RNA World

[Saenger]

RNA World
A new project from the orbit of Rechenkraft.

About RNA World (beta)
RNA World (beta) is a distributed supercomputer that uses Internet-connected computers to advance RNA-related research. You can participate by downloading and running a free program on your computer.

RNA World (beta) is based at the Rechenkraft.net e.V. research facility located in Germany.

* Projectdescription
* Project location & personnel
* Cooperation partners
* Sponsors
* FAQ
* Presentation of the project at the 5th Pan-Galactic BOINC Workshop

The permission to publish stats was given today.

[Bok]

Yup, already done - http://stats.free-dc.org/stats.php?page=proj&proj=rna

Please note that this is not open to the public just yet though. Soon, I'm told Seems to run pretty well so far..

[zombie67]

Tell me about this RNA, of which you speak!

[LAURENU2]

Tell me about this RNA, of which you speak!

RNA World project description
RNA World is a distributed supercomputer that uses Internet-connected computers to advance RNA research. This system is dedicated to identify, analyze, structurally predict and design RNA molecules on the basis of established bioinformatics software in a high-performance, high-throughput fashion.

In contrast to classical bioinformatic approaches, RNA World does not rely on individual desktop computers, web servers or supercomputers. Instead, it represents a continuously evolving cluster of world-wide distributed machines of any type. As such, RNA World is very heterogenous and, depending on the sub-project, currently addresses Internet-connected computers running Linux, Windows and OSX operating systems - your computer could be an important part of it. The fact that hardware and electricity costs are shared among the volunteer contributors raises the possibility of performing interesting analyses which under economical aspects would often not be affordable. In return, RNA World is not for profit, exclusively uses open source code and will make its results available to the public.

Sounds good to me I am asking for a invite

[Bok]

Ribo-Nucleic Acid

[LAURENU2]

Ribo-Nucleic Acid

Is that the invite code Ribo-Nucleic Acid

[Bigred]

Is that the invite code Ribo-Nucleic Acid

Didn't work for me.

[LAURENU2]

Didn't work for me.

Ya they are just Not accepting any new members

[Saenger]

Ya they are just Not accepting any new members

The chief (Dr. Michael Weber) just said that the next bunch of accounts will be available sometimes this month probably.

[Digital Parasite]

The chief (Dr. Michael Weber) just said that the next bunch of accounts will be available sometimes this month probably.

Interesting so that is what he is up to now. I just signed a release form for his new book on Distributed Computing that has articles from a lot of people in the DC scene. It will be available with a CC license I think so anyone can download it and read.

Jeff.

[LAURENU2]

Interesting so that is what he is up to now. I just signed a release form for his new book on Distributed Computing that has articles from a lot of people in the DC scene. It will be available with a CC license I think so anyone can download it and read.

Jeff.

Are they all calling me Crazy Again

[yoyo]

Hi,
currently we are struggling a bit with homogenous redundancy and validating results. We do not want to be unfriendly to the users if they get invalid results. Therefore the project isn't open.
yoyo

[Angus]

Back to the original issue of rechenkraft racking up big credit while no one else can participate -

Will you reset credits when RNA goes public, so the rechenkraft team doesn't have a totally unfair head start?

[Bok]

Personally I would vote NOT to reset the credits, knowing it's added work in order to achieve this.

Once they go live and as long as there is lots of wu's, some of the bigger teams out there like SETI.USA, L'Alliance Francophone and Seti Germany to name just a few would probably get up to the same levels within a few days anyway so it would not make the slightest bit of difference in the long run.

Just my own opinion though.

Bok

[LAURENU2]

Personally I would vote NOT to reset the credits, knowing it's added work in order to achieve this.

Once they go live and as long as there is lots of wu's, some of the bigger teams out there like SETI.USA, L'Alliance Francophone and Seti Germany to name just a few would probably get up to the same levels within a few days anyway so it would not make the slightest bit of difference in the long run.

Just my own opinion though.

Bok

Hay Bok you forgot yo mention LAURENU2

[Bok]

Hay Bok you forgot yo mention LAURENU2

Oh I thought of it, but I kept Free-DC out

[LAURENU2]

[Angus]

I see this thread has now been censored into banality.

[Bok]

No censuring of posts has occurred that I'm aware of. All posts off-topic from this thread were just moved to another. I'll remove yours and this one too at some point soon.

Stay on topic please.

[Angus]

No censuring of posts has occurred that I'm aware of.

This thread used to be two pages, and there are a LOT of missing posts. Where are they now?

[Bok]

re-read my post above that I edited to explain..

new thread is here

[Angus]

I made the mistake of looking in the yoyo@home section. silly me.

[Angus]

Someone tell yoyo that his database is in distress. Web site and BM both get errors.

1/15/2010 5:55:23 PM|RNA World|Message from server: Server can't open database

[Michael H.W. Weber]

Hi guys!

Will you reset credits when RNA goes public, so the rechenkraft team doesn't have a totally unfair head start?

Although we have not yet discussed this in detail, there are no plans to bring credits back to zero when the project goes public. The reason for this is fairness, because these people that helped during development deserve at least to keep their credits which they had earned by carrying out hard work. It should also be kept in mind that most of them contributed much more than CPU cycles since they identified a number of issues and even helped actively resolving them. I am sure you will understand that.

Someone tell yoyo that his database is in distress. Web site and BM both get errors.

1/15/2010 5:55:23 PM|RNA World|Message from server: Server can't open database

Thanks for the information. Issue resolved.
Best regards,
Michael.

P.S.: An exact date for going public is not yet fixed since it depends on the outcome of the final test rounds we are currently cycling through. I actually wanted to make the project go public in November right after my initial project presentation on the BOINC Workshop held in Barcelona last year in October but then a new version of the implemented software came out and we decided to first incorporate that and test it. We just like to be up to date.

P.P.S.: If anyone has questions concerning the RNA World project, just go ahead and ask me.

[Bok]

Thanks for coming on over Michael!

Looking forward to the project running

Bok

[Angus]

Since the 68 or so users in the last 24 hours brought the project's server to it's knees, and the few thousand WUs that were processed filled up their disk, I think they are not quite ready for prime time.

How can anyone go so wrong in the specification for a server?

[yoyo]

Since the 68 or so users in the last 24 hours brought the project's server to it's knees, and the few thousand WUs that were processed filled up their disk, I think they are not quite ready for prime time.

How can anyone go so wrong in the specification for a server?

We are not so well financed as a university. So we used the equipment which we have already. Now you see also why we do not going open, which you claimed above in this thread.
yoyo

[Michael H.W. Weber]

Thanks for coming on over Michael!

Looking forward to the project running

Bok

You are welcome! And thanks for your help with RNA World. It indeed has been quite some time since I last visited this forum, but think I will come for a visit more frequently.

Since the 68 or so users in the last 24 hours brought the project's server to it's knees, and the few thousand WUs that were processed filled up their disk, I think they are not quite ready for prime time.

How can anyone go so wrong in the specification for a server?

Firstly, please note that this server also hosts the Yoyo@home project. Then, these "68 or so users" assigned approx. 400 machines to RNA World, most of which quite powerful. However, it is exactly this why we are still in the testing phase and we have already decided to migrate the RNA World project to a much more powerful machine as a consequence of our testing.

We are not so well financed as a university.

In fact, we have no external funding at all. RNA World at present is financed completely on the basis of Rechenkraft.net mebership fees (of only 2,50 € per month; tax-deductible of course). But as soon as first publishable results pour in, we hope to acquire some additional funding.

Michael.

[LAURENU2]

Long time no see Dr. Michael H.W. Weber
Glad to see your still in the game.

Will you be looking into a cuda App for your project?

And when your really ready to test your platform send me a Invite,
(I sent you a request but with no reply from you)
And I will Port 160 cores (400+ Ghz) to see if your site is ready for DC-ing.

[Michael H.W. Weber]

Long time no see Dr. Michael H.W. Weber
Glad to see your still in the game.

Will you be looking into a cuda App for your project?

RNA World will incorporate several additional apps in the future, and, of course, if it turns out that GPU usage is beneficial in terms of computational output we will do our best to make use of it. At present, however, the implemented programs apparently do not profit from GPUs - they have been tested for it. So, currently GPUs have to stay aside.

And when your really ready to test your platform send me a Invite,
(I sent you a request but with no reply from you)
And I will Port 160 cores (400+ Ghz) to see if your site is ready for DC-ing.

Excellent!

To whom exactly did you send your request (to which email address)? I have actually replied to all requests as mandatory for good project support. But maybe something escaped my attention (e.g. spam folder or something of this sort). However, at present without exceptions (for fairness reasons) we have to reject all further participant requests except the team captains (which are automatically imported). There are some final tests going on including resolving a server issue, and, although spare-time operated, we don't want to start with avoidable glitches wherever possible. ;D

Michael.

[Angus]

<grinch mode on>

Let's debunk some of the grandiose aura of this "RNA WORLD" thing...

"Rechenkraft.net e.V. research facility" is simply some members of a DC team with a server or two either in someones apartment or a co-lo site somewhere in Germany (more likely, since yoyo talks about "renting" another server). There is no "facility" - no pictures of a modernistic lab or ivy-covered science building.

They have no connection to any scientific endeavor - no university, no visible principle scientist, not even a grad student doing his thesis for which he needs this research done.

They seemed to have picked an existing program and wrapped it in BOINC, to do research for which there is no current customer.

They set this thing up, made a pitch for it at the BOINC Pan-Galactic Conference (don't get me started on DA's obvious megalomania), poked at the app for a few months, then imported all the BOINC-wide teams, so now everyone in the BOINC universe is ready and anxious to participate.

But - it isn't ready. They can only let one user per team participate, and it has to be the team founder. No chance for a team to assign one selected active user.

The first sort-of live test falls flat on it's face, because this thing is installed on the same server as yoyo's other wrapper efforts, and somehow the "yoyo@home" project has been assimilated into this Rechenkraft.net e.V. research facility entity.


Now - they want the public to fund this this with thing by donating so they can "rent" (?) a server and bandwidth for one year. What happens at the end of that year, if the apps aren't running, and they haven't been able to sell any tangible results to anyone? another donation campaign?

Maybe we should all just pay them to add BOINC credits to our account, because that's all that's happening here, folks! They are selling credits!

<grinch mode off>


Have at it, moderators.

[Bok]

Have at it, moderators.

Ok if that's what you want as you obviously intend to irritate any and all.

If you have nothing positive to contribute, please don't. You seem to have a personal vendetta against Rechenkraft/Yoyo/RNA world and I'm getting somewhat tired of hearing it. All you are achieving is to make Free-DC look bad.

Further action pending after I talk with the other admins.

Bok

[Angus]

I guess transparency isn't so much encouraged here any more. The "Free" seems to have disappeared from Free-DC where we could freely and openly discuss anything about any project, and be honest with one another. It seems now that any nay-saying is not allowed.



I would have posted on their project site, but they don't have an integrated BOINC message board - only some off-site board somewhere that requires a separate account to post.

[outlnder]

I, personally, don't feel any animosity against Free-DC for allowing Angus to pontificate his opinions. However, it is really making Angus look like an ass. If he wants to continue his childish rants against RNA, let him. He is the only person that looks stupid.

[LAURENU2]

<grinch mode on>

<grinch mode off>

I prefer <grinch mode off> Myself

Sorry

[Angus]

I prefer <grinch mode off> Myself

Sorry

I was led astray by this: Grumpy is good for you

still

[LAURENU2]

Excellent!

To whom exactly did you send your request (to which email address)? I have actually replied to all requests as mandatory for good project support. But maybe something escaped my attention (e.g. spam folder or something of this sort). However, at present without exceptions (for fairness reasons) we have to reject all further participant requests except the team captains (which are automatically imported). There are some final tests going on including resolving a server issue, and, although spare-time operated, we don't want to start with avoidable glitches wherever possible. ;D

Michael.

I am Sorry I think I misspoke I think I only asked in your forum and I did get a responseIt was another project I confused your's with
You have always in the past given good project support.for the projects you worked on

[Michael H.W. Weber]

I am Sorry I think I misspoke I think I only asked in your forum and I did get a responseIt was another project I confused your's with

Well, then everything seems just fine, I guess.

You have always in the past given good project support.for the projects you worked on

Oh yes, I like DC a lot, so I try to put in my time whenever possible. Thank you for that nice remark.

@Angus: Just a few things for clarification (I always try to take comments serious although, sadly, sometimes people make it really very hard by the style they do communicate). RNA World is a bioinformatics project, so we do not need a lab at all. A few computers and a good webserver is sufficient. Still, as you can see from our cooperation partner list, we do clearly have the capabilities of performing lab experiments to validate our computational results. In fact, I work in an RNA lab every day with more than 10 years of practical experience in a diverse set of scientific fields. And yes, we do outsource server hosting to professionals while we keep server administration in house. This, to our experience, is the best and most economic way to do it. And we do indeed have at least some experience since we operate in DC for more than 10 years now. First we "only" participated in DC projects. Then we started the Yoyo@home project to help scientists not too firm with BOINC to acquire more volunteer support for their projects. We achieved that by wrapping a set of clients of non-BOINC projects we liked into the BOINC infrastructure and, apart from your crediting concerns, I think we did a nice job (and Yoyo is the driving force here). This scenario allowed us to gain a lot of practical experience over many years in this "business" (yeah, I hate that word in this context); also in terms of user requirements and support. And now, we are implementing our own scientific project in which we use established software plus own software developments to put into practice our own research ideas. You can say that we have evolved from a DC community to DC project developers. So, what is bad about that?

Finally, concerning myself (since you addressed this issue), maybe you have overlooked that I am not a Ph.D. student; I am holding a doc degree in natural sciences (Dr. rer. nat., chemistry) for quite some time now and I am the principal investigator at Rechenkraft.net you were seemingly looking for (and yes, I do not get paid for doing that like nobody at Rechenkraft.net gets paid for anything; it is just our spare-time interest but that has lasted in a sustained manner over a decade). That said, I would like to say that - as we witness in DC every day - volunteers can contribute significant efforts towards achieving meaningful scientific results. Hence, I do not give much on degrees (although from your writing it appeared to me that it seems important to you). Rather, a nice style of cooperative working together is what I have in mind where everybody can input small ideas. That, taken together, will ultimately give a nice overall picture. I believe, DC is not at all about competition as always claimed. If you look a bit beyond competition in terms of who has the fastest machine, you will find that a bigger goal is achieved COOPERATIVELY. And that, to date, to my opinion, is the most powerful principle in nature - not competition. But maybe let us better keep that aside for now. So to say as a philosophical side remark...

Michael.

[gopher_yarrowzoo]

Micheal I do believe you've hit the protein on the amino acid (if you'll forgive the bad pun), yes I do know about Adenine, Cytosine, Guanine and Urasil (sp) notice I didn't say Thymine since well that's DNA..

Yes many do it for the "I'm bigger than you" but it's all about the science in the end, the more power gets thrown at it the quicker we get to prove / disprove the theory behind the project or prove / disprove that particular drug / protein.

[Angus]

@MHWW thanks for clarifying some of the issues.

I spent a LOT of time yesterday moving through your web sites and pasting bits and pieces into Google Translate trying to get answers for myself. With almost all of the content in German, it's very difficult for a non-German speaker to get any kind of picture of your organization. Do you a plan to provide all the content in English?

This is further compounded by having stuff scattered around through multiple sites. There is no BOINC message board, however there appears to be a rechenkraft message board that I'm not sure is for the team or the organization, but it requires a separate login. There is also some sort of wiki, but it's almost entirely in German too.

One of the more interesting pieces might have been an "RKN roadmap" post that seems to be at the top of many areas of the message boards, but I couldn't find that in English anywhere.

Even the English home page for the RNA project still has at least some German on it, and today the server status pages are coming up in German where they were in English previously.

I think your organization is a victim of self-imposed obscurity by not providing other language content, particularly English.

Just an observation.