IOCBio Kinetics
Project description
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
expected that pip
solution would work for Mac as well.
For Windows, conda
solution is recommended for users that don't have
Python installed already. Otherwise, if using other than Anaconda
Python, consider using pip
solution.
pip
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 pip3
command
below with 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 PATH
.
If the command is missing after installation, check whether the default location
of pip3
installation is in your path. For Linux, it should be ~/.local/bin
.
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://git@gitlab.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 .
Note that --user
is recommended to avoid messing up the system
packages.
For upgrade, add --upgrade
after install keyword. For example,
pip3 install --upgrade --user git+https://gitlab.com/iocbio/kinetics
or
python3 -m pip install --upgrade --user git+ssh://git@gitlab.com/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.
Installation Anaconda
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:
- conda-forge
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
iocbio-kinetics
in Anaconda/Scripts
directory. For convenience, a
shortcut can be created on desktop or Start Menu by the user.
Use with R
If iocbio-banova
is used, some additional packges are needed. Install them following packages in R:
install.packages(c("tidyverse", "BayesFactor"))
Making packages
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 .
in packaging/conda
subfolder.
Copyright
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 markov@sysbio.ioc.ee
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