Kinetics analysis program
IOCBIO Kinetics is a cross-platform application for analysis of different traces, as described by its plugins. While originally developed for analysis of enzyme kinetics, the other types of traces can be analyzed as well.
IOCBIO Kinetics is written for use by Laboratory of Systems Biology, Department of Cybernetics, School of Science, Tallinn University of Technology. At present, the software is not distributed outside the laboratory and its use is permitted for laboratory personnel only.
Installation and Upgrade
There are several ways to install the software. The application requires python3.
For Linux, at present, installation using
pip is recommended. It is
pip solution would work for Mac as well.
conda solution is recommended for users that don't have
Python installed already. Otherwise, if using other than Anaconda
Python, consider using
To be able to install PyQt5 using pip, you have to use python3.5 or
higher. If not available in the system, you can replace
python3 -m pip.
To install published version, run
pip3 install --user iocbio.kinetics
This will install all dependencies and it is expected to add a command
iocbio-kinetics into your
If the command is missing after installation, check whether the default location
pip3 installation is in your path. For Linux, it should be
To install, use the Git repository directly, for HTTPS users:
pip3 install --user git+https://gitlab.com/iocbio/kinetics
and for SSH users:
python3 -m pip install --user git+ssh://email@example.com/iocbio/kinetics.git
For development, use
pip3 install --user -e .
in the source directory. To install the current version from the source, use
pip3 install --user .
--user is recommended to avoid messing up the system
For upgrade, add
--upgrade after install keyword. For example,
pip3 install --upgrade --user git+https://gitlab.com/iocbio/kinetics
python3 -m pip install --upgrade --user git+ssh://firstname.lastname@example.org/iocbio/kinetics.git
conda (Anaconda or Miniconda3)
Installation by conda is not supported at the moment. However, you can install Anaconda environment and then use pip3 solution above in Anaconda Prompt.
Install Anaconda Python environment by downloading it from https://www.anaconda.com/ . The package uses Python 3 language, so, the version supporting it should be installed. At the moment of writing, its Python 3.6.
Installation of channels
For installation from GUI:
- Start Anaconda Navigator
- Add channels by clicking "Channels" on the main screen and adding:
For installation from CLI, start Anaconda Prompt. In the prompt, add channels:
conda config --append channels conda-forge conda config --append channels iocbio
and install software
conda install -c iocbio iocbio-kinetics
and you are all set.
For running iocbio.kinetics in Windows, its possible to start it as an
application from Anaconda Navigator or, directly, from starting
Anaconda/Scripts directory. For convenience, a
shortcut can be created on desktop or Start Menu by the user.
Use with R
iocbio-banova is used, some additional packges are needed. Install them following packages in R:
For making source package, run
python3 setup.py sdist
For Conda packages, install conda (miniconda3 or anaconda3),
conda-build, and run
conda-build -c anaconda -c conda-forge .
Copyright (C) 2018 Laboratory of Systems Biology, Department of Cybernetics, School of Science, Tallinn University of Technology (https://sysbio.ioc.ee).
Software license: GPLv3, see LICENSE.
Contact: Marko Vendelin email@example.com
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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