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OpenSourceMalaria / OSM_To_Do_List

Action Items in the Open Source Malaria Consortium
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Explore pathway enrichment studies for malaria #190

Open egonw opened 10 years ago

egonw commented 10 years ago

From a Google+ post:

https://plus.google.com/u/0/+EgonWillighagen/posts/fzBMxMecx7m

""" Hi all, as you know I have not been able to contribute much, but just want to let you know that in the next seven weeks I have a student work on pathway analysis of micro array expression experiment data in combination with #WikiPathways (e.g. see http://www.bigcat.unimaas.nl/wiki/index.php/March_27,_2014:_Pathway_analysis_in_PathVisio from a recent course).

Who is interested in this kind of work, and likes to talk to us on give this internship a bit more practical focus? """

mattodd commented 10 years ago

Well, I guess it would be useful to have more specifics on what you're looking for here. Can you break up the tasks into discrete things that people can do? For example, when something is submitted here it tends to be a task - a molecule to be made, or a question to be answered, so something quite granular - something that can be done by someone and completed, so that we can close the issue - Issues are "self-immolative" - they can be solved and closed when someone does something. If you're not at the stage of breaking up the task yet, are you asking for PR/spreading the word about the opportunity? And are you thinking (I assume yes) of a pathway relevant to malaria?

egonw commented 10 years ago

Well, our steps at this moment are (and indeed for malaria ;):

  1. take expression data from ArrayExpress (see https://www.ebi.ac.uk/arrayexpress/experiments/search.html?query=malaria)
  2. do pathway enrichment analysis (mostly for human, as we have the largest pathway set, see http://wikipathways.org/index.php/WikiPathways lower right corner; in fact, we do not have any plasmodium at all at this moment)
  3. find hotspots and see if the targets match existing malaria research.

But, I am requesting some collaboration here, an "advisory board" to point us to interesting pathways, perhaps the pathway around the current protein targeted by OSM. And, I like to know whom in the OSM community is doing expression experiments, or other omics level analysis.

So, the goal of this task is to mostly see what is happening. But I will also ask Patricia to work out steps to perform and list those here too! That should happen this week.