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update RegenerateConnectome.py to read data from OpenWorm database instead of a spreadsheet #140
Currently, RegenerateConnectome.py reads synapse position data from a spreadsheet. (I think this one: Steven Cook Data ). See issue 136 for more info. This issue is effectively update "a)" from that issue.
In order to close the data->model loop, we should replace this step with one that reads the data from our currently in-development biological data database
This will serve as the first test case for closing the loop between the biological data repository we are aggregating from the scientific literature and the simulations we plan to run to explore and test this data.
referenced this issue
Sep 25, 2013
This is long overdue - explanation of our current semantic database.
Not sure where it should go on our repositories?
On Wed, Sep 25, 2013 at 8:35 AM, kneuron firstname.lastname@example.org wrote:
@Lambdanaut yes this still needs work. Your help would be appreciated. The description appears to do a good job of explaining the issue. Issue #143 has some notes in one of the comments from me that has example python code that can be used to query data out of the database via rdflib. A version of RegenerateConnectome.py that used these kinds of methods would be very helpful to making the connectome model more rapidly data driven. It provides a great impetus for us to continue populating the database.
@Lambdanaut, thanks so much for offering to help with this. As others have mentioned, it still needs to be done - I assigned it to myself and then disappeared... I'm still around to help, but I don't have a ton of time in the near future to devote to code (maybe over the holiday break). I hope I've made the necessary steps clear in the description above.
I think @pgleeson's suggestion of starting from a fresh copy of the python script is a smart one. (new: RegenerateConnectomeDB.py vs old: RegenerateConnectome.py)
My work schedule has recently changed dramatically and I'm going to have to
On Fri, Jan 3, 2014 at 1:03 AM, Stephen Larson email@example.com: