Release 2017-02 (beta) is the first public release of the PhenoMeNal services. It is the output of 1.5 years of the work conducted in the H2020 project [PhenoMeNal (target site decommissioned)] which stands for Phenome and Metabolome aNalysis. Although properly tested and monitored using our [continuous integration pipeline (target site decommissioned)] it should be used with caution.

Services

Service	Container	Tag	Maintainer	Affiliation	Docs
Galaxy	container-galaxy-k8s-runtime	[v16.07-pheno_cv0.1 (target site decommissioned)]	P. Moreno, L. Pireddu, P. Roger Mele	EMBL-EBI, CRS4, CEA
Jupyter	container-jupyter	[v387f29b6ca83_cv0.4 (target site decommissioned)]	P. Moreno, M. Capuccini	EMBL-EBI, Uppsala University
Luigi	container-luigi	[v2.6.0_cv0.1 (target site decommissioned)]	Marco Capuccini	Uppsala University

Container Tools

Tool	Container	Tag	Maintainer	Affiliation	Docs
batman	container-batman	[v1.2.1.0.7_cv1.0 (target site decommissioned)]	P. Moreno, J. Gao	EMBL-EBI, Imperial College London
ms-vfetc	container-ms-vfetc	[v0.4_cv1.3 (target site decommissioned)]	Michael van Vliet	Leiden University	docs
iso2flux	container-iso2flux	[v0.2_cv1.0 (target site decommissioned)]	Pablo Moreno	EMBL-EBI
ramid	container-ramid	[v1.0_cv0.1 (target site decommissioned)]	Pablo Moreno	EMBL-EBI
midcor	container-midcor	[v1.0_cv0.2 (target site decommissioned)]	Pablo Moreno	EMBL-EBI
mtbls-dwnloader	container-scp-aspera	[v3.5.4.102989-linux-64_cv0.1 (target site decommissioned)]	Pablo Moreno	EMBL-EBI
nmrml2isa	container-nmrml2isa	[v0.3.0_cv0.1 (target site decommissioned)]	P. Moreno, T. Lawson	EMBL-EBI, U. of Birmingham
mzml2isa	container-mzml2isa	[v0.4.28_cv0.2 (target site decommissioned)]	P. Moreno, K. Peters	EMBL-EBI, IPB Halle
metfrag-cli	container-metfrag-cli	[v2.4.2_cv0.2 (target site decommissioned)]	Kristian Peters	IPB Halle
w4m - MetaboLights Downloader	container-mtbls-dwnld	[v1.2.0_cv1.1 (target site decommissioned)]	Pierrick Roger Mele	CEA
w4m - univariate	container-univariate	[v2.2.3_cv1.2 (target site decommissioned)]	Pierrick Roger Mele	CEA
w4m - multivariate	container-multivariate	[v2.3.10_cv1.1 (target site decommissioned)]	Pierrick Roger Mele	CEA
w4m - biosigner	container-biosigner	[v2.2.7_cv1.1 (target site decommissioned)]	Pierrick Roger Mele	CEA
w4m - LC/MS matching	container-lcmsmatching	[v3.1.6_cv1.3 (target site decommissioned)]	Pierrick Roger Mele	CEA
metabolite ID converter	container-MetaboliteIDConverter	[v0.5.1_cv1.0 (target site decommissioned)]	Benjamin Merlet	INRA
NMRMLConv	container-nmrmlconv	[v1.1b_cv0.1 (target site decommissioned)]	Kristian Peters	IPB
metfrag-cli	container-metfrag	[v2.4.2_cv0.2 (target site decommissioned)]	C. Ruttkies, K. Peters	IPB Halle
xcms	container-xcms	[v1.50.1_cv0.4 (target site decommissioned)]	K. Peters, P. Moreno	IPB Halle, EMBL-EBI
MetaboLights ASCP	container-scp-aspera	[v3.5.4.102989-linux-64_cv0.1 (target site decommissioned)]	Pablo Moreno	EMBL-EBI
metabomatching	container-metabomatching	[v0.1.0_cv0.3 (target site decommissioned)]	Rico Rueedi	Unil

Note: maintainers are for containers, not necessarily tool authors.

Workflows

Workflow	PI	Maintainer	Affiliation	Docs
Sacurine workflow	Etienne Thévenot	Pierrick Roger-Mele	CEA	docs
C13 Stationary Fluxomics	Prof. Marta Cascante	Pedro de Atauri, Pablo Moreno	Universitat de Barcelona, EMBL-EBI

Deployment systems

Name	Version	Use case	Maintainer	Affiliation
KubeNow		Manual deployment on OpenStack, AWS, GCE	Marco Capuccini, Anders Larsson	Uppsala University
EBI Portal		Automates deployment of KubeNow on cloud providers	Jose Dianes, Amelie Cornelis, Dario Vianello, Gianni Dalla Torre	EMBL-EBI
PhenoMeNal VRE Gateway		Automated deployment of KubeNow on cloud providers	Sijin He, Pablo Moreno, Kenneth Haug	EMBL-EBI

Supported cloud providers

Provider	Docs
Google Cloud Platform	portal/direct deployment