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oercompbiomed / CBM101

Introduction to Computational Biomedicine and Machine Learning
MIT License
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Network analysis notebooks #7

Open karinSDU opened 5 years ago

karinSDU commented 5 years ago

Dear all I have uploaded three notebooks in network analysis. 1) Basic network terms (still need to finish part four with attributes/colors) 2) Protein-protein ego network (here they apply the basic network terms that they just learned and will learn some more terms incl. very basic matrixplot from nxviz- last part not finished) 3) Using py2cytoscape on a network and applying layouts and styles and saving.

I would like to know if these three elements covers what you think is needed and whether more should be implemented. Could I ask for a respons within 2 weeks?

veitveit commented 5 years ago

There are still a few issues and these notebooks are a very good use case to get them solved:

Installation The installation cell contains code to load the necessary packages but not installation instructions. The user still needs to install them externally. So we either add instructions how to do that (pip or conda) or add code to install the packages. See also issue #8 about this.

custom package As far as I understand, there is a custom package which was probably coming with the original example. I cannot run the notebooks without the files of this package. @karinSDU Did you have to install such a package? Then the files need to be provided, too, and you should also check whether there is any license on the files, so we are sure that we actually can use them.

Loading packages/libraries The corresponding code should got then to the cell Loading data which I will now rename to Loading data and packages

arvidl commented 5 years ago

I think an easy way to do installation of packages (and keep a well separated conda environment) is to follow the guide in 'setup.md' carefully. Using the 'environment.yml' and 'conda env update' mechanisms does all the installations automagically ... @karinSDU / @veitveit

karinSDU commented 5 years ago

I think I have solved the custom problem - or at least partly? I uploaded the first two notebooks successfully to binder: https://mybinder.org/v2/gh/karinSDU/conda/master For this to work I deleted some of the lines with import and made the environment.yml file:

name: example-environment channels:

veitveit commented 4 years ago

That seems to work. @karinSDU Could you add the necessary files to this repository and we then test it on mybinder?