Posts by valterc
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21) Message boards : Science : SARS-CoV-2 virus (Message 1742)
Posted 3 Apr 2020 by Profile valterc
We already published the OneGenE (expansion of all the genes) results for a Vitis vinifera dataset (Vespucci).

The OneGeneE project for Homo sapiens FANTOM-5 gene expression dataset is our 'background' job, and it is a very long one. We normally put genes in the queue in alphabetic order (actually it is by 'number of isoforms', but it would be the same). At the very beginning we started by prioritizing genes related to neurovegetative diseases, then to some types of cancer, right now any gene possibly related to COVID-19 (you guess why...).

Any result we get is immediately available to the scientific community (biologists etc.), for example the ACE2 expansions we completed a few days ago will soon be analyzed by a immunologist, etc.

We are also studying the possibility of doing some work on specific gene datasets recently made up from cells of SARS-CoV-2 infected individuals. In this case we will put 'on hold' the OneGenE Hs project.
22) Message boards : Science : SARS-CoV-2 virus (Message 1737)
Posted 2 Apr 2020 by Profile valterc
Arte these available for RaspberryPi?
Thanks.

We have applications for ARM based devices. It should work, just try.
23) Message boards : Science : SARS-CoV-2 virus (Message 1731)
Posted 2 Apr 2020 by Profile valterc
I just put into the queue all the genes related to SARS-CoV-2 according to this paper https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3

The data we used are available here https://public.ndexbio.org/#/networkset/4b4a9769-6ad1-11ea-bfdc-0ac135e8bacf?accesskey=abb250cd4e341423f3e913d71c171068c75c722e54649a83868feff7f239a548

Description: Interactomes for SARS-CoV-2 (coronavirus) the virus causing COVID-19. Interactomes have been performed in multiple cell lines, including HEK-293T, and a lung cell line, A549.

Workunit's id will start at 165735_Hs to 166977_Hs, that's the expansion of 1242 gene isoforms, each one will be 294 workunits, so there is plenty of work to do...
24) Message boards : Number crunching : We need a brand new Mac OS application (got it!) (Message 1730)
Posted 1 Apr 2020 by Profile valterc
Thank you, just download the source code and try to compile it, you need the BOINC libraries for this. I can provide some other validation tests (a couple of them are in the repository).
25) Message boards : Number crunching : We need a brand new Mac OS application (got it!) (Message 1728)
Posted 31 Mar 2020 by Profile valterc
Hi all, the application available here for Mac OS is not the latest release (i.e. it misses some optimization). We don't have people here with the necessary skills/resources to build it, starting from the source code available here https://bitbucket.org/francesco-asnicar/pc-boinc/.

Is there anyone who likes to volunteer? (the new version should be at least 10% faster)
26) Message boards : Science : SARS-CoV-2 virus (Message 1726)
Posted 28 Mar 2020 by Profile valterc
Added a few genes, related to DPP4, according to StringDB:
INS GIP SLC5A2 SLC5A5 ADA GCG GLP1R
27) Message boards : Science : SARS-CoV-2 virus (Message 1713)
Posted 19 Mar 2020 by Profile valterc
We are actually expanding a lot of human genes, prioritizing them according to the scientists' interests. Among them this one (ACE2) https://www.ncbi.nlm.nih.gov/gene/59272 which is closely related to the SARS-CoV-2 virus. Don't expect we will be able to 'find a cure' but we are trying to add something to better know our enemy.

How about expanding the 400 proteins involved in SARS-CoV-2 processing and replication???

https://www.nytimes.com/2020/03/17/science/coronavirus-treatment.html?action=click&module=Top%20Stories&pgtype=Homepage


Interesting stuff, I will send the information to my colleagues (BTW we already did the expansion of BRD2, cited in the article, in the past).
28) Message boards : Science : SARS-CoV-2 virus (Message 1712)
Posted 19 Mar 2020 by Profile valterc
We just added some other genes related to ACE2, according to this https://string-db.org/cgi/network.pl?taskId=fBQjTFzroyIX

They are AGT AGTR1 AGTR2 REN MME DPP4 PRCP MEP1B MEP1A XPNPEP2, among them we already expanded MME and DPP4. You may see the others' names coded inside the workunits string.
29) Message boards : News : World Gene Expansion Challenge 2020 (Message 1711)
Posted 19 Mar 2020 by Profile valterc
I moved all the SARS-CoV-2 virus posts to the new thread in the Science section
30) Message boards : News : World Gene Expansion Challenge 2020 (Message 1703)
Posted 16 Mar 2020 by Profile valterc
The workunits contain the ACE2 string (not so many, around 800)
31) Message boards : Science : SARS-CoV-2 virus (Message 1698)
Posted 14 Mar 2020 by Profile valterc
We are actually expanding a lot of human genes, prioritizing them according to the scientists' interests. Among them this one (ACE2) https://www.ncbi.nlm.nih.gov/gene/59272 which is closely related to the SARS-CoV-2 virus. Don't expect we will be able to 'find a cure' but we are trying to add something to better know our enemy.

In the mean time, please, take care.
32) Message boards : Cafe : Coronavirus (Message 1694)
Posted 9 Mar 2020 by Profile valterc
Yep, we are close to the 'red' area. The situation is rather 'complicated'. The government is trying to convince anyone not to have 'close', not necessary, contacts with others. The sad thing is that a lot of people don't care unless forced to. I will work from home the next two weeks.
33) Message boards : News : World Gene Expansion Challenge 2020 (Message 1680)
Posted 21 Feb 2020 by Profile valterc
The volunteers belonging to the BOINC.Italy group have organized a challenge on this project, from March 16 at 12:00 UTC up to March 23 at 12:00 UTC.

Have a look at the challenge banner here: https://www.boincitaly.org/media/kunena/attachments/6725/TN-GridCh.jpg and the boincstats announcement/chat page: https://www.boincstats.com/stats/challenge/team/chat/1072
34) Message boards : News : No news is good news (sometimes) (Message 1674)
Posted 13 Feb 2020 by Profile valterc
Just wanted to say that everything is going on smoothly. The server is stable, the scientists are happy with the results and are doing their analysis. Thanks all!
35) Message boards : Number crunching : Help with invalid tasks and computation errors? (Message 1667)
Posted 14 Jan 2020 by Profile valterc
Sometimes, for a lot of different reasons, the computation ends 'correctly' but the results are not. This is the reason we implement the 'redundancy' feature (one result is marked correct if it is bit-wise identical to another one).

We also know we have a small bug in our code (very infrequent, that we were not able to catch). In some cases, when the computation of a task is stopped at the very beginning, before the first checkpoint, the output file become 'inconsistent', thus the computation will produce an 'invalid' result (it can happen if you see 'Start from checkpoint: 1' in the log). Keeping a small workunit queue (thus avoiding BOINC going into 'rush' mode) will mitigate this problem.

Error 194 is sometimes an effect of the computer being unresponsive, too much load, see http://wuprop.boinc-af.org/forum_thread.php?id=402
36) Message boards : Science : Colorectal cancer genes characterization (Message 1664)
Posted 2 Jan 2020 by Profile valterc
PC-IM is the algorithm we use for analyzing gene expression datasets of various organisms, and of different origin. The same algorithm/application can be used for various purposes, so no new category.
37) Message boards : Number crunching : WU / task creation flow (Message 1657)
Posted 19 Dec 2019 by Profile valterc
Hi Valterc,
If i remember right, 1 gene expansion is composed by 294wu (588 vith replication. For every 15minutes = 96 gene/day and 56448 wu/day generated

There is a queue's top limit? why wu "ready to send" are alays around 8-9k and dont raise up?
According to science page we are currently process around 30 gene/day

It would help during challenges

Yes, the work generator starts doing its job if the number of available workunits is lower than a threshold, to optimize server's memory. Currently this number is 9000 and this is usually enough in 'normal' times. I will set the cap to 10000 and see what happens.
38) Message boards : Number crunching : Clear Linux - All results Invalid or Inconclusive (fma, avx, sse) (Message 1654)
Posted 9 Dec 2019 by Profile valterc
all errors , so I applied the workaround

Yep, I sent a mail to the boinc developers about this, no answers yet.
39) Message boards : Number crunching : Clear Linux - All results Invalid or Inconclusive (fma, avx, sse) (Message 1651)
Posted 4 Dec 2019 by Profile valterc
I don't know if it is (technically) a bug, the fact is that the output of pigz (or the 'new' libz) is not, bitwise, the same as gzip, although it is 'compatible' (correctly uncompressed). The side effect here is that the validator checks the results by comparing two output files (just skipping the gzip header), thus failing in this case. I will post this issue to the boinc_projects mailing list, asking for BOINC developers comments.
40) Message boards : Number crunching : Clear Linux - All results Invalid or Inconclusive (fma, avx, sse) (Message 1649)
Posted 3 Dec 2019 by Profile valterc
gzip stores (by default) the file name inside its archive, the test_ubuntu.gzip file is exactly 7 bytes larger than test.gzip. Try with same file name length (and content)


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