paulklemm

import uMAIA
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import warnings
import os

# Define the path to save the data
workdir = '/beegfs/scratch/bruening_scratch/pklemm/2024-01-theodora/uMAIA/data_maldi'

paulklemm

renv::install("BiocManager", prompt = FALSE)
renv::install("languageserver", prompt = FALSE)
renv::install("tidyverse", prompt = FALSE)
renv::install("xaringan", prompt = FALSE)
renv::install("targets", prompt = FALSE)
renv::install("visNetwork", prompt = FALSE)
renv::install("httpgd", prompt = FALSE)
renv::install("patchwork", prompt = FALSE)
renv::install("devtools", prompt = FALSE)
renv::install("roxygen2", prompt = FALSE)

paulklemm

# See https://github.com/randy3k/rtichoke#settings
options(
    # auto match brackets and quotes
    rtichoke.auto_match = TRUE,
    # when using history search (ctrl-r/ctrl-s in emacs mode), do not show duplicate results
    rtichoke.history_search_no_duplicates = TRUE
)

paulklemm

// Future versions of Hyper may add additional config options,
// which will not automatically be merged into this file.
// See https://hyper.is#cfg for all currently supported options.

module.exports = {
  config: {
    // default font size in pixels for all tabs
    fontSize: 16,

    // font family with optional fallbacks

paulklemm

curl -sL https://github.com/seqan/flexbar/archive/v2.7.0.tar.gz | tar xz
# Download required libraries
curl -sL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/linux/tbb2017_20161128oss_lin_0.tgz | tar xz
curl -sL https://github.com/seqan/seqan/releases/download/seqan-v2.1.1/seqan-library-2.1.1.tar.xz | tar xJ
mv tbb2017_20161128oss/include flexbar-2.7.0
mv seqan-library-2.1.1/include/* flexbar-2.7.0/include
cd flexbar-2.7.0
cmake .
make

paulklemm

# Convert GFF3 to GTF file
wget ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/5.0/genome_coordinates/Mus_musculus.GRCm38.gff3.gz
gunzip --verbose Mus_musculus.GRCm38.gff3.gz

# Download gffread source and compile it
mkdir gffread_build
cd gffread_build
git clone https://github.com/gpertea/gclib
git clone https://github.com/gpertea/gffread
cd gffread

paulklemm

AC020968.3
AC021630.11
AC021667.21
AC024069.29
AC024608.4
AC024913.33
AC025622.3
AC025669.19
AC025794.9
AC025913.11

paulklemm

Keybase proof

I hereby claim:

• I am paulklemm on github.
• I am paulklemm (https://keybase.io/paulklemm) on keybase.
• I have a public key ASA2miJvr-QmLL17BrLg8v_l3dv3rxDDw5BgO5H357er6wo

To claim this, I am signing this object:

paulklemm

All criticized points were considered in the revision. I think the paper substantially improved. The distinction between `Kvik` and `Kvik Pathways` is made clear. A list of contributions makes it easier to follow the structure. I think you should consider putting the requirement analysis into a dedicated section.

I see nothing in the paper that gives me a reason to not approve it.

I have noticed two minor typos:
Abstract
Typo: Missing whitespace after sentence „Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.“
Implementation
Missing verb? „Kvik Pathways Cytoscape.js to create a pathway visualization from the list of nodes and edges and overlay the nodes on the pathway image.“
Apart from the paper, I have one comment on your response on my review w.r.t. the differences regarding the NIK paper. You stated that

paulklemm

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console