kinaid 1.1.0

KINAID : Kinase Activity and Inference Dashboard

KINAID

Public webserver version

https://kinaid.princeton.edu

Install library

python3 -m pip install kinaid

install resources

can take up to 3GB HDD memory.

Requires the following libraries

• biopython

• dash

• dash-cytoscape

• mpire

• numpy

• openpyxl

• pandas

• pyxlsb

• scipy

• statsmodels

  cd <DIRECTORY TO INSTALL KINAID RESOURCES>
  kinaid-install
  

add additional organism

Choose organism from DIOPT https://www.flyrnai.org/diopt

usage: kinaid-add [-h] [--organism_name ORGANISM_NAME] [--taxon_id TAXON_ID] [--orthologs_dir ORTHOLOGS_DIR]
                  [--human_kinases_database_file HUMAN_KINASES_DATABASE_FILE] [--threads THREADS]

options:
  -h, --help            show this help message and exit
  --organism_name ORGANISM_NAME
                        Name of organism
  --taxon_id TAXON_ID   DIOPT Taxon ID of organism
  --orthologs_dir ORTHOLOGS_DIR
                        Directory to store ortholog files
  --human_kinases_database_file HUMAN_KINASES_DATABASE_FILE
                        File containing human kinases database
  --threads THREADS     Number of threads to use

Example

kinaid-add --organism_name clawed_frog --taxon_id 8364 --threads 4

Private webserver version

• clone this repository
• change to kinaid root directory

install resources

can take up to 3GB HDD memory.

python3 -m kinaid.utility --threads 4

run dashboard

usage: dashboard.py [-h] [--port PORT] [--host HOST] [--no_debug]

options:
-h, --help   show this help message and exit
--port PORT
--host HOST
--no_debug

python3 dashboard.py

Examples

sandbox.ipynb

basic examples of loading phosphoproteomics data and running library version of kinaid

yeast_tests.ipynb

notebook to generate yeast experiment data for Supplementary Table 4. The data must be loaded by the dashboard.

offline_tests.ipynb

notebook to generate and run experiments for Supplementary Table 3. This experiment evaluated the performance of the library and not the dashboard.