Re: Interest in Codefest in Bergamo, Italy, July 19-20th ff.
On 02/21/2012 03:50 PM, Andreas Tille wrote:
> I admit I can not give any sure confirmation whether I will join or not
> but there is a 60% chance that I will show up at this event. I'm
> specifically interested in extending the time over the weekend
> (21.+22.7.) as it is suggested unofficially.
>
> My work plan would be to work on the Debian Med project and if needed
> give presantations about Debian Med in whatever detail is wanted
> (including packaging training).
My main motivation will be to find new ways to collaborate as
a community. So, it may be good when we are both coming.
I see
a) biological workflows and Debian ... I think I would like a session
on that
b) collection of questions - and answers to those should be given in
that uses the workflows of a)
Now some wild brain storming on example questions and individuals from
which I hope to get some workflow templates at least outlined:
I) I find a couple of transcripts to be co-regulated. And I know others
that are not related at all. My hunch is that some transcription factor
may be in control of the first group. Can I please have some suggestions
for shared binding sites? What other transcripts should I have a closer
look at? (Individuals to propose an answer: Steffen ... there is no
perfect answer, but we should define how far we get with Free tools)
II) Comparing healthy and affected individuals (patients, mice,
whatever, ...) there are about five genes with each 5 nucleotide
differences in the genes most differentially expressed with
Affy/Illumina chip soandso. How can I know that the SNP was not having
an influence on the differential expression measurement? What SNP is
most likely to be relevant for the disease (Individuals to propose an
answer: Steffen, Laszlo, .... )
III) (Let's just presume for a second) I am an expert in Ubiquitin and
all the many forms of associated modifications that we find for various
forms of transport for many proteins in multiple biological processes.
The GeneOntology (GO) is not up to my level of understanding, but I need
those Gene Set Enrichment analyses for the expression data at hand and
would love to have GO enhanced for my purpose. (Individuals to propose
an answer: Steffen ... seeing the OBO tools missing with Debian )
..... add what you want to add ....
It is just another of my hunches, but such questions at a visible
location with understandable and maybe even "working" answers, should
find quite some audience. And those answers should steadily improve as
we improve - in deepness and broadness. The Codefest to me would be the
seed of such an effort. Would I be alone with that?
Steffen
Reply to: