ISAMBARD: An open-source computational environment for biomolecular analysis, modelling and design
Intelligent System for Analysis, Model Building And Rational Design.
Version 2017.2.2 (Aug 16th, 2017), Woolfson Group, University of Bristol.
ISAMBARD (Intelligent System for Analysis, Model Building And Rational Design), is a Python-based framework for structural analysis and rational design of biomolecules, with a particular focus on parametric modelling of proteins. It is developed and maintained by members of the Woolfson group, University of Bristol.
Any publication arising from use of the ISAMBARD software package should cite the following reference:
Christopher W. Wood, Jack W. Heal, Andrew R. Thomson, Gail J. Bartlett, Amaurys A. Ibarra, R. Leo Brady, Richard B. Sessions, Derek N. Woolfson; ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. Bioinformatics 2017 btx352. doi: 10.1093/bioinformatics/btx352
ISAMBARD can be installed straight from PYPI using pip:
pip install isambard
Or if you want to try an experimental build, download from GitHub either by downloading the zipped file or cloning, then navigate to the ISAMBARD folder and type:
pip install .
ISAMBARD has a few Python package requirements, just install them through pip if it asks for them. We recommend using the Anaconda Python 3 distribution, it contains most of the dependencies.
Windows Users - You’ll need to download a C compiler, if you want to use ISAMBARD. This is because we use a package called Cython to make the code run fast. The exact version of Microsoft Visual C++ compiler depends on the python version that you are using. Here are the installation instructions.
You can also use MinGW, but it’s not currently supported. `Instructions here <http://cython.readthedocs.io/en/latest/src/tutorial/appendix.html>`__.
To get the most out of ISAMBARD, a couple of external programs are recommended:
- Scwrl4 - Used to pack sidechains, it’s fast and accurate. Free for non-commercial use.
- DSSP - Used to find secondary structure in models. Free to download.
When you first import ISAMBARD you’ll be asked to give paths to the executables for the dependencies. These are not required to use ISAMBARD, if you don’t want to use any of them, just leave the path blank. Once you’ve finished setting your paths and some other options, a small file called .isambard_settings will be made in your home directory, which contains your settings. If you ever want to rerun the configure script that runs when you first import, you can run the following command:
import isambard isambard.settings.configure()
Chat with us on Gitter if you get stuck (link above), or raise an issue!
Once ISAMBARD is installed…
You might want to take a look at the wiki, there are a range of tutorials that demonstrate various aspects of ISAMBARD. These are IPython notebooks, so please download them and run through them (modify/hack/break them) on your own machine.
Wanting to delve a bit deeper? Take a look at the docs to find out more of the features in ISAMBARD, or just take a look through the code base and hack around. Remember, feel free to contact us on Gitter, email or through the issues if you get stuck.
To ensure that the package is correctly installed unit tests can be run by:
python -m unittest discover unit_tests/
Improved error handling for Residue.backbone.
Adds a large amount of documentation.
Adds new functionality for working with non-canonical amino acids.
ISAMBARD now contains an add ons module containing code for structural analysis of coiled coils.
The release contains a range of tweaks and bug fixes, including a major bug in the model building of anti-parallel helices in coiled coils.
- Derek N. Woolfson
- Email: email@example.com
Developers - Core Dev Team
- Gail J. Bartlett
- Email: firstname.lastname@example.org
- Jack W. Heal
- Email: email@example.com
- Twitter: @JackHeal
- Kieran L. Hudson
- Email: firstname.lastname@example.org
- Andrew R. Thomson
- Email: email@example.com
- Christopher W. Wood
- Email: firstname.lastname@example.org
- Twitter: @ChrisWellsWood
- Caitlin Edgell
- Kathryn L. Porter Goff
BUDE Dev Team
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|File Name & Checksum SHA256 Checksum Help||Version||File Type||Upload Date|
|isambard-2017.2.2-cp35-cp35m-macosx_10_7_x86_64.whl (2.0 MB) Copy SHA256 Checksum SHA256||cp35||Wheel||Aug 16, 2017|
|isambard-2017.2.2-cp35-cp35m-win_amd64.whl (1.9 MB) Copy SHA256 Checksum SHA256||cp35||Wheel||Aug 16, 2017|
|isambard-2017.2.2-cp36-cp36m-macosx_10_7_x86_64.whl (2.2 MB) Copy SHA256 Checksum SHA256||cp36||Wheel||Aug 16, 2017|
|isambard-2017.2.2.tar.gz (1.3 MB) Copy SHA256 Checksum SHA256||–||Source||Aug 16, 2017|