[Mne_analysis] mne-python config file path could not be determined...

[Alexandre Gramfort]

Thanks for sharing.

Please let us know once this gets public.

Best,
Alex


On Wed, May 21, 2014 at 8:55 PM, Peter C. Marks <peter.c.marks at gmail.com> wrote:
> Alex,
>
> Thank you for the reply.
>
> The application will be open source. We are preparing a paper. I pasted the
> abstract at the end of this message. Mne is attributed in the references.
>
> I think I will try the approach that Mads just suggested (Thank you, Mads!).
> I'll post the results.
>
> Best,
>
> Peter
>
> Proposed Abstract:
>
> A wealth of functional genomics data for cardiovascular phenotypes exists in
> many public sources such as GEO (Gene Expression Omnibus,
> http://www.ncbi.nlm.nih.gov/geo/). In the systems biology era, understanding
> of pathways and networks underlying phenotype requires analysis of genomics
> data across multiple platforms (microRNA expression, gene expression, etc.)
> and across multiple experimental conditions, organisms, and systems. While
> many such data sets exist, and while software tools for the analysis of each
> of these individual data sets are prolific, software tools for the
> integrative analysis of genomic data across platforms of genomic expression
> and across experimental conditions are uncommon. We present CardioCPI, a
> freely availably web-based application populated with gene and microRNA
> expression data from GEO. CardioCPI provides seamless analysis and graphing
> of genomic and phenotypic data across platforms and experiments. CardioCPI
> is built in Python using the Model-View-Controller software pattern within
> the Django web application framework, with a LevelDB schema-less data store
> for storing and accessing genomic and phenotypic data. We illustrate the
> utility of CardioCPI with an example of integrated analysis of gene and
> microRNA expression data from a sample of infants with Tetralogy of Fallot
> (TOF), a congenital fetal heart disease, and a set of control infants to
> show gene regulatory pathways and modules that are highlighted through the
> joint and integrated analysis of these two separate data sets. In summary,
> CardioCPI is a flexible user-friendly tool for cross-platform and
> cross-study analysis of gene regulatory pathways underlying cardiovascular
> disease.
>
>
>
> On Wed, May 21, 2014 at 2:34 PM, Alexandre Gramfort
> <alexandre.gramfort at telecom-paristech.fr> wrote:
>>
>> hi Peter,
>>
>> > I'm using mne as part of a browser-based web application - it is using
>> > the
>> > Django framework.
>>
>> sounds exciting !
>>
>> > Development is done using a built-in web server. Yesterday
>> > I moved the application to Apache but I am getting an error (see
>> > below).
>> >
>> > I can see why the error is occurring - mne utils.py is attempting to
>> > open a
>> > config file that is located at $HOME/.mne/mne-python.json but $HOME
>> > doesn't
>> > seem to be set in the Apache environment, hence the error.
>> >
>> > Has anyone had a similar experience using Apache?
>>
>> I doubt it.
>>
>> What we could do is to support an environment variable eg. MNE_CONFIG_DIR
>> that defaults to $HOME but can be overwritten by the user. Would that
>> help?
>>
>> out of curiosity do you plan to open this code? what is the context of
>> this work?
>>
>> Best,
>> Alex
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