From SimBio - A generic environment for bio-numerical simulations

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How to...

...get a login:

Since Aug.2013, the SimBio MediaWiki is open for everyone and does no longer need an account. If you face problems with it, get in touch with the site administrator Daniel.

...join the SimBio mailing-list:

To join the SimBio mailing list, please send an email to simbio-list-subscribe@tu-ilmenau.de.

This SimBio mailing list is meant to distribute information on revisions, the code itself, meetings, new developers etc. To do so, just send an email to simbio-list@tu-ilmenau.de.

For further questions on subscription and using the list, please contact Stephan Lau (simbio-list-owner@tu-ilmenau.de).

...start or edit a page:

There are several ways to start a new page. These can vary based on the type of page started, as well as the wiki and namespace. Just check out the MediaWiki Help for further support

...checkout the SimBio software from sourceforge:

svn checkout svn://svn.code.sf.net/p/neurofem-simbio/code/ SimBio
svn log SimBio

You will then get a full checkout of the SimBio-code. You get a new directory with the name SimBio, in which you find trunk, branch and SimBioPatch. The second command lists recent changes to be aware of. Since 2013, the full SimBio code (IPM and NeuroFEM) is open-source code, please study the license agreement. In SimbioPatch, there are the scripts that Martin Steinisch used to restructure the SimBio-code.

...access the test data repository:

The testdata repository offers a reasonable start with SimBio, you will find some documentation and also some more software that helps working with SimBio. The testdata repository 2014 is available under source forge. Through the file README_StartWithSimBio, well-documented scenarios for forward and inverse source analysis will be available.

Furthermore, we have produced some films that document how to work with the SimBio testdata:

The film EEG forward modeling using FEM documents how to perform full subtraction FEM forward modeling as presented by (Drechsler et al., NeuroImage, 2009).

The film EEG inverse modeling with FEM documents how to use the ddd debugger to step through and understand the code and to perform dipole fits for a set of dipoles with different eccentricities.

The film tES forward modeling with FEM documents how to perform transcranial electric stimulation (tES) FEM forward modeling as presented by (Wagner et al., J. Neur. Eng., 2014). The sourceforge testdata 2014 do not yet contain the data for the simulation of tES yet. For a more up-to-date version of the SimBio testdata (including the tES scenarios), you need to write an email to Carsten Wolters.

Troubleshooting

Problem: You see the error message:

svn: PROPFIND request failed on '/svn/SimBio'
svn: PROPFIND of '/svn/SimBio': could not connect to server (https://svnserv.cbs.mpg.de)

but the server can be pinged:

$ ping svnserv.cbs.mpg.de
PING beryll.cbs.mpg.de (194.95.183.241) 56(84) bytes of data.
64 bytes from beryll.cbs.mpg.de (194.95.183.241): icmp_seq=1 ttl=48 time=321 ms
...

Solution: You are behind a firewall which blocks SVN. Use a VPN client, talk to your network administrator (Good luck!) or do the checkout at home.

Other SVN problems: Read the SVN Handbook.

...access the OLD repository:

Do NOT use this for development purposes

SimBio sources, Revision 232 (write an email to Carsten Wolters to get an account on biomag07.uni-muenster.de):

svn+ssh://user@biomag07.uni-muenster.de/home/neurofem/NeuroFEM_repository 

...cite SimBio:

Please refer to SimBio by citing the Wiki as an online document:

SimBio Development Group. "SimBio: A generic environment for bio-numerical simulations", online, https://www.mrt.uni-jena.de/simbio, accessed Dec 14, 2024.

or use bibtex:

@misc{simbio,
     author        =  "{SimBio Development Group}",
     title         =  "{SimBio}: A generic environment for bio-numerical simulations",
     howpublished  =  "online, https://www.mrt.uni-jena.de/simbio, accessed Dec 14",
     year          =  "2024"
}

The date above is always the current date. Whenever you want to cite SimBio cut&paste the above.