Posts by valterc
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1) Message boards : Number crunching : Connecting to project (Message 1603)
Posted 11 days ago by Profile valterc
Have been having hellish problems these past few days connecting to the project from new clients.

Anyone else seeing same problem?

Which kind of problem? I didn't find anything strange server-side.
2) Message boards : Number crunching : Can we multi-thread the TN-Grid wu's? (Message 1588)
Posted 28 Jun 2019 by Profile valterc
Very briefly: some things are faster done while working in a serial way, others in a parallel way. I found a good explanation here: https://www.quora.com/If-parallel-programming-is-significantly-faster-why-arent-all-programming-problems-solved-using-that-technique. Being able to parallelize an algorithm (like making an efficient multi-threaded version) is usually the first step in the path to CUDA/OpenCL.
3) Message boards : Wish List : Future requests (Message 1584)
Posted 12 Jun 2019 by Profile valterc
Any update on GPU app? It's still in development or is stopped?

It was actually never in 'development', we just spent some time thinking about it but we gave up (at least for the moment) for two reasons:
- not clear enough if it will be useful doing this (because of the algorithm)
- Lack of in-house cuda/opencl progrmmers
4) Message boards : Wish List : Tn-Grid in Boinc Manager project list (Message 1572)
Posted 31 May 2019 by Profile valterc
I definitely agree!!
The vast majority of Bonic users choose a project from that list.

We (I mean the project team) are discussing about this. The main issue is that having a lot more users may have a strong impact on the server.
5) Message boards : Science : Scientific results (Comments) (Message 1571)
Posted 31 May 2019 by Profile valterc
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 advanceĀ”
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)
6) Message boards : Science : Scientific results (Comments) (Message 1561)
Posted 23 May 2019 by Profile valterc
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.
7) Message boards : Science : Scientific results (Publications etc.) (Message 1559)
Posted 22 May 2019 by Profile valterc
Thanks to the invaluable contribution of the gene@home volunteers, we were able to perform a wide number of 'virtual experiments' using two different algorithms: PC-IM (PC Iterative Method) which is done with BOINC and NESRA (Network Expansion by Subsetting and Ranking Aggregation) which further analyzes BOINC results. The experiments were made on various organisms (among them Escherichia coli, Arabidopsis thaliana and Vitis vinifera), expanding different Local Gene Networks. We also did analysis for optimizing the whole computing system and the algorithms' parameters.

After having organized and analyzed the results we started to present some of them to the international scientific community. Here follows the current list of our contributions, links to papers will be provided when published.

  • Discovering Candidates for Gene Network Expansion by Variable Subsetting and Ranking Aggregation
    Luca Erculiani, Francesca Galante, Caterina Gallo, Francesco Asnicar, Luca Masera, Paolo Morettin, Nadir Sella, Thomas Tolio, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser, Enrico Blanzieri

    Poster, Network Biology SIG on July 10, 2015, preceding the main ISMB conference in Dublin (Ireland). http://f1000research.com/posters/4-562

  • Discovering Candidates for Gene Network Expansion by Distributed Volunteer Computing
    Francesco Asnicar, Luca Erculiani, Francesca Galante, Caterina Gallo, Luca Masera, Paolo Morettin, Nadir Sella, Stanislau Semeniuta, Thomas Tolio, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser, Enrico Blanzieri

    Paper, The 13th IEEE International Symposium on Parallel and Distributed Processing with Applications (IEEE ISPA-15), 20-22 August 2015 in Helsinki, Finland, Published in 2015 IEEE Trustcom/BigDataSE/ISPA, https://ieeexplore.ieee.org/document/7345656/

  • TN-Grid and gene@home project: Volunteer Computing for Bioinformatics
    Francesco Asnicar, Nadir Sella, Luca Masera, Paolo Morettin, Thomas Tolio, Stanislau Semeniuta, Claudio Moser, Enrico Blanzieri and Valter Cavecchia

    Paper, BOINC:FAST 2015 (BOINC: Fundamental & Applied Science & Technology), Second International Conference, 14-18 September, 2015, Petrozavodsk, Republic of Karelia (Russia).

    Presentation: http://gene.disi.unitn.it/test/documents/Gene@Home.@BF15.pdf
    Proceedings: http://ceur-ws.org/Vol-1502/

  • NES2RA: Network expansion by stratified variable subsetting and ranking aggregation
    Francesco Asnicar, Luca Masera, Emanuela Coller, Caterina Gallo, Nadir Sella, Thomas Tolio, Paolo Morettin, Luca Erculiani, Francesca Galante, Stanislau Semeniuta, Giulia Malacarne, Kristof Engelen, Andrea Argentini, Valter Cavecchia, Claudio Moser and Enrico Blanzieri

    Paper, International Journal of High Performance Computing Applications, August 22, 2016 (doi:10.1177/1094342016662508, http://hpc.sagepub.com/content/early/2016/08/17/1094342016662508.full.pdf+html)

  • Discovering causal relationships in grapevine expression data to expand gene networks. a case study: Four networks related to climate change
    Malacarne, G., Pilati, S., Valentini, S., Asnicar, F., Moretto, M., Sonego, P., Masera, L. Cavecchia, V., Blanzieri, E. & Moser, C.

    Frontiers in plant science, 2018, 9.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161569/

  • OneGenE: Regulatory Gene Network Expansion via Distributed Volunteer Computing on BOINC
    Asnicar, F., Masera, L., Pistore, D., Valentini, S., Cavecchia, V., & Blanzieri, E. (2019, February).

    In 2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP) (pp. 315-322). IEEE. https://ieeexplore.ieee.org/abstract/document/8671629/



For comments please use this thread: https://gene.disi.unitn.it/test//forum_thread.php?id=112

8) Message boards : Science : Scientific results (Comments) (Message 1558)
Posted 22 May 2019 by Profile valterc
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...
9) Message boards : Science : Scientific results (Comments) (Message 1556)
Posted 21 May 2019 by Profile valterc
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.
10) Message boards : Number crunching : gene_work_generator Not Running (Message 1552)
Posted 3 May 2019 by Profile valterc
Well, the issue was the work generator not able to communicate with the mysql server (Got an error reading communication packets). Being busy with other stuff I wasn't able to actually find the origin of the error. As a last resort I tried a reboot and it worked.... (but I have to find more time to check the issue again).
BTW, it will take some time in order to re-fill the output queue.
11) Message boards : Number crunching : gene_work_generator Not Running (Message 1549)
Posted 3 May 2019 by Profile valterc
I will be out of work shortly. Is this being looked into?

I was able to notice this only now (was out of town, sorry). The work generator had some problems, I restarted it and will investigate what happened. ...
12) Message boards : Science : Scientific results (Comments) (Message 1545)
Posted 9 Apr 2019 by Profile valterc
More publications added
13) Message boards : Getting started : how to create a userteam (Message 1544)
Posted 1 Apr 2019 by Profile valterc
here: https://gene.disi.unitn.it/test/team_create_form.php
14) Message boards : Number crunching : EXXtreme Neverending deathloop wu computation Errors (Message 1541)
Posted 6 Mar 2019 by Profile valterc
The error you got (exit code 1 (0x1)) is because, for some strange reasons, your computer claims to support the AVX instructions set but, actually, it cannot. If I remember correctly you should install W7 SP1 in order to enable AVX (but I may be wrong).
15) Message boards : Number crunching : Report Deadlines (Message 1500)
Posted 15 Feb 2019 by Profile valterc
For a long time TN-Grid had workunits with a 4 days deadline. A couple of months ago I added another day. I could obviously add another day to the deadline, maybe reducing the number of workunits a computer can cache. It's just matter of balancing the overall system. The reason of having a short deadline is mainly because a lot of workunits are really returned too late (even months later).
16) Message boards : Number crunching : AVX != SSE2 (Message 1491)
Posted 1 Feb 2019 by Profile valterc
Hi there, unfortunately I'm not able to check the results output files right now, the invalid one was deleted from the system after validation. We are aware of the issue, one way of solving it is by removing the less significant results (using a threshold) from the output files thus minimizing the possible (precision related) differences. I will increase this threshold for the Hs workunits. As a side effect the output file will be slightly smaller.

The threshold itself is an input parameter of the work generator so it will take some time to be effective (already generated workunits will not be affected by this change).
17) Message boards : Number crunching : Weird hosts (Message 1483)
Posted 9 Jan 2019 by Profile valterc
Ok, I have blacklisted it, setting its max_results_day field to -1, let see what happens.

The problem here is that I do not have any owner's e-mail address (because of the gridcoin pool mechanism)
18) Message boards : Number crunching : New TCGA workunits (TCGAz) (Message 1482)
Posted 9 Jan 2019 by Profile valterc
293 hours because it's prime.
Edit: just looked, think it was between 281 and 282 hours. 281 is prime too...
You received > 7,000 credits. Cool. Wonder why the first guy who finished it didn't get credits?

It didn't validate correctly, nevertheless I just assigned credits.
19) Message boards : Number crunching : Weird hosts (Message 1472)
Posted 5 Jan 2019 by Profile valterc
Dear all, while monitoring the overall situation of the server I just noticed this host: http://gene.disi.unitn.it/test/show_host_detail.php?hostid=33492.
Very fast execution times (suspiciously fast) and no valid results, the format of the output results is also strange.

The host belongs to a gridcoin pool, if someone were able to contact the owner please do it.

If you happen to find other 'strange' hosts, please tell me. I'm also open to suggestions about how to handle this situation.
20) Message boards : Number crunching : New TCGA workunits (TCGAz) (Message 1471)
Posted 4 Jan 2019 by Profile valterc
Yep, thanks, I also cancelled, server side, those workunits. Will check if it worked.


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