The new Vitis vinifera project is underway

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stefania Project scientist Send message Joined: 24 Oct 18 Posts: 3 Credit: 0 RAC: 0	Message 3164 - Posted: 12 May 2023, 16:26:14 UTC Last modified: 16 May 2023, 11:15:48 UTC
Dear all, I am very excited to announce that a new bigger dataset of Vitis vinifera transcriptomic data (Vespucci) is now available for OneGene expansion. The number of experiments has more than tripled. We are still using the results from the previous analyses, finding very interesting gene associations and producing amazing gene networks. We now expect to improve and refine them with this new collection of runs. Many thanks to all of you. If you are interested in the architecture of the transcriptomic dataset, please look at the following article: https://doi.org/10.3389/fpls.2022.815443 ____________
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Falconet Send message Joined: 21 Dec 16 Posts: 105 Credit: 3,092,711 RAC: 0	Message 3165 - Posted: 12 May 2023, 17:02:27 UTC - in response to Message 3164.
Thanks for the update. Will a progress counter be added to the Science Status page? ____________
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valterc Project administrator Project tester Send message Joined: 30 Oct 13 Posts: 623 Credit: 34,677,535 RAC: 2	Message 3166 - Posted: 12 May 2023, 22:19:46 UTC - in response to Message 3165.
By now I just put a few genes into the queue, if everything goes well I will switch to full throttle this Monday, also adding the progress counter.
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Falconet Send message Joined: 21 Dec 16 Posts: 105 Credit: 3,092,711 RAC: 0	Message 3167 - Posted: 13 May 2023, 20:26:53 UTC - in response to Message 3166.
By now I just put a few genes into the queue, if everything goes well I will switch to full throttle this Monday, also adding the progress counter. Thank you. ____________
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[VENETO] boboviz Send message Joined: 12 Dec 13 Posts: 183 Credit: 4,641,505 RAC: 0	Message 3170 - Posted: 16 May 2023, 7:05:15 UTC
Up to now, no error or invalid validation Well done!
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adrianxw Send message Joined: 22 Dec 16 Posts: 36 Credit: 8,489,198 RAC: 0	Message 3172 - Posted: 16 May 2023, 11:31:14 UTC Last modified: 16 May 2023, 11:55:45 UTC
I crunched a few, (8), work units from the test batch on the 12th which all ran to normal completion. Since then, I've not received any. <edit> And less than an hour later, a work unit arrives! It is crunching now. ____________ Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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entity Send message Joined: 20 Jul 20 Posts: 20 Credit: 31,475,949 RAC: 1	Message 3174 - Posted: 16 May 2023, 15:44:50 UTC - in response to Message 3172.
How many WUs are in a gene/isoform and is the last one short like the previous project?
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valterc Project administrator Project tester Send message Joined: 30 Oct 13 Posts: 623 Credit: 34,677,535 RAC: 2	Message 3175 - Posted: 16 May 2023, 16:32:03 UTC - in response to Message 3174.
A single gene expansion is made up by 77 workunits, each one contains 800 small computational chunks (PCs), the last one (#77) contains just 400 of them. (I may change the numbers of chunks per workunit in the future)
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Retvari Zoltan Send message Joined: 31 Mar 20 Posts: 43 Credit: 51,206,467 RAC: 0	Message 3199 - Posted: 23 May 2023, 9:34:57 UTC - in response to Message 3175. Last modified: 23 May 2023, 9:36:36 UTC
A single gene expansion is made up by 77 workunits, each one contains 800 small computational chunks (PCs), the last one (#77) contains just 400 of them. (I may change the numbers of chunks per workunit in the future) So a single gene expansion is 76800+400 chunks, that is 61200 chunks in total. 61200 \| 2 30600 \| 2 15300 \| 2 7650 \| 2 3825 \| 3 1275 \| 3 425 \| 5 85 \| 5 17 \| 17 1 \| There are a few numbers around 800 that can divide 61200 to equal sized workunits: 81675 (1732222)(553) 85072 (17552)(33222) 90068 (553322)(1722) But it is desirable to make longer workunits (to be able to generate enough work for all hosts), if it does not take longer for the workunit generator (you should reduce the maximum allowed workunits at the same time to prevent hoarding): 102060 (175322)(5322) 120051 (5532222)(173) 122450 (1733222)(552) 127548 (17553)(32222) 136045 (1752222)(533) 153040 (175332)(5222) 170036 (175522)(3322) 180034 (5533222)(172) So I would change the workunit size according to the end of this list.
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valterc Project administrator Project tester Send message Joined: 30 Oct 13 Posts: 623 Credit: 34,677,535 RAC: 2	Message 3200 - Posted: 23 May 2023, 10:06:14 UTC - in response to Message 3199.
Sorry for that, but I made a mistake in my previous statement... it's not 800 but 600
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stefania
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Dear all, I am very excited to announce that a new bigger dataset of Vitis vinifera transcriptomic data (Vespucci) is now available for OneGene expansion. The number of experiments has more than tripled. We are still using the results from the previous analyses, finding very interesting gene associations and producing amazing gene networks. We now expect to improve and refine them with this new collection of runs. Many thanks to all of you.
If you are interested in the architecture of the transcriptomic dataset, please look at the following article: https://doi.org/10.3389/fpls.2022.815443
____________

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Falconet
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Thanks for the update.
Will a progress counter be added to the Science Status page?
____________

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valterc
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By now I just put a few genes into the queue, if everything goes well I will switch to full throttle this Monday, also adding the progress counter.

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Falconet
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By now I just put a few genes into the queue, if everything goes well I will switch to full throttle this Monday, also adding the progress counter.

Thank you.
____________

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[VENETO] boboviz
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Up to now, no error or invalid validation

Well done!

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adrianxw
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I crunched a few, (8), work units from the test batch on the 12th which all ran to normal completion. Since then, I've not received any.

<edit>
And less than an hour later, a work unit arrives! It is crunching now.
____________
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

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entity
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How many WUs are in a gene/isoform and is the last one short like the previous project?

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valterc
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A single gene expansion is made up by 77 workunits, each one contains 800 small computational chunks (PCs), the last one (#77) contains just 400 of them. (I may change the numbers of chunks per workunit in the future)

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Retvari Zoltan
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A single gene expansion is made up by 77 workunits, each one contains 800 small computational chunks (PCs), the last one (#77) contains just 400 of them.
(I may change the numbers of chunks per workunit in the future)

So a single gene expansion is 76*800+400 chunks, that is 61200 chunks in total.

61200 | 2 30600 | 2 15300 | 2 7650 | 2 3825 | 3 1275 | 3 425 | 5 85 | 5 17 | 17 1 |

There are a few numbers around 800 that can divide 61200 to equal sized workunits:

816*75 (17*3*2*2*2*2)*(5*5*3) 850*72 (17*5*5*2)*(3*3*2*2*2) 900*68 (5*5*3*3*2*2)*(17*2*2)

But it is desirable to make longer workunits (to be able to generate enough work for all hosts), if it does not take longer for the workunit generator
(you should reduce the maximum allowed workunits at the same time to prevent hoarding):

1020*60 (17*5*3*2*2)*(5*3*2*2) 1200*51 (5*5*3*2*2*2*2)*(17*3) 1224*50 (17*3*3*2*2*2)*(5*5*2) 1275*48 (17*5*5*3)*(3*2*2*2*2) 1360*45 (17*5*2*2*2*2)*(5*3*3) 1530*40 (17*5*3*3*2)*(5*2*2*2) 1700*36 (17*5*5*2*2)*(3*3*2*2) 1800*34 (5*5*3*3*2*2*2)*(17*2)

So I would change the workunit size according to the end of this list.

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valterc
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Sorry for that, but I made a mistake in my previous statement... it's not 800 but 600

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