README.md 2.27 KB
Newer Older
Adelene Lai's avatar
Adelene Lai committed
1
2
3
4
5
6
7
8
9
10
11
12
13

# Additional Supporting Information

## Occurrence and Distribution of Pharmaceuticals and their Transformation Products in Luxembourgish Surface Waters 									

### Randolph R. Singh<sup>1†\*</sup>, Adelene Lai<sup>1,2</sup>, Jessy Krier<sup>1</sup>, Todor Kondic<sup>1</sup>, Philippe Diderich<sup>3</sup>, Emma L. Schymanski<sup>1\*</sup>							



<sup>1</sup> Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg
<sup>2</sup>Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743, Jena, Germany
<sup>3</sup> Water Management Agency, Ministry of the Environment, Climate and Sustainable Development, Luxembourg
<sup></sup> Current affiliation: IFREMER (Institut Français de Recherche pour l’Exploitation de la Mer), Laboratory of Biogeochemistry of Organic Contaminants, Rue de l’Ile d’Yeu, BP 21105,Nantes Cedex 3, 44311, France															
Adelene Lai's avatar
Adelene Lai committed
14
\* Corresponding authors: RRS: randolph.singh@ifremer.fr and ELS: emma.schymanski@uni.lu 		
Adelene Lai's avatar
Adelene Lai committed
15
16
17
18


------
Please cite the code in this repository as:
Adelene Lai's avatar
Adelene Lai committed
19
(placeholder for Zenodo DOI)
Adelene Lai's avatar
Adelene Lai committed
20
------
Adelene Lai's avatar
Adelene Lai committed
21
22
23



Adelene Lai's avatar
Adelene Lai committed
24
25
26
27
28
29
30
31
32
33
This repository contains Additional Supporting Information to the above manuscript. It contains all code and inputs used as described in detail in the Methods section of the manuscript. It is organised into three subdirectories respectively:

1. `metfrag/`						#.R script to run MetFrag as described in Methods section
2. `tps/`						    #generate a Suspect List of pharmaceutical transformation products mined from PubChem
3. `figures/`						#visualise data and generate Figures 2, 3, 4, and 5 in the manuscript


Besides all necessary input files and code, all outputs generated have also been included for completeness.

In `tps/` and `figures/`, all code was originally written and run in Jupyter Notebooks (.ipynb). These Notebook files contain rich explanatory text written using Markdown that is interspersed between cells. Users are recommended to clone this repository and open the original Notebook files on their local machine, as GitLab has documented issues rendering Notebooks properly. However, those unable to open Notebooks locally can view them as rendered .html files which have been included in the subdirs. The code in the Notebooks has also been provided as .R files.