cbmpy-metadraft

CBMPy Metadraft: a flexible and extensible, GUI-based genome-scale model reconstruction tool that supports multiple Systems Biology standards.

UPDATE: July 2024

Metadraft has had a core dependency on the legacy BLAST executables that are now not available or don't work for many new OS versions. I am in the process of rewriting a core part of Metadraft that will remove this dependency, and many others, and simplify its installation. A new release will include a prototype of this fucntionality ... watch this space.

I've also renamed the default branch to 'main' if you have existing clones, either reclone or do the following to update your base branch: shell git branch -m master main git fetch origin git branch -u origin/main main git remote set-head origin -a - Brett

If you clone the Metadraft repository please be sure to include the modelDB modules

Shell cd cbmpy-metadraft git submodule update --init --remote -- modeldb/2019-1/ If you want to switch back to the 2018-1 library and results please edit the _metadraft.cfg file and change the value of the "metadraft_db_version" key to "2018-1" (it is currently set to "2019-1").

• 0.9.7 removes the SIP dependency and is Python 3.10 compatible.

Installation and system dependencies

NEW: The MetaDraft User Guide is now available online and for download from the MetaDraft website.

System dependencies

MetaDraft requires working versions of Python, Perl, Java and NCBI Blast2. Once you have downloaded MetaDraft and it's Python dependencies, please run the system test script to that can be found in the MetaDraft directory python systemtest.py.

Typically the default Java runtime (JRE) installed on your system is all that is require, for Windows this can be obtained from [https://www.java.com/]. On Linux please use your favourite package manager, for example, when using Ubuntu/Debian based oeprating systems, try sudo apt-get install default-jre.

MetaDraft has been successfully tested using Windows 10/11, Ubuntu Linux and is developed on Windows 11 using Anaconda Python 3.10 with PyQt5.

Getting MetaDraft

To install the latest version of MetaDraft, download from GitHub ([https://github.com/SystemsBioinformatics/cbmpy-metadraft]) or directly clone a repository (requires git to be installed).

Clone the cbmpy-metadraft git repository:

shell git clone https://github.com/SystemsBioinformatics/cbmpy-metadraft.git

Getting and installing the MetaDraft template library

MetaDraft ships with a single model template, if you have cloned the repository you can activate the current template set, based on the BiGG2 repository, change into the MetaDraft directory and activate the template submodule:

shell cd cbmpy-metadraft git submodule update --init --remote -- modeldb/2019-1/

If you have downloaded master repository as a zip file or as a release, download the template-models-2019-1.zip template archive provided with the latest release. Unzip this archive into the metadraft/modeldb directory.

MetaDraft is archived on Zenodo, please see CITATION.cff for more details

For the latest code and development pull requests

Once you have cloned the cbmpy-metadraft repository and installed the DB module, switch to the development branch:

shell git checkout dev git pull

You are now working in the development branch where anything can happen and the code can change often, please do a regular git pull. Please use this branch as the base for any metadraft pull requests (PR's).

Creating a custom Anaconda Python environment

You have now downloaded the latest version of MetaDraft, next please run the system test script python systemtest.py to check your installation and then proceed to install the required Python dependencies. How you do this will depend on whether you use Conda or PIP.

The following commands will create custom virtual environments with all the Python dependencies needed to run MetaDraft. It is also possible to install the individual packages using "conda" or "pip" see the requirements.txt file for details of the required packages (see "pip" instructions below).

Setting up a Python 3 CONDA environment (recommended)

Creating the environment, this should work on all operating systems. Open a terminal and type:

shell conda env create -f environment.yml conda activate metadraft3

One Windows run the system test (optional) and start MetaDraft:

shell runwin.bat

One Linux run the system test (optional) and start MetaDraft:

shell sh ./run.sh

Adding the the core packages (minimal) to an existing CONDA environment:

shell conda install -c bgoli -c conda-forge pyqt5-sip pyqt python-libsbml xlrd xlwt cbmpy biopython

Using PyPI to install Python dependencies

For Python 3

Using PyPI it is only possible to use Python 3. You can install the packages useing the requirements.txt file (recommended):

shell pip install -r requirements.txt

Software citation

Please cite this software if you use it (the author(s) enthusiasm to carry on maintaining this project depend on it), see CITATION.cff for more details.

text Brett G. Olivier. (2019, October 8). SystemsBioinformatics/cbmpy-metadraft: Metadraft. Zenodo. http://doi.org/10.5281/zenodo.2398336

(C) Brett G. Olivier (b.g.olivier@vu.nl), Vrije Universiteit Amsterdam, Amsterdam, July 2023. Licence CC-BY 4.0