RefCurv

[Christian Winkler]

Hi everyone,

I would like to connect one of my tools with Simvacular and I think the best way is to use the Python interface. The tool is called RefCurv and you can find the code on GitHub (https://github.com/xi2pi/RefCurv). It would be great to get some feedback from the developers of Simvascular - maybe you have the advice to facilitate the connection.

With RefCurv, users can create pediatric reference curves from data. Let us say you want to fit a "curve model" to the data, you can do that with some simple steps (https://github.com/xi2pi/RefCurv/wiki/Quick-Guide). Here an example for the body mass index (BMI) over the age: https://raw.githubusercontent.com/xi2pi ... xample.png
Working with pediatric cardiologists, I found that they use these reference curves in every day clinical practice. RefCurv is the first tool that enables physicians with some easy steps to create but also analyzes the curves. With this project, I hope to bring both fields, "statistical learning" and "medical applications", closer together.

Simvascular is a great project with high potential for clinical applications. However, I found it difficult to extract information from the computations in a concise way. My idea is that simulation results could be presented as reference curves, as these are used in clinics and doctors understand them quickly. Let us take one of your recent studies as an example (http://journals.sagepub.com/doi/abs/10. ... 5117745026). The results in Figure 6 could be presented as reference curves.
On the other hand, boundaries, parameters, and initial values have to be defined in Simvascular before the simulation. The information for defining the parameters could be extracted from clinical reference curves. There are a lot of curves in literature for all kinds of medical parameters and it would be great to have this information available in Simvascular. Currently, I am working on an easy way to load curves from literature into RefCurv.

If you need more information, take a look at the GitHub repository and feel free to contact me. I would be glad to share my manuscript about RefCurv (planned submission in the Journal of Statistical Software by the end of the year).

Best,
Christian

[Christian Winkler]

Hi everyone,

I am on a Linux machine and install Simvascular via the package installer. Everything works fine and I can open the Python console inside Simvascular.

How do I open Simvascular's Python from outside? Can I access it through the terminal?

I could not really find the location of Simvascular's Python.

Best,
Christian

[Fanwei Kong]

Hi Christian,

You should be able to access SimVascular from command line by following the steps under "Setup SimVascular to run from a terminal" on this page: http://simvascular.github.io/docsInstallation.html.

After finishing the above steps, you could launch SimVascular's Python by typing "simvascular --python"

Best,
Fanwei

[Christian Winkler]

Great, thanks!

The actual thing I would like to do is to install packages for SimVascular's Python (like "pandas", "scipy", etc.). I tried a bit around with "pip" but without success. Is there a fast way how I can achieve that?

Maybe installing the same Python version (3.5.5 for SimVascular 2019-01-27) and using pip with package path definition (Simvascular path) could do the trick?

I guess compiling SimVascular from the source code could be another way but that would take a while.

Is there any other way to connect SimVascular with my "global" Python in Linux?

[Christian Winkler]

I found out that you can open an external script with the command:
simvascular --python -- "test.py"

Could that help?

[Christian Winkler]

I found a way how to couple RefCurv with SimVascular.

Here a short video for everyone who is interested:

https://vimeo.com/315196508