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Message 23021 - Posted: 20 Jan 2012 | 14:52:37 UTC
Last modified: 22 Jan 2012 | 19:47:40 UTC

The Amino acids, components of proteins, the main characters in GPUGRID simulations. Given per total number of credits and milestones in 20 levels, the number of amino acids encoded by the universal genetic code (ordered by molar mass ~weight). Amino acid/credits equivalences below.



The Waters, basic component of life and a distinctive trait of our long and accurate simulations. 7 levels (Plastic, Bronze, Silver, Gold, Ruby, Emerald, Sapphire) to represent relative contribution to our scientific publications. Each water badge will be linked to the corresponding publication and Science topic. Water/percentage equivalences below.



The donor badge is changed to the crown

The complete information is available in the Volunteers page. We will update the server at the start of next week!

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Message 23022 - Posted: 20 Jan 2012 | 14:55:55 UTC - in response to Message 23021.
Last modified: 20 Jan 2012 | 23:14:39 UTC

#AA - Milestone (in Million credits)
Gly 0.5
Ala 1
Ser 5
Pro 10
Val 25
Thr 50
Cys 100
Ile 150
Leu 200
Asn 250
Asp 300
Gln 400
Lys 500
Glu 750
Met 1,000
His 1,500
Phe 2,000
Arg 3,000
Tyr 5,000
Trp 10,000

#Water - Top % contribution (percentiles)
Plastic 100
Bronze 90
Silver 75
Gold 50
Ruby 25
Emerald 10
Sapphire 1

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Message 23023 - Posted: 20 Jan 2012 | 15:33:54 UTC

Amino acids rofl :) Neat idea, and very much in keeping with what GPUGRID is about.

Nicely Done :)

Regards
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Message 23024 - Posted: 20 Jan 2012 | 15:44:09 UTC - in response to Message 23023.

Acknowledgements go to skgiven as well!
His contribution has been crucial in the development of the badge system.

Cheers,
i

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Message 23027 - Posted: 20 Jan 2012 | 17:30:12 UTC

sweet. Implemented partially at Free-DC, given it's just based on credit.

See an example on my CPID page here

standalone for use in signatures

which is {img}http://stats.free-dc.org/badgesgpugrid.php?proj=ps3&id=59511{/img} changing {} to []

Bok

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Message 23028 - Posted: 20 Jan 2012 | 17:55:08 UTC - in response to Message 23027.

Excellent - that didn't take you long =)

This one looks a bit odd,

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Message 23029 - Posted: 20 Jan 2012 | 17:57:02 UTC

I took a guess at that as there was a default badge out there, figured it was a base one everyone got...I should have looked at it first as it was not a good guess perhaps :)

I'll update code to take that out now.

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Message 23030 - Posted: 20 Jan 2012 | 18:02:23 UTC - in response to Message 23029.

The grey badge will be used as a default below 0.5 M credits, in fact!

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Message 23031 - Posted: 20 Jan 2012 | 18:23:41 UTC

Ok cool. Reverted back to how I did it originally :)

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Message 23032 - Posted: 20 Jan 2012 | 18:30:06 UTC - in response to Message 23029.

Thanks for your efforts Bok.

It's way better to have a grey αα than none!

Isoleucine (ILE/I) at it's finest,


The crowns look more appropriate for donations.
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Message 23034 - Posted: 20 Jan 2012 | 18:50:20 UTC

This looks great. I need more compute hardware. ><

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Message 23036 - Posted: 20 Jan 2012 | 20:31:33 UTC - in response to Message 23034.

Those are cool. :)
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Message 23038 - Posted: 20 Jan 2012 | 22:15:44 UTC

How is the water badge calculated? What does (say) top 1% of contribution mean?
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Message 23039 - Posted: 20 Jan 2012 | 23:14:15 UTC - in response to Message 23038.

Water badges are equivalent to percentiles in a ranked table of contributors.
Of all contributors for a paper, the Top 1% are assigned a Sapphire, the top 10% (minus the 1% guys) an Emerald and so on...

cheers
i

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Message 23040 - Posted: 21 Jan 2012 | 0:03:49 UTC - in response to Message 23039.

Thanks. I was not clear on my question. What is the equation? Also, hypothetically, I could be in the top 1% today, but drop out tomorrow. So does this badge represent the highest ever achieved, or just the current ranking?
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Message 23041 - Posted: 21 Jan 2012 | 0:17:57 UTC - in response to Message 23040.
Last modified: 21 Jan 2012 | 0:31:21 UTC

The paper rankings are (barring fixes) "static": they represent the contribution that you have given to a specific paper. Thus, they are only computed when a new paper comes out, by counting the calculations that were used in it. Once a paper is published, new WUs can't enter into it, and therefore - once a badge is given, it's given.

Hopefully I did not confuse your ideas.

In other words:
1. Computations are done; say, they have the "LYSTRYP" name tag
2. A paper on LYSTRYP is written and, hopefully, published.
3. We count who has given what to our LYSTRYP (computations and paper)
4. Contributors are ranked; top 1% of the contributors get sapphire for LYSTRYP, top 10% get ... etc
5. There is no n. 5. New workunits will have different names, and new results won't affect the LYSTRYP badges.

In short, paper-related badges are tokens of appreciation for helping us in reaching specific important goals.

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Message 23042 - Posted: 21 Jan 2012 | 0:33:02 UTC

Where will these badges appear (other than BOK's site)?

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Message 23043 - Posted: 21 Jan 2012 | 0:51:06 UTC - in response to Message 23041.

In short, paper-related badges are tokens of appreciation for helping us in reaching specific important goals.


Ah! I get it now. Thanks!

Okay, then I have a follow-up question. There is a choice between long and short tasks. Are any sub-projects available in only one or the other? In other words, if I chose only long tasks, will I be missing out on contributing to some sub-projects? Or if I choose only short tasks, will I be missing out on contributing to some sub-projects?
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Message 23047 - Posted: 21 Jan 2012 | 2:43:05 UTC - in response to Message 23042.
Last modified: 21 Jan 2012 | 16:42:22 UTC

Where will these badges appear (other than BOK's site)?

Early next week badges will appear beneath your RAC, like this:

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Message 23049 - Posted: 21 Jan 2012 | 3:43:16 UTC - in response to Message 23043.
Last modified: 21 Jan 2012 | 3:43:33 UTC

There is a choice between long and short tasks. Are any sub-projects available in only one or the other? In other words, if I chose only long tasks, will I be missing out on contributing to some sub-projects? Or if I choose only short tasks, will I be missing out on contributing to some sub-projects?

Very good question.
I don't know the long-term answer to that question, but I have an impression of the present situation and can speculate on what I think will/should happen:
At the minute TONI, GIANNI and NATHAN have long tasks (in various numbers) but I have not seen any MJHARVEY or KASHIF long tasks recently, and while I have seen a few normal length NATHAN and TONI tasks, I think these are different projects (but possibly different parts of one project). There has not been many IBUCH tasks recently, of either length, probably because Ignasi has been busy setting up this system and the site.
I expect this will be discussed soon, 'amongst the researchers' if it has not already been agreed upon (related issues have been).
I would speculate that it's most likely there will be both long and normal tasks for as many projects as possible fairly soon. My worry would be that some ongoing research might require step continuity, but for future projects I don't see any reason why there could not be both short and long tasks for all ongoing research. It's sort of set and forget vs interactive & fun. Either way, so long as we know what's happening we can crunch accordingly. We should all be able to reach plastic for every project by crunching a few short (or even long) tasks now and again.

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Message 23052 - Posted: 21 Jan 2012 | 5:37:28 UTC - in response to Message 23047.

Early next week badges will appear beneath your RAC, like this:


Sweet...thanks skgiven!

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Message 23054 - Posted: 21 Jan 2012 | 7:18:02 UTC - in response to Message 23049.

Thanks for the reply. I see a problem for badge-chasers like me. How do we make sure we maximise our chance to win? Rather than a choice for long/short, we need sub-project selections.
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Message 23056 - Posted: 21 Jan 2012 | 11:18:03 UTC - in response to Message 23054.

Skgiven's guesses of the short/long tasks are rather accurate.
Our usage of either of these is primarily based on the experiment/researcher needs.

Now, regarding zombie67 concerns about sub-project selection, I can say that we will NOT implement it. Unlike other DC projects that do so trough the differnet apps they deploy, GPUGRID runs a single app for all of its WU types (only splitted in two weight categories—short/long). Moreover, sub-project selection would result in a competition for resources between GPUGRID scientists and we don't want that, we are single research group with common goals.

The most you can do is to use short/long WU to indirectly select between experiements (i.e. HIV is only running on short)...

Finally, and adding up on Toni's words, let me remark the fact that as scientists our goal is to get our work published. Publications are the measure of performance and success and they are the means to communicate our findings and developments. Publication Badges are designed to acknowledge your contribution to the achievement of these goals. In fact, they will be linked to each and every one of the publications done so far using GPUGRID. AFAIK and correct me if I am wrong but, this is a unique feature in the DC community that I am sure you will appreciate.

Cheers,
i

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Message 23062 - Posted: 21 Jan 2012 | 18:58:10 UTC

I'm just going to venture a guess that Stoneageman is going to have a lot of sapphire badges. O_o

Are the water badges retroactive? Or will they only be for publications going forward from the implementation of this badge system?

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Message 23065 - Posted: 21 Jan 2012 | 20:10:13 UTC - in response to Message 23062.
Last modified: 21 Jan 2012 | 20:19:44 UTC

One amino badge for contribution (total credit based), and one water badge per published project - implemented retrospectively (for existing completed work). For existing projects, the badges will be added when the projects finish and the research is published.

Badges will look like this

You can read about the Badges in this thread and in the Volunteers page.
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Message 23066 - Posted: 21 Jan 2012 | 20:43:04 UTC

Well that's great recordkeeping as far as who's contributed what to each publication. It sounds like you've been planning for this badge system for awhile now.

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Message 23075 - Posted: 22 Jan 2012 | 12:40:55 UTC - in response to Message 23047.

Where will these badges appear (other than BOK's site)?

Early next week badges will appear beneath your RAC, like this:

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Ah that was the answere i was looking for, thx :)
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Message 23077 - Posted: 22 Jan 2012 | 14:41:09 UTC - in response to Message 23022.
Last modified: 22 Jan 2012 | 14:46:10 UTC

#AA - Milestone (in Million credits)
Gly 0.5
Ala 1
Ser 5
Pro 10
Val 25
Thr 50
Cys 100
Ile 150*
Leu 200*
Asn 250
Asp 300
Gln 400*
Lys 500*
Glu 750
Met 1,000
His 1,500
Phe 2,000
Arg 3,000
Tyr 5,000
Trp 10,000


I think the proper order is:

Gly 0.5
Ala 1
Ser 5
Pro 10
Val 25
Thr 50
Cys 100
Leu 150*
Ile 200*
Asn 250
Asp 300
Lys 400*
Gln 500*
Glu 750
Met 1,000
His 1,500
Phe 2,000
Arg 3,000
Tyr 5,000
Trp 10,000

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Message 23087 - Posted: 22 Jan 2012 | 19:59:10 UTC - in response to Message 23077.


I think the proper order is:
...
Leu 150*
Ile 200*
...
Lys 400*
Gln 500*
...


Mmmm not really... Ile/Leu are the same (131.17 Da) but Gln/Lys are 146.14/146.19 Da...
But anyway, it's just to define an order.

Thanks!

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Message 23088 - Posted: 22 Jan 2012 | 20:42:43 UTC - in response to Message 23077.
Last modified: 23 Jan 2012 | 17:51:09 UTC

There are all sorts of grouping arguments that could have led to many different orderings. For example, groups (small, nucleophilic, hydrophobic, aromatic, acidic, amides, basic), fluorescence, pKa, abundance, their codon letters/weights, alphabetical names, hydropathy index, wet and/or dry weight... Many possibilities were considered, as was the αα count itself (20, 21, 22, numerous non-standard variants)!

IIRC the system chosen was entirely based on 'dry' molecular weight, for which Leucine and Isoleucine have an identical molecular weight (molar mass) of 113.16 Dalton - so their order is moot. I might have went with Leucine and then Isoleucine too, but it’s of little importance to the badge system. Maybe this was just done alphabetically (I,L)? Gln is slightly lighter than Lys – 128.14 and 128.17 respectively.

Are the water badges retroactive?

- edit Yes, retroactive/applied retrospectively for completed work.

It sounds like you've been planning for this badge system for awhile now.
There was a lot to consider and decide upon before implementing anything, and the site and server code had to be updated and tested first.
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Message 23092 - Posted: 23 Jan 2012 | 9:30:33 UTC - in response to Message 23087.


I think the proper order is:
...
Leu 150*
Ile 200*
...
Lys 400*
Gln 500*
...


Mmmm not really... Ile/Leu are the same (131.17 Da) but Gln/Lys are 146.14/146.19 Da...
But anyway, it's just to define an order.

Thanks!


Okay, I was just going by the way they were pictured ... :)

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Message 23094 - Posted: 23 Jan 2012 | 11:30:09 UTC - in response to Message 23088.


Are the water badges retroactive?
No, and neither are the amino acids, though they could be; you can use heavy αα's as a biological tracking technique.


Indeed! They are! We will assign water badges per past projects too.
Amino-acid badges will be on current total credits too.

cheers
i

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Message 23101 - Posted: 23 Jan 2012 | 17:33:41 UTC

Yeah he said they were retroactive, and then contradicted his earlier response. I see now that they do give credit for previous work. Outstanding! I wish I'd started this project earlier, I'm missing so many badges.

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Message 23103 - Posted: 23 Jan 2012 | 18:04:51 UTC - in response to Message 23101.
Last modified: 23 Jan 2012 | 18:18:16 UTC

Sorry, was in a rush and misread as 'radioactive'! Thought someone was being funny and referring to the water molecule colours; tritium, tritium... Hence the research tool tangent.

Corrected below and definitely retroactive.

Yeah, I'm also missing a few badges - but I never learn.
This morning I set one of my profiles to crunch on both long and short tasks, so as not to miss out on any more.

Just in case somebody doesn't notice, move your mouse over the badges...
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Message 23105 - Posted: 23 Jan 2012 | 18:43:09 UTC

Yeah well, it happens. I know, trust me. ^^

I just turned off short runs because of the ridiculously low credits I was getting on some of the units. Some were running as long as the long runs, and giving 25-30% of the credit. I'm sure you've already heard that before. I want to contribute to all of the subprojects without feeling like I'm being shorted. Is there anything to be done about this?

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Message 23107 - Posted: 23 Jan 2012 | 19:09:55 UTC - in response to Message 23105.
Last modified: 23 Jan 2012 | 19:46:15 UTC

Of course; you could make a suggestion in the Wish list. Add your reasons.

Presently there is at least one project that only uses short tasks, perhaps more than one project. Tasks for new projects will probably be available in long and short lengths (steps).
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Message 23111 - Posted: 23 Jan 2012 | 22:20:12 UTC

I'm still wondering, which of the amino acids resembles Chuck Norris the most? :)
Good work! It's a very clever badge system.

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Message 23117 - Posted: 24 Jan 2012 | 9:51:17 UTC - in response to Message 23111.

I'm still wondering, which of the amino acids resembles Chuck Norris the most? :)




;)

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Message 23118 - Posted: 24 Jan 2012 | 12:13:36 UTC

*atomrofl*
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