REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
FPKM for the time-series study (GSE148729)	MDC-berlin	https://filetransfer.mdc-berlin.de/?u=CVXckugR&p=MACT6Xw9
Read counts of the severity study (GSE147507)	NCBI GEO	https://ftp.ncbi.nlm.nih.gov/geo/series/GSE147nnn/GSE147507/suppl/GSE147507_RawReadCounts_Human.tsv.gz
Formulation of the viral biomass function	BioModels	https://www.ebi.ac.uk/biomodels/MODEL2003020001#Files
DrugBank V5	DrugBank	https://go.drugbank.com/releases/latest
Drug repurposing hub mode of actions	Clue.io	https://s3.amazonaws.com/data.clue.io/repurposing/downloads/repurposing_drugs_20200324.txt
GHDDI broad-spectrum antiviral agents	GHDDI	https://ghddiai.oss-cn-zhangjiakou.aliyuncs.com/file/Antivirus_Drug_Profile_k2.csvv
Recon 2	VMH	https://www.vmh.life/#downloadview
Recon3D	VMH	https://www.vmh.life/#downloadview
Software and algorithms
rFASTCORMICS	Pacheco et al. (2019)	https://github.com/sysbiolux/rFASTCORMICS
COBRA Toolbox	GitHub	https://github.com/opencobra/cobratoolbox/tree/master/src
IBM CPLEX solver		https://www.ibm.com/products/ilog-cplex-optimization-studio
RStudio		https://www.rstudio.com/
R CRAN (FactoMineR, networkD3, ggplot2 & dependencies)		https://cran.r-project.org/
Bioconductor (edgeR, DESeq2 & dependencies)		https://www.bioconductor.org/