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We are ready to start another experiment on Escherichia coli, using the same expression dataset of the previous one but changing one of the algorithm's parameters.
Execution times should slightly faster than the last one on Vitis vinifera.
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Confirming I received them, they are much quicker than the Vitis vinifera WUs.
Will the science page on the homepage updated with the % of work done?
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valtercProject administrator
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Confirming I received them, they are much quicker than the Vitis vinifera WUs.
Will the science page on the homepage updated with the % of work done?
We need some time in order to find the 'optimal' generation parameters (the target execution time should be around one hour for average cpus), I will update the science page in the next days.
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Thanks for the new "science meter". I really appreciate that you created a separate meter for the new experiment instead of lumping it all into one and recalculating the percent complete based on total work done. With separate meters, it feels like we are going forward. Recalculating the percentage would feel like we're going backward. Plus, we can track the progress of each experiment individually.
Keep up the good work!
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I've just added another experiment on Vitis vinifera (same dataset as the last one but different algorithm's parameter). This is computationally faster but the work generator will take the same time as before to create a work unit. This means that it would be difficult to build up a large queue of ready-to send workunits...
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there is nothing to sent when i look at serverstatus
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Felix, work is being generated, but it is downloaded immediately by hosts which are asking for work often enough. Hence the server status page shows 0 tasks ready to send practically all the time.
In other words, computer capacity available from contributors currently exceeds the pace of the work generator.
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oh okay thank you
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At this moment we are able to create 97*2 workunits every ~4 minutes (2910 per hour, 69840 per day). The average computing time is around one hour.
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well...
i would say thats to less new created work
can you do sth about this?
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Could I take a look on code of your work generator and some sample input data? I wonder if I could optimize it a bit.
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valtercProject administrator
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Could I take a look on code of your work generator and some sample input data? I wonder if I could optimize it a bit.
Thank you for this, I will contact Francesco (who is the main author of the program) and let you know about his comments. Beware that the core of the program is written in Python, I'm planning to rewrite it in C++.
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Could I take a look on code of your work generator and some sample input data? I wonder if I could optimize it a bit.
Thank you for this, I will contact Francesco (who is the main author of the program) and let you know about his comments. Beware that the core of the program is written in Python, I'm planning to rewrite it in C++.
No problem, I know Python too :)
BTW, have you tried to use PyPy (https://pypy.org/) or something like this?
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But i continue to download and crunch Vitis Vinifera....
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But i continue to download and crunch Vitis Vinifera....
...as explained a few posts above... The E. coli experiment is almost finished (see the 'science' link from the home page)
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valtercProject administrator
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I've just added another experiment on Vitis vinifera (same dataset as the last one but different algorithm's parameter). This is computationally faster but the work generator will take the same time as before to create a work unit. This means that it would be difficult to build up a large queue of ready-to send workunits...
Could you please explain what is the difference here in more layan terms? I Think a lot of people would like to know exactly what's happening with our submitted results. :) I see that it's marked with the same algo as the E. Coli dataset, but I couldn't find where are the differences or what the end goal of them is.
Thanks!
Simply speaking the algorithm implemented here is able to find (causal) relations between variables (on various domains). We apply it on 'expression data' obtained from different organisms. A typical computational result is the information that gene X has some kind of relationship with gene Y (this knowledge will help biologists to better understand the biological processes associated with the specific genes). We apply the algorithm (with different parameters) to the organisms of interest of the biologists we are working with. If you want to know more about please look at the 'science' section of the forum.
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But i continue to download and crunch Vitis Vinifera....
...as explained a few posts above... The E. coli experiment is almost finished (see the 'science' link from the home page)
Ok, thank you.
P.S. i thinked that the new experiment on e.coli could bring new work. My misunderstanding
Always waiting for Pseudomonas :-P
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valtercProject administrator
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Simply speaking the algorithm implemented here is able to find (causal) relations between variables (on various domains). We apply it on 'expression data' obtained from different organisms. A typical computational result is the information that gene X has some kind of relationship with gene Y (this knowledge will help biologists to better understand the biological processes associated with the specific genes). We apply the algorithm (with different parameters) to the organisms of interest of the biologists we are working with. If you want to know more about please look at the 'science' section of the forum.
Thanks. The openness and the friendly replies are exactly why I'm crunching for you. :)
One more thing, I've noticed that the current VV database has only 3611 genes to compute, right? Does that mean these are "cherry picked" genes that need further expansion?
Also, if that's the case, the science meter on the page is not working properly, as it reports 1212 genes as being 4.33%. Sorry if I'm being dumb here.
The number 3611 (DB column) that you see right now means that 3611 out of 28013 genes are inserted into our queuing system, ie. ready to be used for creating workunits. The other ones will be inserted later, when the need arises. We do this in order to keep our db small.
Maybe the word 'QUEUED' is more explanatory than 'DB' (I just changed it)
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valtercProject administrator
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But i continue to download and crunch Vitis Vinifera....
...as explained a few posts above... The E. coli experiment is almost finished (see the 'science' link from the home page)
Ok, thank you.
P.S. i thinked that the new experiment on e.coli could bring new work. My misunderstanding
Always waiting for Pseudomonas :-P
We are still doing experiments on Pa (in direct contact with some biologists here), but not using the BOINC system, A single gene expansion on this organism is *really* fast, a simple dedicated (not too powerful) workstation is enough for now.
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FYI, I see that you are out of tasks to work on but the server is not reporting that to the client (Out of Work).
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