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Profile [VENETO] boboviz
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Message 507 - Posted: 10 Jun 2015, 17:32:28 UTC - in response to Message 505.

Well done, boys!!

Profile [AF>Amis des Lapins] Phil1966
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Message 508 - Posted: 10 Jun 2015, 18:00:30 UTC

Great ! Thank You for the update :)

[AF>Le_Pommier] Jerome_C2005
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Message 509 - Posted: 11 Jun 2015, 7:10:30 UTC

Thanks to share this, happy to see that we are helpful :)

Profile [VENETO] boboviz
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Message 515 - Posted: 5 Oct 2015, 7:20:18 UTC - in response to Message 505.

Here follows the current list of our contributions, links to papers will be provided when published.


Any news??

Profile valterc
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Message 1545 - Posted: 9 Apr 2019, 9:17:06 UTC

More publications added

Jim1348
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Message 1546 - Posted: 9 Apr 2019, 11:28:36 UTC - in response to Message 1545.

I don't understand the science, but you seem to have found one of the better biomedical applications for BOINC.
It appears to have wide applicability, and is the type of thing that no single company would do. It benefits from public volunteer participation.

Profile [VENETO] boboviz
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Message 1547 - Posted: 25 Apr 2019, 7:35:40 UTC - in response to Message 1545.

More publications added


Great!!

JaviF
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Message 1553 - Posted: 16 May 2019, 12:12:16 UTC

Hi team,

It would be rather nice to read something clearer about what are we doing, what do we want to achieve, how many work units (experiments) are planned, what would be a possitive finding...etc.

I feel I know very little about this project.

Thx¡
Javi

adrianxw
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Message 1555 - Posted: 21 May 2019, 15:06:13 UTC

Something to remember with research, is that it is rarely possible to say in advance, how long, how many, how much etc. What tends to happen is that a project starts with a good idea of where it is going, but as the results start drifting back, some suprises appear, these can lead to additional types of jobs, different techniques etc. If you look at the history of other BOINC projects, you will see this again and again.

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Message 1556 - Posted: 21 May 2019, 15:19:28 UTC - in response to Message 1555.
Last modified: 21 May 2019, 15:22:23 UTC

Something to remember with research, is that it is rarely possible to say in advance, how long, how many, how much etc. What tends to happen is that a project starts with a good idea of where it is going, but as the results start drifting back, some suprises appear, these can lead to additional types of jobs, different techniques etc. If you look at the history of other BOINC projects, you will see this again and again.

Exactly. In our case, being the algorithm we use rather general, the number of problems we may try to solve could be very large. Simply speaking we implement an algorithm for 'causal relationships' between variables (something stronger than correlation), look at this simple description of the concept: https://medium.com/datadriveninvestor/goodbye-correlation-say-hello-to-the-era-of-causal-inference-f238065c156b.
At his moment our 'variables' are 'gene expression values' of different organisms (bacteria, plants, humans). To put it simply we try to figure out if a gene X is somewhat related with a gene, or a network of genes Y that we already know are involved in some kind of biological process, thus increasing the overall knowledge of the process itself.

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Message 1557 - Posted: 22 May 2019, 8:05:11 UTC - in response to Message 1556.

Hi,

Somehow, I agree and disagree at the same time :D

Technically speaking, we "know" what are we sending to crunch. There must be a "start" and "end" set of possibilities, and we also know if there is something interesting in case X, we investigate deepper (which we can't predict, I agree).

Now is like crunching all genes of the world or?

If we go to science status, all 3 organism are "on hold"...

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Message 1558 - Posted: 22 May 2019, 9:24:31 UTC - in response to Message 1557.

Hi,

Somehow, I agree and disagree at the same time :D

Technically speaking, we "know" what are we sending to crunch. There must be a "start" and "end" set of possibilities, and we also know if there is something interesting in case X, we investigate deepper (which we can't predict, I agree).

Now is like crunching all genes of the world or?

If we go to science status, all 3 organism are "on hold"...

They are "on hold" because we already expanded all the genes (using one set of the algorithm's parameters) and some of the possible gene networks; results were good and some have been already published. We may go further with the same organism, maybe changing some algorithm's parameter, expanding some other networks or using a different gene expression dataset. The decision is up to the biologists we work with. The choice of the organism to analyze is also up to the biologists.

The scientific focus, right now, is on the Vitis vinifera (grapevine) which is of interest to https://www.fmach.it/eng/CRI/general-info/organisation/Chief-scientific-office/Genomics-and-biology-of-fruit-crops (they are actually preparing a new gene expression dataset).

The computational part is now mainly dedicated to Homo sapiens, see https://gene.disi.unitn.it/test//forum_thread.php?id=217#1329

It would be interesting to 'crunch' all the genes of the world, but obviously not realistic...

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Message 1560 - Posted: 23 May 2019, 7:27:13 UTC - in response to Message 1558.

In that case...wouldn't be interesting to add something to "science status" link?

If you go there, all is on hold and you can get no clue how far are we with current experiment (no need to know the exact % but the current information is almost useless...we dont know whether 1 day or 1 billion years is remaining).

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Message 1561 - Posted: 23 May 2019, 10:09:06 UTC - in response to Message 1560.

In that case...wouldn't be interesting to add something to "science status" link?

If you go there, all is on hold and you can get no clue how far are we with current experiment (no need to know the exact % but the current information is almost useless...we dont know whether 1 day or 1 billion years is remaining).

OK, good point, I just updated the science page with some new info.

JaviF
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Message 1562 - Posted: 23 May 2019, 10:42:10 UTC - in response to Message 1561.

It looks definetely better¡

Thx for the updates :)

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Message 1566 - Posted: 29 May 2019, 8:58:09 UTC - in response to Message 1562.

By the way...It would be rather interesting to understand what is included in each "task / work unit".
What is it's relation to each Gene/Isoform?

We can see X tasks being crunched and Y Genes per day, number are quite different.

I am just curious...

Thx in advance¡
Javi

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Message 1571 - Posted: 31 May 2019, 9:38:16 UTC - in response to Message 1566.
Last modified: 31 May 2019, 9:38:44 UTC

By the way...It would be rather interesting to understand what is included in each "task / work unit".
What is it's relation to each Gene/Isoform?

We can see X tasks being crunched and Y Genes per day, number are quite different.

I am just curious...

Thx in advance¡
Javi

In the current experiment the expansion of a single gene is made up by 294 workunits.
A workunit name like '154374_Hs_T068364-SERPINB7_wu-29_1559223285745_2', can be read as follow:
id_organism_isoform_gene_wu-N_timestamp (where N is up to 294)

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Message 1575 - Posted: 3 Jun 2019, 16:32:09 UTC - in response to Message 1571.
Last modified: 3 Jun 2019, 16:32:42 UTC

Great.

So a total of 87554 genes /isoforms * 294 tasks / each (we dont count here resends) = 25.74 Million tasks.

We need at least 2 tasks to have a "valid" result so: 25.74 * 2 = 51.48 Millions tasks.

If we are doing now 26 genes a day (average) this means a returning rate of 26 * 254 ( * 2 to be valid) = 13K tasks / day?

If this is the case, we definetely need to gain computing power somewhere :D

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Message 1576 - Posted: 9 Jun 2019, 11:29:14 UTC - in response to Message 1575.

>>> we definetely need to gain computing power somewhere

I wonder how many times that has been said by the folk at the various projects!

I think one of the biggest problems is that the projects and BOINC in general, are not well known. I sent e-mails to the companies that do the "after the news" evening chat shows suggesting a five minute slot to push BOINC generally, but never had a reply.

Another problem I discovered is the licensing of BOINC, it contains wording with warnings saying that it "has never caused problems", "used without issue by millions", etc. etc. I tried to get permission from the local council to put BOINC on the general purpose computers in the local library, they refused saying they could not trust it because of this, rather soft, wording. I could assure the council it was harmless as I'd never had any trouble with it, or the older Seti@Home that was the predecessor of BOINC in the last centuary, but that is just me.
____________
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Jim1348
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Message 1577 - Posted: 9 Jun 2019, 11:56:24 UTC - in response to Message 1576.

Probably the best way to get known is just to list TN-Grid in the BOINC projects list. I hope they have taken care of that for the next BOINC release. Otherwise, it will be an uphill struggle.

A GPU version would do it. There are volunteers around on the various projects who may have the expertise to do it, if they know about it.

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