diff --git a/README.md b/README.md
index 3050e65..848fed9 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 
 | MacOS / Linux | Windows | License | Test Coverage | Documentation | Lifecycle |
 | --- | ---- | ------ | ------ | ---- |
-|[![Travis](https://img.shields.io/travis/compbiocore/VariantVisualization.jl/master.svg?style=flat-square)](https://travis-ci.org/compbiocore/VariantVisualization.jl)|[![Build status](https://ci.appveyor.com/api/projects/status/67hyn6rckulwr2dj/branch/master?svg=true)](https://ci.appveyor.com/project/fernandogelin/variantvisualization-jl/branch/master)|[![License](https://img.shields.io/badge/license-MIT-orange.svg?style=flat-square)](https://github.com/compbiocore/VariantVisualization.jl/blob/clean-up/LICENSE.md)|[![Codecov](https://img.shields.io/codecov/c/github/compbiocore/VariantVisualization.jl.svg?style=flat-square)](https://codecov.io/gh/compbiocore/VariantVisualization.jl/branch/master) | [![Docs](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://compbiocore.github.io/VariantVisualization.jl/stable) [![Docs](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://compbiocore.github.io/VariantVisualization.jl/latest) | ![Lifecycle](https://img.shields.io/badge/lifecycle-active-green.svg?style=flat-square) |
+|[![Travis](https://img.shields.io/travis/compbiocore/VariantVisualization.jl/master.svg?style=flat-square)](https://travis-ci.org/compbiocore/VariantVisualization.jl)|[![Build status](https://ci.appveyor.com/api/projects/status/67hyn6rckulwr2dj/branch/master?svg=true)](https://ci.appveyor.com/project/fernandogelin/variantvisualization-jl/branch/master)|[![License](https://img.shields.io/badge/license-MIT-orange.svg?style=flat-square)](https://github.com/compbiocore/VariantVisualization.jl/blob/clean-up/LICENSE.md)|[![Coverage Status](https://coveralls.io/repos/github/compbiocore/VariantVisualization.jl/badge.svg?branch=master)](https://coveralls.io/github/compbiocore/VariantVisualization.jl?branch=master)|[![Docs](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://compbiocore.github.io/VariantVisualization.jl/stable) [![Docs](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://compbiocore.github.io/VariantVisualization.jl/latest) | ![Lifecycle](https://img.shields.io/badge/lifecycle-active-green.svg?style=flat-square) |
 
 ## Overview
 
diff --git a/src/VariantVisualization.jl b/src/VariantVisualization.jl
index bd50bde..625dfe2 100644
--- a/src/VariantVisualization.jl
+++ b/src/VariantVisualization.jl
@@ -49,7 +49,6 @@ export
     translate_genotype_to_num_array,
     translate_readdepth_strings_to_num_array,
     genotype_heatmap_with_groups,
-    jupyter_main_new,
     returnXY_column1!,
     pass_genomic_range_siglist_filter,
     pass_genomic_range_filter,
diff --git a/src/batch_julia_runtimes.jl b/src/batch_julia_runtimes.jl
deleted file mode 100644
index 3090e00..0000000
--- a/src/batch_julia_runtimes.jl
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/bin/bash
-#=
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf -l test/test_files/significantList_for_proteinstructures.csv --heatmap genotype`)
-println("time to run sig_list heatmap:")
-toc()
-
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf -r chr1:0-400000000 --heatmap genotype`)
-println("time to run chromosome range heatmap:")
-toc()
-
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf --pass_filter -r chr1:0-400000000 --heatmap genotype`)
-println("time to run pass filter and chromosome range heatmap:")
-toc()
-
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf --pass_filter -x test/test_files/select_column_list.txt --heatmap genotype`)
-println("time to run pass filter select 4 patients heatmap:")
-toc()
-=#
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf --pass_filter --group_samples test/test_files/sample_phenotype_matrix.csv control,case --heatmap genotype`)
-println("time to run pass filter group samples by trait heatmap:")
-toc()
-
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf -l test/test_files/significantList_for_proteinstructures.csv --heatmap genotype --avg_dp samples`)
-println("time to run sig_list heatmap and avg dp scatter plot for samples:")
-toc()
-
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf -l test/test_files/significantList_for_proteinstructures.csv --heatmap genotype --avg_dp samples`)
-println("time to run sig_list heatmap and avg dp scatter plot for variants:")
-toc()
-
-tic()
-run(`julia viva_cli.jl -f combine_haplo-exo_AC_gatk406.vcf -x test/test_files/select_column_list.txt --heatmap genotype`)
-println("time to run select columns with no filters heatmap:")
-toc()
diff --git a/src/open_jupyter_notebook.jl b/src/open_jupyter_notebook.jl
deleted file mode 100644
index bcac03b..0000000
--- a/src/open_jupyter_notebook.jl
+++ /dev/null
@@ -1,2 +0,0 @@
-using IJulia
-notebook()