Posts by Aegis Maelstrom

1) Message boards : Rosetta@home Science : protein-protein docking at Rosetta@Home (Message 76040)
Posted 9 Sep 2013 by Aegis Maelstrom
Post:
Hello Lei,

thank you for your explanations, it keeps many people motivated. Are there any news after first three months to share or are you waiting with everything for the publication? :)

Best Regards,
a.m.
2) Message boards : Rosetta@home Science : CASP 10 (Message 72970)
Posted 2 May 2012 by Aegis Maelstrom
Post:
Hi, I second Sid Celery in his proposals.

My guess is that a majority of R@h crunchers is not meeting your 1-2 days deadline for a task requirement. To be effective they need to be forced (or at least informed) to change their behaviour. As the CASP10 has already started, we would need to inform them in a blink.
Furthermore, let\'s be honest - a vast majority of crunchers does not read information from the projects or their teams on a daily basis. They even lag severly in e-mail communication. Moreover, even if they learn about new requirements a fair amount of participants will forget, be unable etc. to adjust their crunching pattern.

In this situation changing the deadlines for WUs in addition to the information about the issue (very important for computers without permanent access to the Internet, used for a small amount of time per day, set on longer run times etc.) seems to be the best option.

That or sending CASP10 WUs strictly basing on behavioural patterns (only to \"fast\" crunchers, if their computing power is big enough).

Best Regards and Happy Crunching.
3) Message boards : Cafe Rosetta : Join the protest against ACTA / SOPA / PIPA (Message 72166)
Posted 17 Jan 2012 by Aegis Maelstrom
Post:
As you may be aware, legislators across the globe are thinking on implementation of new laws, which are putting more restrictions on Internet and citizen freedoms within it.

Because of this fact, a number of services are going to protest against the new legislature. This is a wide movement, including not only numerous Free/Libre/Open Source Software and citizen rights sites, but big names like Wikipedia, Google, Mozilla, Reddit&ArsTechnica as well.

My team, BOINC@Poland, and our affiliated project Radioactive@home are supporting the protest.

Our side portal http://www.boinc.com.pl will be blacked out, and the main services like http://www.boincatpoland.org and http://radioactiveathome.org/pl/ will highlight our message.

We invite all the projects, BOINC teams and volunteers to support the protest, in a way you feel would be appropriate.

Just let me pass the ask of a sysop of Radioactive@home:


Welcome

Because of acceptance of ACTA agreement, and also other attempts of forcing legal solutions targeting increase of legal control over internet, administrators of Radioactive@home decided to place note of protest on the project site, with the following information.

\"With regard to the ACTA (so-called Anti-Counterfeiting Trade Agreement) accepted by European Union, we feel obliged to warn you that our website may be unavailable in some countries soon.

ACTA Agreement was initiated by organizations describing themselves as \"defending artists from bad pirates\" and has been enforced on EU in secret negotiations initiated by US Government. Non government
organizations from all over the world agreed on condemning both the way of negotiations ware taken and allowing by this agreement cutting off websites \"uncomfortable\" for governments of countries that
signed ACTA, without proving infringements of any laws.\"


We would like Your project to join this action. We plan to publish this note on Wednesday, 18.01.2012 on 0.00am.

Regards,

Krzysztof \'krzyszp\' Piszczek


Best Regards to you all and happy crunching,

aegis maelstrom
BOINC@Poland
4) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 72163)
Posted 17 Jan 2012 by Aegis Maelstrom
Post:
Great to hear from you!

When only I get some free time, I\'ll make some translations & news basing on your posts. I am pretty sure MadMax and others will be happy as well.

Kind regards from BOINC@Poland,
a.m.
5) Message boards : Number crunching : Looking into Rosetta\'s source code? (Message 72110)
Posted 13 Jan 2012 by Aegis Maelstrom
Post:
Regarding the general question of ability to take a look into the Rosetta source code - have you thought of external \"consulting\" from the volunteering programmers from the BOINC or Free/Libre/Open Source Software community?

I do realize there can be many secrets and fears of being copied involved - but additional IT resources could be very potent: both in generating new and higher quality, reviewed code as well as higher reliability and recognition within our communities.

For instance, as an active member of BOINC@Poland team\'s community and forum, I see questions regarding Rosetta\'s efficiency, possibility and gains from 64-bit version, use of additional instructions and registers like SSEs and AVX, general recompiling etc. etc. quite often. These are understandable concerns which we have sometimes a hard time to answer.

My teammates do run a few (however smaller) BOINC Projects and introduced a few improvements to some other existing ones so there is some expertise even within a single team, not mentioning the broad BOINC/FLOSS communities.

I remember seeing on this forum a very brief remark of a volunteer who saw some actual code and I thought it was a positive experience for both sides. Even should you need to show only some less biology specific part of the code, use some NDAs etc. etc., maybe you could coin some mechanism to share the knowledge, gain some good PR and grasp improvements?

Best regards,
a.m.
6) Message boards : Rosetta@home Science : Bakerlab update for 2012 (Message 72109)
Posted 13 Jan 2012 by Aegis Maelstrom
Post:
Hi,

and let me join you in the \"give us more information\" club.

I think Rosetta misses its trains to gather more crunchers again and again. For instance, there has been an update of the software to 3.19 version - but we have not been informed what is new (new protocols? improved algorythms?) with it.

Similarily both core projects as well as all the recent CASPs, side projects run by visiting scientists etc. lack of publicity and explanation.

Rosetta is not the only neither the most credit rewarding game in town - I think more information would help to convince me - and many crunchers - to put more resources into R@h (and even generally into BOINC).

Best regards from BOINC@Poland,
a.m.
7) Message boards : Cafe Rosetta : Merry Christmas / Happy Holidays! (Message 71885)
Posted 25 Dec 2011 by Aegis Maelstrom
Post:
All of ye good people of Rosetta@home: fellow crunchers, project scientists and technicians, fans and supporters and specifically you, ModSense :) - please accept the best wishes of health, warmth, joy and good luck in your lives.

Let the world be a better place around you and thanks to you.

Happy BOINCing!

Kind Regards from BOINC@Poland,
aegis maelstrom

Wesołych Świąt!
8) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 71811)
Posted 16 Dec 2011 by Aegis Maelstrom
Post:
Hello,

as I have described in the LigDes thread originated by Mr. Moretti, I am pretty interested in the scientific progress of Rosetta@home, including projects mentioned in this thread like Ebola virus surface glycoprotein research.

As it would be nice to keep up everyone with your science, please do not hesitate to post us some updates! :) They are always very welcome. :)

Best Regards from Warsaw,
a.m.
BOINC@Poland
9) Message boards : Rosetta@home Science : Design of protein-small molecule binding (Message 71808)
Posted 16 Dec 2011 by Aegis Maelstrom
Post:
Hi,

thank you for your fast response. I understand that the things are not always as easy as we thought they would be.

If I understand you correctly, everything what was reasonable to crunch for your project on this stage has been crunched and now we are waiting for the validation in an actual wet lab. Your collaborators from George Church\'s lab need to iron out two things: 1. a complete procedure of validating the computed results (as you wrote \"good binder vs. bad binder\") and 2. a proper method to actually synthetize the proteins to test them.

In such a case I should wish you good luck with physical proteins and many exciting computational projects. :)

Best regards,
a.m.
10) Message boards : Rosetta@home Science : Design of protein-small molecule binding (Message 71800)
Posted 15 Dec 2011 by Aegis Maelstrom
Post:
Hello there,

thank you for your detailed description. You may not see all the feedback that you should get but many people are pretty involved in the scientific side of BOINC and distributed computing in general, especially including projects like Rosetta@home where the science is a key appeal. However, there is some stir, not only on this site.

Several months ago I have put a brief summary of your post in Polish for my teammates in BOINC@Poland (link to the B@P wiki). I think you have already guessed that 1. not all the volunteers use the fora of the projects (but some of them heavily use the teams\' communication channels) 2. not everyone\'s command in English is good enough to easily comprehend even popular-scientific texts in biology. This is why sometimes the volunteers act as a kind of \"broadcasters\" and \"preachers\" of the projects. :)

Now, as roughly 6 months passed, I would like to kindly ask you for some summary / follow-up post about your successes, failures and general work so far. I am quite sure that many people are interested in your project(s) and achievement(s) and more information would attract more volunteers.
Moreover, I don\'t need to mention that I would be pretty happy to provide my teammates a yet another reference point and a summary. :) I think it is very encouraging for many people to participate in distributed computing efforts.

So please, write us some updates if you find some time. :)

Best Wishes and happy crunching for everyone,
greetings from Warsaw,
a.m.
BOINC@Poland
11) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (5) (Message 71388)
Posted 6 Oct 2011 by Aegis Maelstrom
Post:
Great news regarding the \"excited state\" proteins.

Congratulations for the whole team and the crunching family!
12) Message boards : Number crunching : Lack of communication from project (Message 71035)
Posted 12 Aug 2011 by Aegis Maelstrom
Post:
Having a secondary project does not solve all the issues.

Especially manual swithing on and off is not acceptable for the users who want to have a fairly stable project (because they will be offline, they have a machine or more in distant location without a working remote access, because they don\'t want to care that much). Far better solution is having a secondary project turned on with something like 0.1% of CPU time enabled. Then it will do work when the primary project fails.

However, all of this does not resolve a huge PR problem. How can we convince other users that Rosetta needs them and their computers can help the science when the project itself does not have anything to do? Of course, it is very good that the project does not want to run empty WUs and we know that the computing power will be needed in future. But the problem lays in timing. If we run a promo campaign of Rosetta@home while it does not need more volunteers, it will be countereffective. Everyone would be better off if we wait with that a month or two.

This is a valid example why the better communication is required.
13) Message boards : Number crunching : Lack of communication from project (Message 71026)
Posted 11 Aug 2011 by Aegis Maelstrom
Post:
Regarding the issue of the limited number of WUs in R@h explained by Rocco it would be great how the close future looks like, eg. the rest of August and September.

My team, BOINC@Poland, is seriously considering Rosetta@home to be, once again, our Project of the Month. Before we (and I personally) start encouraging people to devote more and more resources to R@h, take a look on the project etc., it would be reasonable to know if the project plans to have tasks to crunch, if we should expect some additionale glitches, new system requirements, new exciting science and so on and so forth. I am sure that we are not the only ones in a such position.

In BOINC World the communication is not only done by Projects and individual users on the Projects\' sites, mailing lists etc., but on the teams communication channels as well. This is particularly important for English non-natives and highly integrated teams. The projects should remember that their information is broadcasted and discussed in many places all over the Internet - and it is highly appreciated even if not stated directly on a forum like this one.

Best regards from Warsaw, and I am seeing for more information regarding the close future.
14) Message boards : Number crunching : Nice and steady 120+ TFlop estimate. (Message 69621)
Posted 10 Feb 2011 by Aegis Maelstrom
Post:
The estimate on this site is apparently derived from the \"Credits last 24h\". Does this mean that 1 million R@H credits in one day is the equivalent to 1 TFLOP? Which means... that 1 TFLOP is 1 million credits divided by the seconds in one day...

Am I going in the right track?

Rosetta main page (Server Status) calculate FLOPS estimate from \"Credits last 24h\" (1 million credits per day = 10 TFLOPS @ 24/7)
Boinc stat (http://boincstats.com/stats/project_graph.php?pr=rosetta&view=credit) calculate FLOPS estimate from Recent average credit (RAC - sliding average from last ~30 days), but shows only half of it (50%) cuz 1 gobblestone (credit) composed from 50% of integer speed and 50% floating point speed.
So major(2х) difference is (TFLOPS only) vs (TFLOPS + TIOPS).
Minor difference is RAC (last 30 days) vs (last 24h) and affected by last big downtime of project in January.
Then RAC stabilise BOINC will show ~ 60-65 TFLOPS, and R@H ~ 120-130 TFLOPS.



they cant both be right..... boinc shows active computers
how long do you think before it stabilizes??


As Mad Max nicely explained, there are two major differences between methodologies on BoincStats and Rosetta sites.

Firstly, boincstats site uses RAC, which takes an average from the last thirty days. Thus, it takes 30 days since the come back after outage to \"stabilize\".

On the contrary, Rosetta site uses only last 24 hours.

Secondly, boincstats uses a different translation between cobblestones (BOINC points) and FLOPSes. It seems to assume that 1 cobblestone = 5 MegaFLOPSes.
On the other side, Rosetta estimates 1 cobblestone = 10 MegaFLOPSes.

Regarding this second difference - which approach is more reliable?
My guess is that Rosetta team knows better the nature of their calculations and can adjust the multiplier (cobblestones / FLOPSes).
On the other hand, boincstats makes one general assumption on all the BOINCprojects, which obviously are not uniform.

Summing up, I would prefer the number provided by the Rosetta Team (however taking it with a grain of salt).

I hope I helped.

Best from Warsaw, BOINC@Poland. :)

P.S. Sidenote: FLOPS (FLoating Operations Per Second) is singular. FLOPSes is plural; thus 130 TFLOPS is O.K. (like 130 m or 130 kg) but a TFLOP is a big flop. ;P
15) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 66619)
Posted 21 Jun 2010 by Aegis Maelstrom
Post:
I think it would be a good idea to make the publications stand out a bit more. I suggest:


  • Updating the Publications list (as linked to on the front page)
  • Splitting the \'About\' heading on the front page into \'About\'* and \'Research\'.


* There might be a more appropriate heading than \'About\'!?!

The Research section should be in big lights, but at the moment it doesn\'t stand out and it\'s the most important thing for a lot of people.



I do agree with dcdc. I would also consider posting a new news item, to attract more attention from the visitors on this website, as well as readers of BoincStats and other BOINC news broadcasters.

P.S. Of course, my sincere congratulations for the whole team!
16) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 65904)
Posted 30 Apr 2010 by Aegis Maelstrom
Post:
Way to undersell it! That\'s phenomenal news! I\'ve had the potential CO2 capture work mentioned in my profile for about a year now - it\'s great to see genuinely progressive action on the subject from the US government, and hopefully this news, along with the influenza work will bring a new crowd to R@H to supply the computers to help power the research. :D

True, I will post a news item for my Polish folks - few people look up here, many cruchers prefer their team sites and fora.
17) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 65714)
Posted 9 Apr 2010 by Aegis Maelstrom
Post:
Does this mean what I think it means?

I think we got another \'wow\'.


Congratulations for the whole team and keep us informed! :)
18) Message boards : Rosetta@home Science : Results to any use so far? (Message 65535)
Posted 12 Mar 2010 by Aegis Maelstrom
Post:
I was wondering if the research that has been made has been to any use so far when it comes to science?


How about reading these shiny sticky topics on this forum? =P
I would recommend starting with the top 2: this and this one. I am sure you will find some interesting information.

This fulfills any use. If you want to know something more specific, please look for it firstly and than ask. I am sure someone will try to help you: provide you answers or maybe support your questions.

Best regards and happy crunching, =]
a.m., B@P.
19) Message boards : Rosetta@home Science : Possible cancer cure found in plant (Message 65296)
Posted 12 Feb 2010 by Aegis Maelstrom
Post:
Hi guys,

regarding the frustration - I think I know a bit of what you mean, Otto. Arrogance and cluelessness one can meet every day, Dilbertian jobs and wasted efforts, apathy and bureaucracy you can see anywhere from capitalistic US to the last communist states, pseudoscience and ignorance, political, cultural, religious fixations, and many, many more...

However, people are people and Rome wasn\'t built in a day. We have made many mistakes and we will make many more - but it only says we should only try harder.

In weird communist times one of Polish cabaret singers made a song \"Róbmy swoje\" (let\'s do our stuff) addressed to inteligentsia and I think it remains valid.
Regardless of actions of all the other people you have your own life, duties and path of conduct. I believe the English-speaking world knows this thought at least from another Pole, Joseph Conrad. :)

That\'s all from Polish Culture 101 now. ;) So let\'s do our stuff - crunch BOINC, bug test, make science popular. There is a long way ahead - we have made great achievements but who knows for how long will we preserve them in the future and what happens within next one hundred years? Think of it, XIX century men of Europe considered themselves as so modern but they would hardly understand our \"western world\" as of today. :) The future is now and yet it escapes like the Zeno\'s Achillean tortoise. :) It may be a reason to be in dispair, it may be a reason to feel excitement and fun.

Regarding the health care in US - AFAIR it asks for some tweakings and it\'s not only the \"treat all the people\" issue. One example: AFAIK still in US, Australia etc. if the branded medicine is prescribed, it cannot be changed by a patient/pharmacist even if a proper generic (and far cheaper) drug is available. This is an outrageous waste and invitation to corruption (sponsoring practicioners to win their prescriptions). In EU any patient has a right to ask in a pharma for the cheapest generic equivalent.

Health insurances is a big business, like pharma, health care, health research or health law suits and they are worth of reconsideration.

Finally, regarding the clinical trials and BOINC: as far as I know Rosetta and other usable methods are far from precision to replace the trials. They are non-deterministic and base on still not fully developed algorythms. Thankfully, presently they can give, each year better, drug candidates for further testing.
Even if our computing power and methods improve enough to have high quality protein-protein docking etc. to have perfect drug candidates, it still does not solve zillions of potential interactions which would need to be checked - and that\'s a lot of computing power.

Summing up, for me it\'s a very distant shot. However, \"perfect\" or \"near-perfect\" drug candidates would be great enough to bring us a new level of medicine.

Nevertheless once again, BOINC platform had an ambition to be not only a \"computing power sharing network\" but a whole \"creative minds in cooperation network\". And that could bring some hope, just as you say!

Best regards ladies and gentlemen,
a.m.
20) Message boards : Number crunching : Jobs lock up and never finish (Message 65284)
Posted 11 Feb 2010 by Aegis Maelstrom
Post:
I had this problem as well, nothing really helped. It looked a bit like a RAM issue or just \"another application issue\" - the WU was being heavier and heavier crunched and in some moment, i.e. switching to some app, killing the browser etc. - this happens. For me it was like a quiet BOINC/Rosetta crash.

That was a final straw for me for some time. I\'ll wait with Rosetta till some new WUs or a new computer, preferably. :) Rosie seems to want more than I can always provide.


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