Posts by valterc
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1) Message boards : News : A mid-summer ping (Message 3413)
Posted 6 Dec 2024 by Profile valterc
Hello! What's the situation?

No news (don't know if it is good news...)
2) Message boards : News : A mid-summer ping (Message 3411)
Posted 18 Sep 2024 by Profile valterc
Hi, i see few tasks in progress.

Could you please provide more info about science part of this, maybe update the http://gene.disi.unitn.it/test/gene_science.php page ?

Thank you!

Well, it's just a single expansion of a FANTOM related gene network (about 700 workunits). As requested by the scientist... No news about future big experiments.
3) Message boards : News : A mid-summer ping (Message 3408)
Posted 22 Aug 2024 by Profile valterc
Hope all of you got a great vacation and work in progress had a great result.

Instead of of ask when work is available i would take time and ask if goal will remain or change with new experiment?

What is the next goal?

The next big goal, from the computational point of view, would be to find a way to re-arrange the really big single cell RNA datasets we are playing with in order to make them compatible with our casual discovery algorithm. It's not that easy...
4) Message boards : News : A mid-summer ping (Message 3403)
Posted 30 Jul 2024 by Profile valterc
Just a ping to state that the project is alive and running.
The last year I was way too optimistic in forecasting that a big new experiment would have started soon. I was wrong, in the last months just a handful of workunits were distributed. Anyway, even in this strange and hot summer, the scientists are working, and the project is making progress, although we cannot say when new job will be available.
BTW, if you want to check something we did recently, although still in beta stage, just go to https://onegene-causality-weaver.disi.unitn.it/
5) Message boards : Number crunching : AVX Applications (Message 3388)
Posted 19 Apr 2024 by Profile valterc
The SIMD optimizations were made by a volunteer many years ago, by adding specific ASM code for SSE2, AVX and FMA. If I remember correctly, at that time, the benefits of using FMA instructions were minimal. I don't know if our algorithm will really make good use of AVX512...
6) Message boards : Unix/Linux : "Computation error" with anonymous platform (Message 3381)
Posted 18 Apr 2024 by Profile valterc
Just a guess, maybe you need some old compiling environment, or older boinc libraries, something might have changed from years ago. The CLI executable you used is the official one or the result of your compilation?
7) Message boards : Number crunching : A very short experiment (Message 3376)
Posted 15 Apr 2024 by Profile valterc
Another small batch is on its way


Are larger ones in the works?

Yes, they are, but no ETA right now...
8) Message boards : Number crunching : A very short experiment (Message 3374)
Posted 15 Apr 2024 by Profile valterc
Another small batch is on its way
9) Message boards : Number crunching : A very short experiment (Message 3370)
Posted 20 Mar 2024 by Profile valterc
I just put into the queue the expansion of ten genes of an old dataset of Vitis vinifera. A short experiment (around 1k workunits) that we need to do for a statistical analysis.
10) Message boards : Science : Transcriptome and translatome from Mus musculus (Message 3369)
Posted 8 Mar 2024 by Profile valterc
Where are results?

The results, as usual, will be available to the scientific community only after a necessary validation phase, discussions, etc., usually at the same time of a publication... (it will take some time, usually months)
11) Message boards : Science : Transcriptome and translatome from Mus musculus (Message 3365)
Posted 19 Feb 2024 by Profile valterc
Yes. I just started with the second (and last, for now) dataset, please look at the "Science status" page (from the main menu) if you want to know how things are going on.
12) Message boards : Number crunching : Optimization (Message 3356)
Posted 14 Feb 2024 by Profile valterc
I don't exactly know the details of that command line (and of your hardware) but, anyway, feel free to compile the application the way you want (and modify it, if you are brave enough). It would be successful if the obtained result is exactly the same of the original one.
13) Message boards : News : New experiment on Spinal muscular atrophy (SMA) from Mus musculus (Message 3350)
Posted 13 Feb 2024 by Profile valterc
We just started two experiments (gene expansion) on two different datasets (rnaseq, riboseq). There will be a total of about 140k workunits (2x tasks), each one relatively fast, distributed in batches.
If interested please follow the discussion here: https://gene.disi.unitn.it/test/forum_thread.php?id=384
14) Message boards : News : Happy New Year! (Message 3348)
Posted 7 Feb 2024 by Profile valterc
I just modified it, thank you for having noticed.
15) Message boards : News : Happy New Year! (Message 3340)
Posted 29 Dec 2023 by Profile valterc
Just a very brief update: People here are working on submitting papers, analyzing the FANTOM and Vitis vinifera data and so on. A nice Web application to look and play with the results is almost ready. Unfortunately there is yet no ETA on the new experiments to be done here.
Happy New Year to everybody listening!
16) Message boards : Science : Human-specific genes in acute lymphoid leukemia (Message 3327)
Posted 27 Nov 2023 by Profile valterc
I just started to distribute the workunits. Please be aware that the experiment is very short, a total of around 3000 (x 2) will be probably out in just a few hours.
17) Message boards : News : Summer break (Message 3298)
Posted 27 Oct 2023 by Profile valterc
We have done research on grape in collaboration with the Edmund Mach Foundation, funded by our regional government, the Autonomous Province of Trento. It's important for our local economy, from the agricultural point of view grape (and it's side product, wine), apples and small fruits are among the relevant products.
See https://www.fmach.it/eng
18) Message boards : News : Summer break (Message 3293)
Posted 24 Oct 2023 by Profile valterc
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
19) Message boards : News : Summer break (Message 3290)
Posted 24 Oct 2023 by Profile valterc
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.
20) Message boards : News : Summer break (Message 3284)
Posted 27 Sep 2023 by Profile valterc
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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