you could get the Top predictions to be more or less automated each month, and that users on their result page could access their current top prediction at any time. Maybe even have a Java-applet where you can navigate inside your protein structure(s) and have various options for display.

* More information about the various proteins we run WU on. Provide link to various databases on proteins for example. It looks like several of your users like to learn about the science, so it would be nice to know in what biological processes the proteins participate in, what class/family of protein do they belong to and so on. I am sure some of this could be automated with lookups to current protein databases.
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I'd like that too.




Edit: fix up some formatting & spelling

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[quote]Just thought I'd clarify and add some thoughts.



Also to Dr DB I would suggest you also post a sort of blog or online diary, frustrations, annoyances, wins and set backs (I don't mean human relationships you understand, just the problem(s) at hand).



could I do this in the message board format--maybe a dedicated thread? certainly there has been a lot of all of the above the last couple of months! I'm not sure how interesting this is to people...

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A simple suggestion that could be rather fast to implement if you guys want to.

On our results we see the name of the protein as:

Name: HBLR_1.0_1dtj_323_3093_1
Name: HBLR_1.0_1hz6_323_1593_0

which is not very informative for the average user, unless you know that the letters in the middle is the pdb id, and that you can look it up in protein databases.

What if you made the name a clickable link that linked to your robetta server?

E.g for my examples:

Name: HBLR_1.0_1dtj_323_3093_1
Name: HBLR_1.0_1hz6_323_1593_0

You then get a quick overview over what the protein/domain does, and can click on further links to get more information.

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What if you made the name a clickable link that linked to your robetta server?

WOW! That is an excellent idea! I had no idea where to look up that info before. I'd still like to see an updated english description.

I have to respectfully disagree with some earlier statements saying that lack of information about the project has been preventing participation in it. I think the responsiveness of late has been outstanding, and the way the app stands now it is better than many other projects. Basically, anything you do on this front is preaching to the choir - your attracting people who already know about the project. Of course I would love to have more info about what is going on, but at a certain point I have to say I'm a CS guy not a biologist so I have no idea what the info contained in the above database means...

I can't say that I know with certainty what will get the crunchers out in force for your project, but one thing that I would like to see is more platform optimized apps. I know that someone mentioned that a lot of work had been put into optimizing the algorithm, but more can be done in using a good optimizing compiler for a specific architecture. I recognize that you're hampered by the details the boinc architechture provides, and that you'd have to implement redundency to prevent cheating (or errors) if you released it open source, cancelling out anything you'd stand to gain by increased crunching. Thus I'd suggest this solution:

Compile a few versions that might see the most benefit; maybe for P4 (sse3 or 2), Pentium M, and one for AthlonXP/p3 on windows and linux. And maybe 2 for the newer Macs. Mainly, do the ones that would see the most benefit. You could release these as executables with an app-info.xml.

But finally, there's no substitute for partnerships/advertisement. I'm thiking about what the bbc did with cpdn recently; they managed to attract quite a few users that would never have heard about it otherwise.

Keep up the good work!

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Also to Dr DB I would suggest you also post a sort of blog or online diary, frustrations, annoyances, wins and set backs (I don't mean human relationships you understand, just the problem(s) at hand).



could I do this in the message board format--maybe a dedicated thread? certainly there has been a lot of all of the above the last couple of months! I'm not sure how interesting this is to people...

A dedicated thread such as "Informal Updates" on a weekly or so basis, just a paragraph or two, briefly saying what happened in the past week, might be helpful. This would be in addition to any comments you might respond to specifically from commenters.

Communication from the project, even briefly, on a regular basis seems to me to be like water on a garden, it should help keep the participants happy! :)

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Regards,
Bob P.

I like the idea of a dedicated thread with short but frequent posts.

What if you made the name a clickable link that linked to your robetta server?

E.g for my examples:

Name: HBLR_1.0_1dtj_323_3093_1
Name: HBLR_1.0_1hz6_323_1593_0

You then get a quick overview over what the protein/domain does, and can click on further links to get more information.

Great idea ! But perhaps a direct link to the color pic would be more suitable for the non-expert ? Of course this doesn't explain the first part of the WU name that describes the algorithmic flavor ('HBLR_1.0' in this case). So what about adding a few lines of text for each WU type to give us a rough idea about the algorithmic flavor that is being tested - perhaps something similar to this folding@home page where they give brief descriptions of each of their socalled 'projects' ?

As a general comment to the feedback discussion in this thread, perhaps the interval since the last science news update was simply a little bit too long (the credit/day started to drop off about two weeks after the initial post in the science news section). I have the impression David only wanted to give us the 'breakthroughs' and 'mayor advances' on that page. But of course science (and live) doesn't consist of a sequence of successes (which is something everyone can relate to). It would be perfectly ok to say something like 'this and that didn't quite work out as intended, so we now want to try something else' (think of this in terms of a crime story where the perpetrator/'the best algorithm' is found after many dead alleys have been followed - in fact this is what keeps the viewers or readers glued to the screen or book). Anyway, I hope there weren't more than the usual amount of 'frustrations and annoyances' for David in the last couple of months. ;-)

the click throughs to the various databases detailing the protien we are currently crunching although a good idea, the descriptions, unless you are a biological science major or in the medical sciences are basicly greek to me.

Maybe just a quickie in the Science news saying our next group of protiens with such and such WU's names are from this biological source and we hope to use this algorithium improvement to get such and such native structure within this many angstroms. would enlighten many of us to just what our computer is doing.

Knowing within reason what our machines are crunching is something much apprctiated by many users and to a surprisingly high number of people a prerequiste to project participation.

Media partnerships in your endeverors are probly the best way of increasing the host count. The ultimate would be to have say NOVA do a show on Rosetta@home.

see ya all....cheers....

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could I do this in the message board format--maybe a dedicated thread? certainly there has been a lot of all of the above the last couple of months! I'm not sure how interesting this is to people...

this is excellent.

Of course I can't talk for everyone, but I'm extremly interested in everything you have to say about the project, I want to know what's happening, I want to feel involved and I want to feel my, though it is small, contribution is really helping in the next vast step in human health (and of course all of the animal and vegetable kingdom ramifications that no-ones even comtemplated yet).

I noticed today we're up to 27 TereFLOPS, I think that's more down to the dial-up users coming back :)


Again forgive the spelling as I havn't had time to re-install OpenOffice

Edit: a nuance that I certainly didn't mean, and some spaces at the bottom of the post

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There are tons of great ideas on this page! I put the clickable links that you guys suggested to the EBI database pages (with cartoons, biological descriptions, etc.) from the news page and the top predictions page. We're looking into setting up a page for "What's next". And also a guide to what the cryptic "HBLR_1.0" stuff means... stay tuned for explanations of these new scientific strategies. And please keep making suggestions!

What if you made the name a clickable link that linked to your robetta server?

E.g for my examples:

Name: HBLR_1.0_1dtj_323_3093_1
Name: HBLR_1.0_1hz6_323_1593_0

You then get a quick overview over what the protein/domain does, and can click on further links to get more information.

Great idea ! But perhaps a direct link to the color pic would be more suitable for the non-expert ? Of course this doesn't explain the first part of the WU name that describes the algorithmic flavor ('HBLR_1.0' in this case). So what about adding a few lines of text for each WU type to give us a rough idea about the algorithmic flavor that is being tested - perhaps something similar to this folding@home page where they give brief descriptions of each of their socalled 'projects' ?

As a general comment to the feedback discussion in this thread, perhaps the interval since the last science news update was simply a little bit too long (the credit/day started to drop off about two weeks after the initial post in the science news section). I have the impression David only wanted to give us the 'breakthroughs' and 'mayor advances' on that page. But of course science (and live) doesn't consist of a sequence of successes (which is something everyone can relate to). It would be perfectly ok to say something like 'this and that didn't quite work out as intended, so we now want to try something else' (think of this in terms of a crime story where the perpetrator/'the best algorithm' is found after many dead alleys have been followed - in fact this is what keeps the viewers or readers glued to the screen or book). Anyway, I hope there weren't more than the usual amount of 'frustrations and annoyances' for David in the last couple of months. ;-)

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