= MOLGENIS suite overview: modules and products =
Here you can find summaries and links on the components listed in the ticket system. In the software, these components become packages. For example: org.molgenis.db for shared pacakes or org.col7a1 for application specific packages. We distinguish two groups of components as listed below. Also the use of '''keywords''' is explained which we use to clarify relationships from shared packages to application. For example: tickets in the 'auth' component can be marked with keywords 'animaldb' to enable tracking by the animaldb team.

|| ||end product: || '''[wiki:PhenoFlow biobankcatalog]''' || '''[wiki:AnimaldbStart animaldb]''' || '''ngs''' || '''[wiki:MutationStart mutationdb]''' || '''[wiki:XgapStart xqtl]''' || '''[wiki:ImputationStart gwas]''' || '''mass_spec''' || '''[wiki:MageStart microarray]''' ||
|| || lead: || joris, despoina || erik || freerk, jessica, wil || robert || joeri, danny || alex, roan || george || alex jessica ||
|| [[BR]][[BR]][[BR]]module: || users:[[BR]][[BR]][[BR]] || lifelines [[BR]]bbmri [[BR]]bioshare[[BR]]nbic || fwn[[BR]][[BR]][[BR]] || bbrmi [[BR]]medgen[[BR]]nbic[[BR]] || nbic [[BR]]col7a1 [[BR]]chd7[[BR]] || panacea [[BR]]euratrans[[BR]]bioshare[[BR]]sysgenet || lifelines[[BR]]bioshare[[BR]]medgen[[BR]] || nbic[[BR]]npc[[BR]]fwn[[BR]] || bbmri[[BR]][[BR]][[BR]] ||
|| '''db''' || morris, joris || y || y || y || y || y || y || y || y ||
|| '''ui''' || erik || y || y || y || y || y || y || y || y ||
|| '''[DataModel datamodel]''' || morris, erik, joeri || y || y || y || y || y || y || y || y ||
|| '''[ConvertorModule convertor]''' || joeri roan || y || || || || y || y || || y ||
||'''[AuthModule auth]''' ||robert, erik || y || y || y || y || y || y || y || y ||
||'''[SearchModule search]''' || despoina || y || y || || || || || || ||
||'''[MatrixModule matrix]''' || joeri, joris || y || y || || y || || || || ||
||'''[LimsModule lims]''' || erik, jessica, joris || || y || y || || || || || ||
|| '''[PipelineModule pipeline]''' || joeri, george, morris || || || y || || y || y || y || ||
|| '''ngs_pipeline''' || freerk wil || || || || || || || || ||
|| '''trac''' || roan despoina || || || || || || || || ||
|| '''servers''' || ger, robert, freerk, joeri || y || y || y || y || y || y || y || y ||

{{{#!graphviz

digraph g {

  node [shape=box,style=filled,color=white] rankdir="RL"

  subgraph cluster_0 {

  style=filled; color=lightgrey; label = "partner & user groups";

  lifelines; bbmri; nbic; panacea; sysgenet; euratrans; gen2phen; gbic; medgen; fwn_chronobiology; npc_mass_spec_center; gids; col7a1;  chd7; amc_nbic;

  }

subgraph cluster_1 {

  style=filled; color=lightgrey; label = "apps"; biobankcatalog animaldb mutationdb xqtl_workbench ngs_workbench gwas_workbench ms_workbench ma_workbench jamboreecards

}

subgraph cluster_2 {

  style=filled; color=lightgrey; label = "molgenis"; phenoexplorer; db; ui; auth; molgenis; workbench; lims; convertors; datamodels; xgap; pheno;

}

#relations between projects and apps

col7a1 -> mutationdb; chd7 -> mutationdb;

fwn_chronobiology -> animaldb;

bbmri -> biobankcatalog;  nbic -> biobankcatalog; lifelines -> biobankcatalog; gen2phen -> biobankcatalog; gids -> biobankcatalog;

gbic -> xqtl_workbench; panacea -> xqtl_workbench; sysgenet -> xqtl_workbench; euratrans -> xqtl_workbench;

npc_mass_spec_center -> ms_workbench;

bbmri -> ngs_workbench; medgen -> ngs_workbench; medgen -> ngs_workbench;

bbmri -> ma_workbench;

bbmri -> gwas_workbench lifelines -> gwas_workbench; gids -> gwas_workbench; medgen -> gwas_workbench;

amc_nbic -> jamboreecards;

#relations between apps and components

ngs_workbench ->workbench; gwas_workbench -> workbench; xqtl_workbench -> workbench; ms_workbench -> workbench; ma_workbench -> workbench;

biobankcatalog -> phenoexplorer; animaldb -> phenoexplorer;  mutationdb -> phenoexplorer; workbench -> phenoexplorer;

animaldb -> lims; workbench -> lims;

workbench -> convertors;

jamboreecards -> molgenis;

#relations between components and sub-components

molgenis -> auth; molgenis -> db; molgenis -> ui;

lims -> datamodels; workbench -> datamodels; phenoexplorer -> datamodels; convertors -> datamodels;

datamodels -> molgenis; datamodels -> pheno; datamodels -> xgap;

}

}}}

== Shared components ==
these are reusable models (or 'semi-finished module) used across multiple molgenis applications.

||'''component''' ||'''summary''' ||'''used''' ||
||db ||molgenis database backend including mysql and jpa ||all systems ||
||ui ||molgenis user interface framework ||all systems ||
||compute ||molgenis compute framework including 'cluster' and 'script submission' tools ||impute, xqtl, ngs ||
||[wiki:XgapStart xgap] ||high-throughput low variability data model for markers, snps, probes, qtls etc ||xqtl-workbench, ngs-lims, gwas-workbench ||
||pheno ||low-throughput data model high variability data model for phenotypes ||col7a1, animaldb, biobank-warehouse ||
||data ||data model, user interface & back-end to browse and search available data in a matrix form ||col7a1, animaldb, biobank-warehouse ||
||convertors ||convertors that transform external file formats into org.molgenis data models so they can be imported automatically ||
||[wiki:AuthModule auth] ||Authentication and authorization plugin ||all systems ||

== Application components ==
These are specific applications (or 'end-product') build for a particular project or user group.

||'''application''' ||'''description''' ||'''projects that participate in this component''' ||
||data-explorer ||datawarehouse application to explore all available observation data ||lifelines, bbmri, gids, animaldb ||

== Dependencies and other keywords ==
Obviously there can be a dependency between components. For example, 'animaldb' depends on 'auth'. To make this dependency visible and queryable we use the keywords field. For example: if 'animaldb' and 'col7a1' both have a dependency on a ticket in the auth component this ticket will have keyewords 'animaldb col7a1'.