Code

The code for running experiments and analysing data is all stored on gitlab.

How can I access Gitlab?

Login to gitlab with your Science Faculty account. Then ask Marc to gain access to biophysics and biophysics_labs

How can I get (clone) the code from the repository?

You can get the code from the repository in several ways, all with their own advantages.

Download zip-file

<todo>

Command Line Instructions

• Instal the GitHUB client for Windows or for Mac, and add the repository via Command line instructions:
  • Git global setup
    • git config --global user.name "Your Name"
    • git config --global user.email "your.e@mail.adress"
  • Create a new repository
    • git clone https://gitlab.science.ru.nl/username/projectname.git
    • cd test
    • touch README.md
    • git add README.md
    • git commit -m "add README"
    • git push -u origin master
  • Existing folder or Git repository
    • cd existing_folder
    • git init
    • git remote add origin https://gitlab.science.ru.nl/username/projectname.git
    • git push -u origin master

Use SourceTree

• Install the Git client Atlassian Sourcetree, and Clone the repository via a button press

How can I get the changes others have made (fetch/pull)?

• In Github for Windows: the Sync button
• In Atlassian Sourcetree: the Pull button

How can I put my changes of the code in the repository (commit/push)?

You should have Master rights to be able to upload your changes to the remote repository. If you do not have own, you should work in a branch.

• In Github for Windows and in Atlassian Source Tree: push the Branch button, and give it a meaningful name (i.e. your first name)

Then you can upload

• In Github for Windows: Sync
• In Atlassian SourceTree: stage files - commit - push when commit

Which repositories exist, and what are they for?

Biophysics

For experiments with sound localization, to analyse fast eye and head movements, to do bayesian data anaysis, and some other utilities

Matrix

MATLAB program for speech vs. noise experiments with vocoder options. The speech consists of 5 word sentences in Dutch or German.

N.B. The speech files are available on [\\mbcogro-srv.science.ru.nl\mbcogro\ruurd\##BIOFYSICA\#P115 Matrix program\OLSA\Sounds mbcogro]

fNIRS

For analysis of NIRS measurements