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Profile bozz4science
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Message 3112 - Posted: 21 Mar 2023, 9:27:34 UTC
Last modified: 21 Mar 2023, 9:30:04 UTC

I am curious as to how the project currently foresees its future regarding the approaching finalization of the gene expansion of the OneGenE FANTOM-1 set. At the moment we should be finishing up the current work on 31st of March 2023. On the website you do list other data sets currently on hold or on testing. Any chance you could elaborate on the future work envisioned for TN Grid? What about a possible timeline for the continuation of the project? What will happen with the finished work? Are you targeting a publication?

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Message 3113 - Posted: 21 Mar 2023, 17:49:34 UTC - in response to Message 3112.

I am curious as to how the project currently foresees its future regarding the approaching finalization of the gene expansion of the OneGenE FANTOM-1 set. At the moment we should be finishing up the current work on 31st of March 2023. On the website you do list other data sets currently on hold or on testing. Any chance you could elaborate on the future work envisioned for TN Grid? What about a possible timeline for the continuation of the project? What will happen with the finished work? Are you targeting a publication?

Best

Very briefly, after the end of the FANTOM experiment we will collect all the data, do some statistical and biological analysis. The targets will be one (or more) publication and a web service to make the results available to the scientific community.
For the future: we are playing with a brand new Vitis vinifera dataset and will probably continue to do something related to the mouse. The main new task should be related to single-cell data (still working on this).
I may guess that after the end of FANTOM there may be a period with shortage of workunits but I hope that it will not last long.

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Message 3117 - Posted: 25 Mar 2023, 14:09:42 UTC - in response to Message 3113.

I am curious as to how the project currently foresees its future regarding the approaching finalization of the gene expansion of the OneGenE FANTOM-1 set. At the moment we should be finishing up the current work on 31st of March 2023. On the website you do list other data sets currently on hold or on testing. Any chance you could elaborate on the future work envisioned for TN Grid? What about a possible timeline for the continuation of the project? What will happen with the finished work? Are you targeting a publication?

Best

Very briefly, after the end of the FANTOM experiment we will collect all the data, do some statistical and biological analysis. The targets will be one (or more) publication and a web service to make the results available to the scientific community.
For the future: we are playing with a brand new Vitis vinifera dataset and will probably continue to do something related to the mouse. The main new task should be related to single-cell data (still working on this).
I may guess that after the end of FANTOM there may be a period with shortage of workunits but I hope that it will not last long.



Thanks for the update.
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Message 3119 - Posted: 29 Mar 2023, 13:01:16 UTC

Thanks for the update valterc! Much appreciated and looking forward to new data sets!

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Message 3134 - Posted: 8 Apr 2023, 0:50:31 UTC - in response to Message 3119.

I too hope you get the new tasks out asap so users don't get lost by going elsewhere during the shortage.
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Message 3135 - Posted: 8 Apr 2023, 5:21:14 UTC - in response to Message 3134.

Just leave TN-Grid on and when work comes it'll pick it up. Probably not immediately unless you get lucky and BOINC checks in at the right time.

That's what I do with DENIS@home and Rosetta.

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Message 3136 - Posted: 8 Apr 2023, 20:33:29 UTC

Haven't gotten work in several hours and the server status page shows a declining number of tasks in progress.
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Message 3137 - Posted: 8 Apr 2023, 21:21:06 UTC
Last modified: 8 Apr 2023, 21:21:23 UTC

You can run lhc@home on vmware workstation player.
vmware vm image with configured cvmfs for lhcathome Theory Simulation and Atlas native

https://archive.org/details/lhcathome-cvmfs-login-user-password-1

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Message 3138 - Posted: 9 Apr 2023, 19:55:08 UTC - in response to Message 3137.

You can run lhc@home on vmware workstation player.
vmware vm image with configured cvmfs for lhcathome Theory Simulation and Atlas native

https://archive.org/details/lhcathome-cvmfs-login-user-password-1

Not sure why talking about LHC here?
I will also leave BOINC in priority for TNGrid project, to be sure getting work when available!

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Message 3139 - Posted: 17 Apr 2023, 9:27:37 UTC - in response to Message 3138.
Last modified: 18 Apr 2023, 8:41:23 UTC

As you may see from the server status page we are waiting for a very small number of workunits before the complete end of the FANTOM-1 project (right now there are still 37 genes/isoforms to be completed).
In the meantime I will distribute another small batch of "mouse" related workunits, biologists seem happy with the preliminary results.

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Message 3140 - Posted: 17 Apr 2023, 22:51:37 UTC - in response to Message 3139.

I'm getting a few mouse units.
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Technologov
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Message 3142 - Posted: 19 Apr 2023, 0:39:46 UTC - in response to Message 3139.
Last modified: 19 Apr 2023, 0:40:59 UTC

I think the last few units got "stuck", and maybe if it doesn't finish by tomorrow; improve parallelisation by re-destributing remaining work units to several more BOINC workers ? (status: 88848 / 88856 completed; 8 more to go)

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Message 3143 - Posted: 19 Apr 2023, 12:06:28 UTC - in response to Message 3142.

Only 5 genes left now.
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Message 3144 - Posted: 19 Apr 2023, 21:25:36 UTC - in response to Message 3142.

Any results that need to be sent out again will be sent out when the deadline is reached/past for the current results that are out in the field.

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Message 3146 - Posted: 21 Apr 2023, 15:12:48 UTC

Last work unit stuck for a day

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Message 3147 - Posted: 22 Apr 2023, 11:16:32 UTC - in response to Message 3146.

Stuck for 2 days already

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Message 3148 - Posted: 22 Apr 2023, 11:59:29 UTC - in response to Message 3147.

It's fine. They'll get resent in a few days if they returned within the deadline.
Only 89 tasks out there and a few are probably from the "mouse" batches.
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rsNeutrino
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Message 3149 - Posted: 24 Apr 2023, 19:43:11 UTC
Last modified: 24 Apr 2023, 19:47:55 UTC

Is this the very last FANTOM-1 WU?

https://gene.disi.unitn.it/test/workunit.php?wuid=42164142
Took a bit to track it down.
The WU is doing its rounds since the 07 Apr 2023, it is on its fifth task now, had two timeouts and a validation mismatch it seems.

Host:
https://gene.disi.unitn.it/test/results.php?hostid=71977
Host has 10 of the remaining 12 tasks currently in progress according to the statistics page. Also a single user remaining, must be the host's owner.
Last successful task by that host was 22 Apr 2023, 10:43:42 UTC.
Next timeout for these tasks would be around 27 Apr 2023.

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Message 3150 - Posted: 25 Apr 2023, 16:54:31 UTC

Looks like it's done. The remaining 3 tasks probably belong to the "mouse" batch.
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rsNeutrino
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Message 3151 - Posted: 25 Apr 2023, 17:18:13 UTC - in response to Message 3149.

Last WU 42164142 has finished.
Name: 233143_Hs_T195812-ARL13A_wu-218_1680830651578

Two tasks were returned today and the following 3 validated successfully, from hosts:
81828___7 Apr 2023, 19:47:11 UTC__authorized result
81179__25 Apr 2023, 15:11:30 UTC__late runner
71977__25 Apr 2023, 16:03:12 UTC__last return

88856 of 88856 genes/isoforms executed

You win! ;)

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