Posted 5 days ago by
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...
Posted 5 days ago by
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?
Posted 9 days ago by
valterc
Another small batch is on its way
Are larger ones in the works?
Yes, they are, but no ETA right now...
Posted 9 days ago by
valterc
Another small batch is on its way
Posted 20 Mar 2024 by
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.
Posted 8 Mar 2024 by
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)
Posted 19 Feb 2024 by
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.
Posted 14 Feb 2024 by
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.
Posted 13 Feb 2024 by
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
Posted 7 Feb 2024 by
valterc
I just modified it, thank you for having noticed.
Posted 29 Dec 2023 by
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!
Posted 27 Nov 2023 by
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.
Posted 27 Oct 2023 by
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
Posted 24 Oct 2023 by
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
Posted 24 Oct 2023 by
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.
Posted 27 Sep 2023 by
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 ...
Posted 8 Sep 2023 by
valterc
Just a brief update:
- No new experiment ready yet (people are working on but no ETA)
- The latest batch on Vitis vinifera has been collected and validated, ready for further biological analysis and publication
- I am re-organizing all the (many years of) data that we collected, trying to optimize the whole system
- Some of us will be here https://grapedia.org/annual-meeting/
Posted 18 Aug 2023 by
valterc
I hope to be able to restart the system with a new project at the beginning of August.
Is there any news on the new project?
Not yet, most of the people here is either on vacation or around for conferences/workshops etc. I was probably too optimistic in my previous statement, I guess we will have some news in September.
Posted 11 Aug 2023 by
valterc
Fixed, thanks for having noticed it.
Posted 11 Jul 2023 by
valterc
The plan is to going around, by car, through Bosnia, Croatia, Montenegro and Albania, moving from place to place and eventually stop if we really like one...
I'm happy you enjoined your volcano "climbing". When I was younger I went on top of Stromboli, starting from the sea level, and spent the night up there on a sleeping bag (it was a wonderful experience).