Ivo Hofacker
2D structure, SHAPE probing
For Windows Users: Please install in advance Windows Subsystem for Linux (WSL). This can be installed from Windows app store. See this page for more details. Once installed, you can access a Linux subsystem by typing wsl in windows shell.
We will use jupyter notebook for the tutorial. We recommend to use conda to install jupyter and other dependencies.
1. Install conda or mamba. Download installer script from conda/mamba and execute it from command line. See this page for detailed instructions. Then run
conda init
2. Set up conda channel, note that we need to prioritize Bioconda over conda-forge.
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
3. Create an environment for AlgoSB and activate it. Here we preinstall python 3.12, you can change it according to other course (though we will need at least 3.11)
conda create -n algosb25 python=3.12
conda activate algosb25
4. Install all dependencies for the Monday course
conda install numpy ipykernal jupyter pillow
conda install viennarna
5. Install additional dependencies for the Friday course
conda install infrared
The hands on assignment is available at:
https://github.com/ViennaRNA/ViennaRNA-Tutorial
Sebastian Will
RNA design
1. Download the assignment sheet:
git clone https://gitlab.inria.fr/amibio/algosb-infrared.git
2. Install various dependencies through:
conda create -n algosb_rnadesign 'viennarna=2.7' numba nunmpy scipy matplotlib pandas infrared
Kalli Kappel
Modeling RNA-protein interactions
Before the hands-on session on Tuesday, December 9, install Rosetta and PyMOL.
[Detailed instructions to install Draffter]
Downloading Rosetta
Download Rosetta 3.13: https://downloads.rosettacommons.org/downloads/academic/3.13/
(Free for academic users)If you are working on a Linux machine, download “Rosetta 3.13 source + binaries for Linux – as one bundle (18G)”
If you are working on a Mac, download “Rosetta 3.13 source + binaries for Mac – as one bundle (14G)”
These are big files, so the download may take a while.
Installing PyMOL
The educational license is free and suitable for our purposes. Download here: https://pymol.org/edu
Follow the installation instructions to install on your computer.
Liuba Mazzanti
Integrative RNA modeling: SAXS and MD simulations
Windows users: Please install Windows Subsystem for Linux as explained above, and use it to pretend you’re a perfectly normal Linux user.
Mac OS X user: Everything should be available/installable, as long as you
have XCode installed
Dependencies:
- Fortran + C compilers (tested with gfortran + gcc)
- Python + libraries: NumPy, MatplotLib, MDAnalysis
- Chimera or VMD
A distribution of further software, analysis scripts and data needed for the tutorial can be downloaded from:
https://filesender.renater.fr/?s=download&token=ff5bc9ad-4160-4f01-8d9f-bf8f1f7d506d
and further instructions can be found within a README file in the 01-Code_GMIN_HiRE_SAXS subdirectory.
Magnus Marcin
From sequence to 3D structure
- install PyMOL, if you can select install PyMOL 2.5
- install rna-tools
https://github.com/mmagnus/rna-tools
(with pip install rna-tools), this include BioPython (hopefully this will go smoothly 😉 if not, then let Magnus know)