New experiments: Pseudomonas aeruginosa
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Profile FrancescoAsnicar [SSC11]
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Message 1042 - Posted: 10 Apr 2017, 1:25:30 UTC

Hello all,
here a brief description of some new experiments coming out in the next days!

Pseudomonas aeruginosa is a bacterium that can be harmful for plants and animals, including us, humans. P. aeruginosa is in general a multidrug resistant bacterium that have been associated with serious illnesses. (https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa)

For this reason, the World Health Organization (WHO), early this year, included P. aeruginosa in its list of bacteria for which there is urgent need of antibiotics. (http://www.who.int/mediacentre/news/releases/2017/bacteria-antibiotics-needed/en/)

Thanks to a collaboration we are starting with a biologist, who is specifically studying this bacterium, we will start in the next days a bunch of new experiments. The first experiments will test several different parameters using a very well known (by the biologists) gene network of P. aeruginosa that controls the number of bacterial cells, named quorum sensing (https://en.wikipedia.org/wiki/Quorum_sensing). If everything turns out well, with our results we can help the biologist we are collaborating with, as she will study our predictions in her in-vitro experiments! :)

Many thanks again to all of you for your support to our project.
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Message 1043 - Posted: 10 Apr 2017, 9:45:34 UTC - in response to Message 1042.
Last modified: 10 Apr 2017, 9:45:56 UTC

We started to feed the system with Pa experiments. At the beginning we'll investigate the algorithm's parameter space to find the optimal ones. From the computational point of view this means (very simple speaking) that the execution time of a single Pa workunit may vary a lot.

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Message 1053 - Posted: 16 Apr 2017, 9:17:05 UTC - in response to Message 1043.
Last modified: 16 Apr 2017, 9:17:31 UTC

We started to feed the system with Pa experiments.


Any roadmap? I'm continuing to download vitis vinifera....

Profile FrancescoAsnicar [SSC11]
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Message 1055 - Posted: 17 Apr 2017, 16:45:37 UTC - in response to Message 1053.

Any roadmap? I'm continuing to download vitis vinifera....

We just submitted to system a bunch of experiments with very different parameter values. We'll now collect and process them. Then, we need to evaluate the results to find the best set of params to use for the "real" experiments. Some of the experiments were too fast to compute and there were users complaining about the bandwidth consumption, so we need to carefully define these new experiments to be suitable within the BOINC environment.
I believe that we can start again new experiments on Pseudomonas aeruginosa by the end of May.
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Message 1087 - Posted: 27 Jun 2017, 18:40:37 UTC - in response to Message 1055.

I believe that we can start again new experiments on Pseudomonas aeruginosa by the end of May.


News? I'm interested in this research

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Message 1088 - Posted: 28 Jun 2017, 23:45:28 UTC - in response to Message 1055.

We just submitted to system a bunch of experiments with very different parameter values. We'll now collect and process them. Then, we need to evaluate the results to find the best set of params to use for the "real" experiments. Some of the experiments were too fast to compute and there were users complaining about the bandwidth consumption, so we need to carefully define these new experiments to be suitable within the BOINC environment.
I believe that we can start again new experiments on Pseudomonas aeruginosa by the end of May.


Some of us don't have a problem with bandwidth, maybe you can do a sub-project of fast units and a slower sub-project of longer ones to keep both sets of people happy.

Profile FrancescoAsnicar [SSC11]
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Message 1090 - Posted: 29 Jun 2017, 23:15:24 UTC - in response to Message 1087.

We are still waiting for some validations from the biologist involved in this project, based on the bunch of workunits that we ran.
This step is fundamental to understand if we need to adjust some parameters before starting doing the complete set of experiments.

I hope we can start soon with these experiments.

Many thanks to you all for your support to our project,
Francesco
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Message 1116 - Posted: 26 Sep 2017, 6:40:05 UTC

Pseudomonas


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