Posts by luca@gene [SSC11]
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1) Message boards : Science : New experiment: gene network expansion of human pathologically relevant genes (Message 1368)
Posted 21 Sep 2018 by Profile luca@gene [SSC11]
Moving to the FANTOM project dataset has been a big challenge for us. The original input contains a slightly different type of data (RNAseq instead of micro-array contrasts) and has 10 times the variables of the biggest data matrix we used so far.

Human is known to have around 20.000 protein-coding genes and 5.000 non-coding ones, but the technology employed in the FANTOM project allowed them to analyze expression at a higher resolution, reporting data also for alternative splicing. The raw dataset reports expression levels for more then 200.000 transcripts in 1829 conditions, wich would been too big to be explored, so we had to filter it.
A strongly related challenge comes from the highly specificity of certain transcripts, that are expressed only in few conditions. This is translated in lines of data with very few non-zero entries that are very likely to correlate one with another.

We are currently testing two version of the input dataset. The first one is a general filtering on the lines that have no HGNC code (www.genenames.org). The second is a more fine grained filtering, where we have removed also transcripts with less then 10% non-zero entries and gene-isoforms too similar one with another.

Most of the work in this moment is focused toward understanding which one of the two dataset is performing "better".

Thank you for all your support.
2) Message boards : Science : DREAM5: the S. cerevisiae dataset (Message 1002)
Posted 21 Mar 2017 by Profile luca@gene [SSC11]
Hi all,
We are back online and very pleased to see you are still joining our project with a great computational power, this is really nice, thank you all!

In parallel with the expansion of the vitis genes, we are working on the comparison of our algorithm with the state of the art methods that participated to the DREAM5 competition on Gene Networks Inference. With your great contribution we almost completed one of the network of the challenge (oge_dream5_net3), so we will move to the next dataset, i.e. oge_dream5_net4.
These dataset covers a wide portion of the baker's yeast with almost 800 experiments. Hereafter a brief introduction on the organism.

Saccharomyces cerevisiae (baker's yeast) is the model organism for unicellular eukaryotes. Indeed, despites being unicellular, it shares most of basic biological processes with pluricellular complex organisms. Moreover, its relatively compact genome makes the baker's yeast the perfect target for bioinformatic methods that want to start addressing eukaryotes without dealing with the computational cost of vegetables or mammalian.

Thanks in advance for your contribution,

Luca
3) Message boards : Number crunching : Tasks won't suspend (Message 133)
Posted 21 Dec 2013 by Profile luca@gene [SSC11]
I have some ideas, did you use void boinc_get_status(BOINC_STATUS*); http://boinc.berkeley.edu/trac/wiki/StatusApi?
BOINC_STATUS boinc_status; boinc_get_status(&boinc_status); if (boinc_status.quit_request || boinc_status.abort_request || boinc_status.suspended)) { /// do things // boinc_end_critical_section(); // boinc_finish(0); }

Should we threat the three different status in the same way?

Does boinc_finish(0) implies the upload of the file to the server?

Isn't better to use a different finish code?




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