iocbio.kinetics 1.0.1

IOCBio Kinetics

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://[e-mail]/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://[e-mail]/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 [e-mail]