Posts by valterc
log in
1) Message boards : Science : SARS-CoV-2 virus (Message 1850)
Posted 8 days ago by Profile valterc
The first batch of genes related to COVID-19 has been completed. We sent the results, for further analysis, to the Univ. of Modena & Reggio Emilia School of Medicine, Italy. Starting from today we added another batch of genes, per request of the aforementioned institution. Most of them are antibodies, so the focus right now is the immune system.

Here is the list of the genes: PTPRC CD28 CCR7 PDCD1 SNCA SPATA2 CD27 B3GAT1 IL7 IL2RA ISG20 FAS PTPN13 CD38 CD74 CD24 CR2
2) Message boards : Web site : Change avatar error (Message 1842)
Posted 15 days ago by Profile valterc
I think I have fixed it, please retry
3) Message boards : Number crunching : Android applications on ARM (Message 1841)
Posted 15 days ago by Profile valterc
Doing some tests we noticed that the recently built applications for OpenWrt/Linux should also run on ARM based Android systems. If you have BOINC running on one of the following platforms

arm-android-linux-gnu Android running on ARM armeabi-v7a (32-bit) aarch64-android-linux-gnu Android running on ARM 64-bit arm64-v8a

you could try to configure your BOINC client to use the alt_platform method inside yours cc_config.xml and request to download the proper application

<alt_platform>arm-openwrt-linux-muslgnueabi</alt_platform> (32-bit) <alt_platform>aarch64-openwrt-linux-musl</alt_platform> (64-bit)

After some testing (I need only a few days if there will be enough statistic) I will start to distribute the Androd/ARM applications "the official way"

[edit] we already have vfpv3/vfpv4 applications for ARM 32-bit
4) Message boards : Science : Scientific results (Comments) (Message 1837)
Posted 16 days ago by Profile valterc
Just send me a PM with your email and I will send it to you, tomorrow.
5) Message boards : Wish List : Android app? (Message 1829)
Posted 18 days ago by Profile valterc
I would wait a few days in order to see if the current OpenWrt/ARM applications will produce correctly validated results on Android systems. After that I will provide the applications directly.

What I need is the platform name, can you confirm the following two for Android on ARM ?

arm-android-linux-gnu Android running on ARM armeabi-v7a (32-bit)
aarch64-android-linux-gnu Android running on ARM 64-bit arm64-v8a
6) Message boards : Wish List : Android app? (Message 1823)
Posted 22 days ago by Profile valterc
OK, the "No such file or directory" error is a little bit misleading. Anyway, the recently added applications for Linux/OpenWrt on ARM were statically built (OpenWrt doesn't support libc). You may try to use those using the following alt_platforms:

x32: arm-openwrt-linux-muslgnueabi
x64: aarch64-openwrt-linux-musl

another way to see if it works is the anonymous platform method.
7) Message boards : Wish List : Android app? (Message 1820)
Posted 23 days ago by Profile valterc
Not an Android expert at all... But you could try to run the application form the command line and look at the error messages. Did you check the executable bit of the application? If not try: chmod a+x gene_pcim_v1.10_armv8-a
8) Message boards : Number crunching : WU / task creation flow (Message 1814)
Posted 25 days ago by Profile valterc
Hi team,

It seems from server_status, we are running out of tasks...

Maybe is just a display issue, I can't say :)

Thx for checking¬°
Javi F

Someone (with a large number of computers) is getting a lot of tasks, the number of "Tasks in progress" is much larger than yesterday. Usual problem here, slow server and slow work generator.....
9) Message boards : Number crunching : SSE3 optimization and Android binary (Message 1810)
Posted 28 Apr 2020 by Profile valterc
The optimized versions (SSE2, AVX, FMA) of the application ...

Somewhat off-topic, but are there any plans to add Windows FMA app?
It would not impact my computer, but at least some of those Windows machines currently running AVX app should be able to benefit, right?

We had problems with v1.10 Windows FMA version (mainly for AMD cpus, early bioses) so we decided not to build it when switching to v1.11, also the speed increase was minimal (in some cases the AVX version performed better). I may try to rebuild it and put it on beta, have to think about it.
10) Message boards : Science : SARS-CoV-2 virus (Message 1808)
Posted 28 Apr 2020 by Profile valterc
Already received work from other batches ahead of 166977.
Are these still SARS-CoV-2 related or from the Homo Sapiens (OneGenE - FANTOM-1) data set?

mixed, for now, for instance ENPEP and TMPRSS2 should be related to SARS-CoV-2. Keep in mind that all genes/isoforms are taken from the FANTOM dataset. We are prioritizing those (human) genes related to the Covid-19 disease, infection and/or pathology.
11) Message boards : Number crunching : Please fix computer #57018 - only invalids! (Message 1803)
Posted 23 Apr 2020 by Profile valterc
Thank you Daniel
12) Message boards : Number crunching : Please fix computer #57018 - only invalids! (Message 1800)
Posted 22 Apr 2020 by Profile valterc
You can limit number of WUs sent to hosts which returned high number of invalid WUs recently. Limit of 1 WU per host and scheduler request delay set to 12h should reduce this problem a lot.

Do you remember the server config option for enabling this? Well, I will try to find out... (Is not that easy for me, working at home)
13) Message boards : Science : SARS-CoV-2 virus (Message 1794)
Posted 20 Apr 2020 by Profile valterc
I've found a group that should be willing to provide some new users for TN-Grid, although not as many as WCG.

However, what I've seen at TN-Grid indicates that I should wait to see if you want them contacted.

Muscular Dystrophy Association

https://www.mda.org/

I'd recommend that you write at least a paragraph giving a good explanation of what gene expansion is, to have it ready to send to them.

Thank you for the info, I just forwarded this to our biologists.
14) Message boards : Science : SARS-CoV-2 virus (Message 1793)
Posted 20 Apr 2020 by Profile valterc
I've found a group that should be willing to provide some new users for TN-Grid, although not as many as WCG.

However, what I've seen at TN-Grid indicates that I should wait to see if you want them contacted.

Muscular Dystrophy Association

https://www.mda.org/

I'd recommend that you write at least a paragraph giving a good explanation of what gene expansion is, to have it ready to send to them.


Rosetta is now providing work most of the time.

Thank you for the info, I just forwarded this to our biologists.
15) Message boards : Science : SARS-CoV-2 virus (Message 1758)
Posted 4 Apr 2020 by Profile valterc
We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.

I was just thinking that this is like Sputnik, where everybody rushed into science and engineering (my masters degree was paid for by the government).
You will have more resources than you know what to do with before long.

Yep, in 'normal' times no one (politics, majority of people) really cares about education, healthcare and basic research. We needed a crisis like this one in order to open a discussion about the errors made in the past, at least here in Italy, we'll see after that...
16) Message boards : Science : SARS-CoV-2 virus (Message 1754)
Posted 4 Apr 2020 by Profile valterc
What do you think to make a public announcement on other medias and / or the front page news, that TN-Grid is also computing COVID-19?

If it's public published, it can attract a lot of more users to the BOINC and also TN-Grid.

In the moment, there is a big run onto Rosetta and Folding@home.
Both projects have not permanently work.

Same old reason: our very limited server resources. The server is running right now at almost its full speed, say that doubling the users will just hassle the server with no real benefits. We just submitted a project to answer a governmental call (COVID-19 related), among other things we asked for a server, hoping to get some money for it.
17) Message boards : Number crunching : We need a brand new Mac OS application (got it!) (Message 1753)
Posted 4 Apr 2020 by Profile valterc
We got it! Thanks to Dotsch we have a brand new Mac application 1.10 (sse2), this one is updated to the latest version of the source code, thus providing substantial speed benefits.
18) Message boards : Science : SARS-CoV-2 virus (Message 1751)
Posted 4 Apr 2020 by Profile valterc
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.

Outstanding!!! Are these Covid-19 patients from a specific cohort??? E.g., the hyperimmune, deceased, etc.

I do not know the details yet, the biologists are looking at it, I will keep you updated if there is any news.
19) Message boards : Number crunching : SSE3 optimization and Android binary (Message 1746)
Posted 3 Apr 2020 by Profile valterc
The optimized versions (SSE2, AVX, FMA) of the application were built not only by giving the right directives to the compiler but also by writing some specific assembly code. Nevertheless the obtained speed gain was relatively small. The dramatic speed increase relative to the first version was mainly obtained by cleverly rewriting the source code. It seems to me that, because of the 'intrinsic' nature of our code, SIMD optimizations are not *very* useful.

Having a Android version of the application would be really fine. The application uses little RAM so it should fit, but I'm completely ignorant about Android development....
20) 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.


Next 20

Main page · Your account · Message boards


Copyright © 2020 CNR-TN & UniTN