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Profile valterc
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Message 3270 - Posted: 10 Jul 2023, 16:21:42 UTC
Last modified: 10 Jul 2023, 16:41:01 UTC

I just put the last Vitis vinifera genes into our queue. With the current pace it will take about a week, maybe less, to distribute them all. The new datasets are not ready yet... Also, I will be on vacation the next two weeks, and it wouldn't be advisable to start a new work without having the possibility to easily oversee the system.
Therefore, in a few days, the work generator will not be able to produce new tasks, only resends will be floating around.
I hope to be able to restart the system with a new project at the beginning of August.

Thank you all!

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Message 3271 - Posted: 11 Jul 2023, 7:57:25 UTC

Have a good holiday, going anywhere interesting? My wife and I spent a couple of weeks around Naples earlier this year, had a nice time. We climbed Vesuvius, sounds dramatic doesn't it! Okay, a bus drives up to a large car park about 150m from the crater rim, but you have to walk that last bit!!!
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Message 3272 - Posted: 11 Jul 2023, 10:35:52 UTC - in response to Message 3271.
Last modified: 11 Jul 2023, 15:32:31 UTC

The plan is to going around, by car, through Bosnia, Croatia, Montenegro and Albania, moving from place to place and eventually stop if we really like one...
I'm happy you enjoined your volcano "climbing". When I was younger I went on top of Stromboli, starting from the sea level, and spent the night up there on a sleeping bag (it was a wonderful experience).

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Message 3276 - Posted: 14 Aug 2023, 19:33:16 UTC - in response to Message 3270.

I hope to be able to restart the system with a new project at the beginning of August.


Is there any news on the new project?

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Message 3277 - Posted: 18 Aug 2023, 9:45:50 UTC - in response to Message 3276.

I hope to be able to restart the system with a new project at the beginning of August.


Is there any news on the new project?

Not yet, most of the people here is either on vacation or around for conferences/workshops etc. I was probably too optimistic in my previous statement, I guess we will have some news in September.

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Message 3278 - Posted: 18 Aug 2023, 10:01:59 UTC - in response to Message 3277.

Thanks for the update.
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Message 3279 - Posted: 8 Sep 2023, 9:46:24 UTC - in response to Message 3278.

Just a brief update:
- No new experiment ready yet (people are working on but no ETA)
- The latest batch on Vitis vinifera has been collected and validated, ready for further biological analysis and publication
- I am re-organizing all the (many years of) data that we collected, trying to optimize the whole system
- Some of us will be here https://grapedia.org/annual-meeting/

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Message 3280 - Posted: 8 Sep 2023, 18:26:44 UTC - in response to Message 3279.

Thanks for the update!
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Message 3283 - Posted: 26 Sep 2023, 22:17:02 UTC - in response to Message 3279.

Just a brief update:
- No new experiment ready yet (people are working on but no ETA)
- The latest batch on Vitis vinifera has been collected and validated, ready for further biological analysis and publication
- I am re-organizing all the (many years of) data that we collected, trying to optimize the whole system
- Some of us will be here https://grapedia.org/annual-meeting/



We are about to enter October. has there been any updates from the development teams on the next application ?

Thanks
Bill F

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Message 3284 - Posted: 27 Sep 2023, 12:15:58 UTC - in response to Message 3283.

Hi all,
No news yet from the researchers.

BTW, I have to solve a new problem. With the last batch of experiments we completed more than 250k gene expansions, the post-processed results are two files for any expansion, so more than 500k... and this hits a limit on the number of files that we can store in a single directory on Google drive. Have to rewrite a lot of scripts and move a lot of things ...

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Message 3285 - Posted: 13 Oct 2023, 10:03:26 UTC

Thanks for the update.
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Message 3286 - Posted: 14 Oct 2023, 6:49:30 UTC - in response to Message 3284.

One easy hack might be to simply store each file pair in it's own subfolder, within the parent folder that would otherwise hold the 500k files.

That's probably the easiest solution to script.

A better solution would be to do that, AND break up the parent folder into groups of, let's say 100k, so if you reuse the same code for a project that ends up larger, there won't be any issues as the results grow.

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Message 3287 - Posted: 19 Oct 2023, 19:05:47 UTC

Hello all :)

Any ETA regarding the start of a new experiment ? I'm also curious about what it will be about: should we expect more Vitis vinifera or maybe some Mus musculus ?

Anyway, I'm looking forward to crunching again for this project :)

Best regards, Samuel

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Message 3288 - Posted: 21 Oct 2023, 2:13:12 UTC - in response to Message 3284.
Last modified: 21 Oct 2023, 2:13:52 UTC

Hi all,
No news yet from the researchers.


Is there any way to give the new tasks a different name than the same name you've been using for a long time? A new name for the Application because it's a new year, a new range or type of data etc etc would bring in more crunchers looking to crunch for the latest new name for an Application.

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Message 3289 - Posted: 21 Oct 2023, 6:23:12 UTC - in response to Message 3288.
Last modified: 21 Oct 2023, 6:23:24 UTC

Is there any way to give the new tasks a different name than the same name you've been using for a long time? A new name for the Application because it's a new year, a new range or type of data etc etc would bring in more crunchers looking to crunch for the latest new name for an Application.

Sounds like a pointless fashion statement to me.

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Message 3290 - Posted: 24 Oct 2023, 11:01:38 UTC - in response to Message 3287.

Hello all :)

Any ETA regarding the start of a new experiment ? I'm also curious about what it will be about: should we expect more Vitis vinifera or maybe some Mus musculus ?

Anyway, I'm looking forward to crunching again for this project :)

Best regards, Samuel

No news unfortunately... The biologist are mostly busy analyzing the huge amount of work that we/you already have done.
Talking about the future I guess that the priority is Homo sapiens, grapes and mice are also possible.

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Message 3291 - Posted: 24 Oct 2023, 12:37:55 UTC - in response to Message 3290.

Hello all :)

Any ETA regarding the start of a new experiment ? I'm also curious about what it will be about: should we expect more Vitis vinifera or maybe some Mus musculus ?

Anyway, I'm looking forward to crunching again for this project :)

Best regards, Samuel

No news unfortunately... The biologist are mostly busy analyzing the huge amount of work that we/you already have done.
Talking about the future I guess that the priority is Homo sapiens, grapes and mice are also possible.


Perhaps you could make a new application and make the BOINC volunteers do part of the analyzing of the data themselves?

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Message 3292 - Posted: 24 Oct 2023, 13:36:19 UTC - in response to Message 3291.

Perhaps you could make a new application and make the BOINC volunteers do part of the analyzing of the data themselves?
I assume this analysis requires a degree in biology, and isn't something done by computer.

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Message 3293 - Posted: 24 Oct 2023, 14:00:49 UTC - in response to Message 3292.
Last modified: 24 Oct 2023, 14:02:53 UTC

Perhaps you could make a new application and make the BOINC volunteers do part of the analyzing of the data themselves?
I assume this analysis requires a degree in biology, and isn't something done by computer.

Well, the initial phase is done by a computer: data collection, some consistency checks and basic statistical analysis. It takes just some days to do that, no need of tremendous computational power. Then you need to look at the results from a very specific biological point of view, by looking at the genes you are interested to and their mutual relationships. If you browse the published papers list you may get some hints about the pipeline.
Also it may be important to notice that here every result (any so-called expansion) is potentially useful. In some other kinds of computation you search for something (like a prime number or the minimum energy of a protein configuration) and keep only the best one discarding all the rest.
In the meantime we are also working in setting up a web service for "publishing" all our results and make them available to the biological community in a easy (and fancy) way. Just check this, for example: http://vitis.onegenexp.eu

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Message 3294 - Posted: 25 Oct 2023, 15:10:52 UTC

Is the reason that we have been working on wine grapes due to the existence of private funding?

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