The new Vitis vinifera project is underway

Author	Message
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 ____________
ID: 3164 · Reply Quote

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? ____________
ID: 3165 · Reply Quote

valterc Project administrator Project tester Send message Joined: 30 Oct 13 Posts: 623 Credit: 34,677,535 RAC: 3	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.
ID: 3166 · Reply Quote

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. ____________
ID: 3167 · Reply Quote

[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!
ID: 3170 · Reply Quote

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.
ID: 3172 · Reply Quote

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?
ID: 3174 · Reply Quote

valterc Project administrator Project tester Send message Joined: 30 Oct 13 Posts: 623 Credit: 34,677,535 RAC: 3	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)
ID: 3175 · Reply Quote

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.
ID: 3199 · Reply Quote

valterc Project administrator Project tester Send message Joined: 30 Oct 13 Posts: 623 Credit: 34,677,535 RAC: 3	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
ID: 3200 · Reply Quote

Author

Message

stefania
Project scientist
Send message
Joined: 24 Oct 18
Posts: 3
Credit: 0
RAC: 0

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
____________

ID: 3164 · Reply Quote

Falconet
Send message
Joined: 21 Dec 16
Posts: 105
Credit: 3,092,711
RAC: 0

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

ID: 3165 · Reply Quote

valterc
Project administrator
Project tester
Send message
Joined: 30 Oct 13
Posts: 623
Credit: 34,677,535
RAC: 3

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.

ID: 3166 · Reply Quote

Falconet
Send message
Joined: 21 Dec 16
Posts: 105
Credit: 3,092,711
RAC: 0

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.
____________

ID: 3167 · Reply Quote

[VENETO] boboviz
Send message
Joined: 12 Dec 13
Posts: 183
Credit: 4,641,505
RAC: 0

Up to now, no error or invalid validation

Well done!

ID: 3170 · Reply Quote

adrianxw
Send message
Joined: 22 Dec 16
Posts: 36
Credit: 8,489,198
RAC: 0

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.

ID: 3172 · Reply Quote

entity
Send message
Joined: 20 Jul 20
Posts: 20
Credit: 31,475,949
RAC: 1

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

ID: 3174 · Reply Quote

valterc
Project administrator
Project tester
Send message
Joined: 30 Oct 13
Posts: 623
Credit: 34,677,535
RAC: 3

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)

ID: 3175 · Reply Quote

Retvari Zoltan
Send message
Joined: 31 Mar 20
Posts: 43
Credit: 51,206,467
RAC: 0

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.

ID: 3199 · Reply Quote

valterc
Project administrator
Project tester
Send message
Joined: 30 Oct 13
Posts: 623
Credit: 34,677,535
RAC: 3

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

ID: 3200 · Reply Quote