Vladimir (Vlad) Kiselev wikiselev

🏠

Working from home

Building Scalable Bioinformatics & AI Solutions | Cloud Infrastructure, Pipelines & Data Science Expert, Single-Cell, Drug Discovery

wikiselev / create-azure-batch-pool-nf.py

Created December 15, 2022 16:25

A script to configure (file share and blob container mounting) and create an Azure Batch pool suitable for Nextflow Tower.

	from azure.identity import DefaultAzureCredential
	from azure.mgmt.batch import BatchManagementClient
	import os
	from dotenv import load_dotenv
	import sys

	load_dotenv()

	AZURE_SUBSCRIPTION_ID = os.getenv('AZURE_SUBSCRIPTION_ID')
	AZURE_BATCH_RESOURCE_GROUP_NAME = os.getenv('AZURE_BATCH_RESOURCE_GROUP_NAME')

wikiselev / easy-Report.sh

Created November 2, 2013 22:58

Quick run of easy-Report script All output files will be located in 'report' folder

	git clone https://github.com/wikiselev/easy-Report.git
	cd easy-Report
	Rscript easy-Report.R script.Rmd report

wikiselev / copasi_api_model_sbml_load.py

Created January 8, 2013 15:13

	# Acquire the model from an SBML file
	dataModel = CCopasiRootContainer.addDatamodel()
	dataModel.importSBML("model_name.xml")
	model = dataModel.getModel()

wikiselev / IGV_snapshot_combine.tex

Created October 19, 2012 15:57

Tex script to combine snapshot created by IGV genomic browser

	\documentclass[landscape,letterpaper]{article}

	\renewcommand{\rmdefault}{phv} % Arial
	\setlength{\oddsidemargin}{-0.9in}
	\setlength{\textwidth}{10.7in}
	\setlength{\textheight}{7in}
	\setlength{\topmargin}{-1.0in}
	\setlength{\headsep}{0.25in}
	\setlength{\parskip}{1.2ex}
	\setlength{\parindent}{0mm}

wikiselev / IGV_script.txt

Created October 19, 2012 15:37

Script for IGV automated snapshotting

	new

	load /Users/Vladimir/IGV/protein_list/protein1.BED,/Users/Vladimir/IGV/protein_list/protein2.BED # all other protein data files

	snapshotDirectory /Users/Vladimir/IGV/snapshots/

	goto gene1_location
	snapshot gene1.png

	goto gene2_location

wikiselev / gene_list

Created October 19, 2012 15:31

gene_list example

	# Examples of the values:
	gene1 # PTGS2
	gene1_full_name # Prostaglandin-endoperoxide synthase 2 (COX-2)
	gene1_url # http://www.ncbi.nlm.nih.gov/gene/5743
	gene1_location # chr1:186,640,920-186,641,060

	gene2
	gene2_full_name
	gene2_url
	gene2_location