REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical Commercial Assays
Amaxa P3 Primary Cell 4D-Nucleofector X Kit S	Lonza	V4XP-3032
4D-Nucleofector Core Unit	Lonza	AAF-1002B
4D-Nucleofector X Unit	Lonza	AAF-1002X
MiSeq Reagent Kit v2 (300-cycles)	Illumina	MS-102-2002
MiSeq Sequencing System	Illumina	N/A
QuickExtract DNA Extraction Solution	Lucigen	QE09050
Cell Culture Lysis Reagent	Promega	E1531
Luciferase Assay Reagent	Promega	E1500
Deposited Data
P. berghei relative growth rate phenotypes in blood stages	Bushell et al., 2017	https://doi.org/10.1016/j.cell.2017.06.030
P. berghei RNA-seq data in blood stages	Otto et al., 2014	https://doi.org/10.1186/s12915-014-0086-0
P. berghei RNA-seq data in liver stages	Caldelari et al., 2019	https://doi.org/10.1186/s12936-019-2968-7
Compiled metabolomics dataset from P. falciparum	Chiappino-Pepe et al., 2017a	https://doi.org/10.1371/journal.pcbi.1005397
P. berghei ANKA protein sequences (fasta file)	PlasmoDB	Release 26
K-orthology groups sequences for enzymatic functional annotation	KEGG database	2015
Genome-scale metabolic model of P. falciparum iPfa	Chiappino-Pepe et al., 2017a	https://doi.org/10.1371/journal.pcbi.1005397
P. falciparum 3D7 protein sequences (fasta file)	PlasmoDB	Release 11.1
The ATLAS of Biochemistry	https://lcsb-databases.epfl.ch/atlas/	2018
Metabolic reactions in the malaria parasites	MPMP database	2016-2018
Reactions producing iron sulfur clusters	iJO1366	N/A
Experimental Models: Cell Lines
Arrayed library of E. coli TSA cells harboring linear plasmids containing P. berghei gene targeting vectors.	PlasmoGEM resource	https://plasmogem.sanger.ac.uk/search
HeLa cells	ECACC	93021013
Experimental Models: Organisms/Strains
Rat: RCC Han Wistar outbred (female)	Envigo+++	RccHan:WIST
Mouse: BALB/c inbred (female)	WTSI & Envigo & Janvier	BALB/cOlaHsd
Mouse: C57BL/6JRj	Janvier	C57BL/6JRj
Mouse: OF1 mice	Charles River	OF1, 612
P. berghei: ANKA cl15cy1 wild-type parasites	N/A	cl15cy1
PbANKA-mCherryhsp70+Luceef1α(1868cl1)	Prado et al., 2015	www.pberghei.eu (RMgm-1320)
PbmCherry	Burda et al., 2015	www.pberghei.eu (RMgm-928)
E. coli: BigEasy-TSA	Lucigen	60224
Anopheles stephensi mosquitoes, STE2	MR4, BEI resources	MRA-128
Software and Algorithms
TEX-FBA	www.github.com/EPFL-LCSB/texfba	1.0
matTFA	www.github.com/EPFL-LCSB/matTFA	1.0
MATLAB	Mathworks	R2016a and R2017a
CPLEX	IBM	12.71
COBRA Toolbox (used updated version within matTFA)	https://opencobra.github.io/cobratoolbox/stable/	2.0
RAVEN Toolbox	https://github.com/SysBioChalmers/RAVEN	1.08
The R Project for Statistical Computing	https://www.r-project.org/	3.5.0
Tidyverse	https://www.tidyverse.org/	1.2.1
TargetP	http://www.cbs.dtu.dk/services/TargetP/	1.1
MitoProtII	https://ihg.gsf.de/ihg/mitoprot.html	1.101
ApicoAP	https://bitbucket.org/wsu_bcb/apicoap/src/master/	2.0