diff --git a/.jenkins/build-pod.yaml b/.jenkins/build-pod.yaml new file mode 100644 index 0000000..4dfbab9 --- /dev/null +++ b/.jenkins/build-pod.yaml @@ -0,0 +1,17 @@ +apiVersion: v1 +kind: Pod +metadata: + name: jenkins-agent +spec: + containers: + - name: jekyll + image: molgenis/jekyll:1.1.2 + imagePullPolicy: IfNotPresent + command: + - cat + tty: true + resources: + requests: + cpu: "1" + memory: "1Gi" + restartPolicy: Never \ No newline at end of file diff --git a/CNAME b/CNAME new file mode 100644 index 0000000..a7b6c19 --- /dev/null +++ b/CNAME @@ -0,0 +1 @@ +molgenis.org \ No newline at end of file diff --git a/MOLGENIS_Privacy_Policy.pdf b/MOLGENIS_Privacy_Policy.pdf index da33352..bcf297b 100644 Binary files a/MOLGENIS_Privacy_Policy.pdf and b/MOLGENIS_Privacy_Policy.pdf differ diff --git a/deploy/nginx/redirect.conf b/deploy/nginx/redirect.conf index 570f3c8..b29a074 100644 --- a/deploy/nginx/redirect.conf +++ b/deploy/nginx/redirect.conf @@ -11,18 +11,15 @@ # EXPIRES: 01-01-2019 # rewrite ^/path https://www.example.com permanent; - - - # DESCRIPTION: Download server that provides data for all research we do on GCC # MAINTAINER: ops-team, data-team # EXPIRES: never -rewrite ^/downloads(.*) https://molgenis26.gcc.rug.nl/downloads/$1 permanent; +rewrite ^/downloads(.*) https://download.molgeniscloud.org/downloads/$1 permanent; # DESCRIPTION: Contains the releases for all our customer artifacts # MAINTAINER: ops-team # EXPIRES: never -rewrite ^/releases https://molgenis26.gcc.rug.nl/releases permanent; +rewrite ^/releases https://download.molgeniscloud.org/releases permanent; # DESCRIPTION: This is our system genetics information page # MAINTAINER: Morris Swertz @@ -42,48 +39,48 @@ rewrite ^/jenkins http://jenkins.dev.molgenis.org/ permanent; # DESCRIPTION: ? # MAINTAINER: ? # EXPIRES: ? -rewrite ^/regenotyper https://molgenis26.gcc.rug.nl/downloads/regenotyper permanent; +rewrite ^/regenotyper https://download.molgeniscloud.org/downloads/regenotyper permanent; # DESCRIPTION: The documentation of all our processes and workflows. # The ticket system trac is here hosted as well. # MAINTAINER: dev-team, Morris Swertz # EXPIRES: never -rewrite ^/wiki http://wiki.gcc.rug.nl permanent; +rewrite ^/wiki http://trac.molgeniscloud.org permanent; # DESCRIPTION: Redirect to reports at trac # MAINTAINER: dev-team, Morris Swertz # EXPIRES: never -rewrite ^/report http://wiki.gcc.rug.nl/report permanent; +rewrite ^/report http://trac.molgeniscloud.org/report permanent; # DESCRIPTION: Tickets at trac ticket/xxxx # MAINTAINER: dev-team, Morris Swertz # EXPIRES: never -rewrite ^/ticket http://wiki.gcc.rug.nl/ticket permanent; +rewrite ^/ticket http://trac.molgeniscloud.org/ticket permanent; # DESCRIPTION: The research documentation # MAINTAINER: Morris Swertz # EXPIRES: never -rewrite ^/research http://wiki.gcc.rug.nl/wiki/research permanent; +rewrite ^/research http://trac.molgeniscloud.org/wiki/research permanent; # DESCRIPTION: xQTL documentation # MAINTAINER: Joeri van der Velde? # EXPIRES: never -rewrite ^/xqtl http://wiki.gcc.rug.nl/wiki/xQTL permanent; +rewrite ^/xqtl http://trac.molgeniscloud.org/wiki/xQTL permanent; # DESCRIPTION: Diagnostic workflow documentation # MAINTAINER: Morris Swertz # EXPIRES: never -rewrite ^/diagnostic http://wiki.gcc.rug.nl/wiki/diagnostic permanent; +rewrite ^/diagnostic http://trac.molgeniscloud.org/wiki/diagnostic permanent; # DESCRIPTION: 5GPM # MAINTAINER: Morris Swertz # EXPIRES: never -rewrite ^/5gpm http://wiki.gcc.rug.nl/wiki/5gpm permanent; +rewrite ^/5gpm http://trac.molgeniscloud.org/wiki/5gpm permanent; # DESCRIPTION: Genomics documentation # MAINTAINER: Morris Swertz # EXPIRES: never -rewrite ^/genomics http://wiki.gcc.rug.nl/wiki/genomics permanent; +rewrite ^/genomics http://trac.molgeniscloud.org/wiki/genomics permanent; # DESCRIPTION: MOLGENIS server list # MAINTAINER: data-team, @@ -97,19 +94,19 @@ rewrite ^/molgenis-imputation https://molgenis.github.io/molgenis-imputation p # DESCRIPTION: Genomics documentation # MAINTAINER: Chao Pang -# EXPIRES: never -rewrite ^/connect https://molgenis17.gcc.rug.nl permanent; +# EXPIRES: 09-09-2021 +rewrite ^/connect https://molgenis.org/retired_server_molgenis_connect.html permanent; # DESCRIPTION: SORTA annotation tool # MAINTAINER: Chao Pang # EXPIRES: never -rewrite ^/sorta https://molgenis19.gcc.rug.nl permanent; +rewrite ^/sorta https://sorta.molgeniscloud.org permanent; # Deprecated? # DESCRIPTION: SNP Visualization Diagnostics -# MAINTAINER: data-team +# MAINTAINER: Connor Stroomberg # SINCE: 01-01-2017 -rewrite ^/upd-tool https://molgenis74.gcc.rug.nl/menu/main/apps/aaaacxzu6j3or6qwhzap6qyaae permanent; +rewrite ^/upd-tool https://snptool.molgeniscloud.org permanent; # DESCRIPTION: Ase # MAINTAINER: Patrick Deelen @@ -131,26 +128,16 @@ rewrite ^/capice https://capice.molgeniscloud.org permanent; # EXPIRES: ? rewrite ^/vkgl https://vkgl.molgeniscloud.org permanent; -# DESCRIPTION: Glia Open Access Database (GOAD) -# MAINTAINER: Dennis Hendriksen -# EXPIRES: ? -rewrite ^/goad https://molgenis13.gcc.rug.nl permanent; - # DESCRIPTION: E-rare -# MAINTAINER: data-team +# MAINTAINER: Marielle v Gijn # EXPIRES: ? -rewrite ^/said https://molgenis77.gcc.rug.nl permanent; +rewrite ^/said https://infevers.umai-montpellier.fr/web/index.php permanent; # DESCRIPTION: Global Screening Array # MAINTAINER: Joeri van der Velde # EXPIRES: ? rewrite ^/gsa https://gsa.molgeniscloud.org permanent; -# DESCRIPTION: Deconvolution -# MAINTAINER: Niek de Klein, Mericko Yang -# SINCE: 30-11-2018 -rewrite ^/deconvolution https://molgenis79.gcc.rug.nl/deconvolution permanent; - # DESCRIPTION: Human Pathway database # MAINTAINER: Miranda # EXPIRES: 12-02-2021 @@ -166,25 +153,22 @@ rewrite ^/c2cards https://molgenis.org/retired_server_c2cards.html # EXPIRES: ? rewrite ^/insaid https://insaid.molgeniscloud.org permanent; - - +# DESCRIPTION: Biobank Universe(mausoleum) +# MAINTAINER: Chao Pang +# EXPIRES: 13-09-2-21 +rewrite ^/biobankuniverse https://molgenis.org/retired_server_biobank_universe.html permanent; # DEPRECATED? # DESCRIPTION: 1000ibd.org # MAINTAINER: Floris Inham # EXPIRES: ? -rewrite ^/infevers https://molgenis40.gcc.rug.nl permanent; +rewrite ^/infevers https://1000ibd.gcc.rug.nl permanent; # DESCRIPTION: BBMRI WP2 Biobank plots # MAINTAINER: data-team # EXPIRES: ? -rewrite ^/bios https://molgenis78.gcc.rug.nl/menu/main/apps/aaaacxuvnfmp76qwh2zcadyaae permanent; - -# DESCRIPTION: Deconvolution 2 -# MAINTAINER: Mericko Yang -# EXPIRES: 31-12-2018 -rewrite ^/decon2 https://molgenis04.gcc.rug.nl permanent; +rewrite ^/bios https://omics-explorer.gcc.rug.nl/menu/main/apps/aaaacxuvnfmp76qwh2zcadyaae permanent; # DESCRIPTION: Variant Interpretation using Biomedical literature Evidence (VIBE) # MAINTAINER: Dennis Hendriksen diff --git a/get.md b/get.md index 065689c..fa6ee05 100644 --- a/get.md +++ b/get.md @@ -1,40 +1,57 @@ --- title: GET MOLGENIS -intro: MOLGENIS is open source and free to download, install and use. There are also hosting services if you don't want to install yourself. +intro: MOLGENIS is open source and free to download, install and use. There are also hosting services if you don't want to install and maintain yourself. layout: blue --- -You can freely copy and install MOLGENIS on your own machines (Licence: LGPLv3). See [Releases](https://github.com/molgenis/molgenis/releases) for overview of versions. There are also organisations who can host MOLGENIS for you and provide data management support. And programmers can take MOLGENIS code and customize it. Each option is described below: +# Data platform + +MOLGENIS original product is its FAIR data platform. You can freely copy and install MOLGENIS data platform on your own machines (Licence: LGPLv3). + +The actively developed MOLGENIS is codenamed 'exm2' and you can see [Releases](https://github.com/molgenis/molgenis-emx2/releases) here. It is easier to install as compared to previous version, see README at https://github.com/molgenis/molgenis-emx2. This package also includes pre-packaged the 'catalogue', FAIR genomes and beacon v2 tools. + +The previous generation of MOLGENIS is still in maintances and you can see [Releases](https://github.com/molgenis/molgenis/releases) for overview of versions. + +There are also organisations who can host MOLGENIS for you and provide data management support. And programmers can take MOLGENIS code and customize it. Each option is described below. + +# Analysis tools + +In addition to the data platform quite a range of additional tools have emerged> + +*** DataSHIELD armadillo *** +For federated analysis using the DataSHIELD protocol we have Armadillo. This can be found here https://github.com/molgenis/molgenis-service-armadillo + +*** Variant interpretation pipeline (VIP) *** +For NGS DNA variant analysis we have the VIP toolbox. This can be found here https://github.com/molgenis/vip + +*** CAPICE *** +CAPICE is a modern machine learning based variant pathogenicity classifiction predictor for DNA variants. See https://github.com/molgenis/capice + +*** NGS_DNA pipeline *** +NGS_DNA is a NGS DNA best practice pipeline for Illumina sequencing - alignment, variant calling, annotation and QC. See https://github.com/molgenis/NGS_DNA + +*** Compute *** +Compute is a simple workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers. eSee https://github.com/molgenis/molgenis-compute + +*** TRE/Sandbox for HPC *** +For setting up trusted research environments for large genome analysis projects (such as Solve-RD) we operate HPC clusters on OpenStack, in close collaboration with University of Groningen center for information technology. See https://docs.gcc.rug.nl/ + # Hosting and support -At least two hosting organisations provide MOLGENIS hosting as a service. E.g. for 200 euro/month UMCG hosts 1 MOLGENIS servers and for 250 euro/month 3 MOLGENIS servers. This includes basic data management support with functional application management. In addition, hosting providers can deliver support on a tailor made basis. Please contact one of the support groups below for details and costs regarding tailored support. +Our team provide MOLGENIS hosting as a service. Please contact us for details and costs regarding tailored support: -**Genomics Coordination Center** +**Genomics Coordination Center (GCC)** University Medical Center Groningen email: -Example service agreement: [here](/attachments/MOLGENIS_DVO_annex4_20201120.pdf) -Acceptable Use policy: [here](/attachements/MOLGENIS_AUP.pdf) - -**TraIT service desk, TraIT foundation** -Lygature, Utrecht -website: -# Install on Linux +# Install on server for multiple users and data persistence -To install on Linux you need -* MOLGENIS 'WAR' file (Choose download WAR [here](https://search.maven.org/search?q=g:org.molgenis%20AND%20a:molgenis-app here)) -* Java Platform (JDK) -* Apache Tomcat -* PostgreSQL -* Elasticsearch -* Optional: OpenCPU (enables R scripting feature) -* Optional: Python (enables Python scripting feature) -See for details on versions used the [Manual](https://molgenis.gitbook.io/molgenis/quickstart/guide-tomcat.html). +If our hosting solution is not suitable and you want to host your own molgenis instance in your own cloud or on your own premise. Please take a look at our [ansible galaxy repo](https://galaxy.ansible.com/molgenis) where the setup and requirements are explained. -# Install using Docker (experimental) +# Install locally for single user testing with Docker (experimental) -For testing purposes we now use Docker. We have the ambition to also use it for production but then you need to configure data persistence. However feel free to use our docker as a starting point. Get [Docker Images](https://github.com/molgenis/docker) +For local testing purposes we provide a Docker image. Get [Docker Images](https://github.com/molgenis/docker) # For programmers The complete source code of MOLGENIS is open source available at [Github](http://github.com/molgenis/molgenis) diff --git a/images/retired/biobank_universe/Figure1_overall.jpg b/images/retired/biobank_universe/Figure1_overall.jpg new file mode 100644 index 0000000..1483b72 Binary files /dev/null and b/images/retired/biobank_universe/Figure1_overall.jpg differ diff --git a/images/retired/biobank_universe/example_1.png b/images/retired/biobank_universe/example_1.png new file mode 100644 index 0000000..c090ac5 Binary files /dev/null and b/images/retired/biobank_universe/example_1.png differ diff --git a/images/retired/biobank_universe/example_2.png b/images/retired/biobank_universe/example_2.png new file mode 100644 index 0000000..c1f0e52 Binary files /dev/null and b/images/retired/biobank_universe/example_2.png differ diff --git a/images/retired/biobank_universe/example_3.png b/images/retired/biobank_universe/example_3.png new file mode 100644 index 0000000..751a7ea Binary files /dev/null and b/images/retired/biobank_universe/example_3.png differ diff --git a/images/retired/molgenis_connect/example_2.png b/images/retired/molgenis_connect/example_2.png new file mode 100644 index 0000000..b0b3289 Binary files /dev/null and b/images/retired/molgenis_connect/example_2.png differ diff --git a/images/retired/molgenis_connect/example_3.png b/images/retired/molgenis_connect/example_3.png new file mode 100644 index 0000000..ab0dd87 Binary files /dev/null and b/images/retired/molgenis_connect/example_3.png differ diff --git a/images/retired/molgenis_connect/example_4.png b/images/retired/molgenis_connect/example_4.png new file mode 100644 index 0000000..4b8380d Binary files /dev/null and b/images/retired/molgenis_connect/example_4.png differ diff --git a/retired_server_biobank_universe.md b/retired_server_biobank_universe.md new file mode 100644 index 0000000..dbff54d --- /dev/null +++ b/retired_server_biobank_universe.md @@ -0,0 +1,46 @@ +--- +title: BiobankUniverse +intro: BiobankUniverse is archived on the 22th of September 2021. +layout: blue +--- + + +# **Project is archived** - Welcome to BiobankUniverse + + +## Introduction +Welcome to BiobankUniverse. The demonstration website has been archived on the 13th of September 2021. Below for your convenience an overview of what you would have found. The features of BiobankUniverse have been merged with the MOLGENIS 'mapping service'. + +BiobankUniverse was a data discovery and matching system for biobanks built in ([MOLGENIS](https://github.com/molgenis/molgenis)) that could automatically tag biobank attributes (metadata) with ontology terms from Unified Medical Language System (UMLS) and based on which generate candidate attribute matches between biobanks. In addition, BiobankUniverse could calculate the overall similarities between biobanks so that users can quickly get an approximation of how close/far the biobanks are to each other. Please note that this server is shelved, for the greatest and latest features of MOLGENIS look ([here](https://www.molgenis.org)). + +The instruction on how to deploy it in tomcat 7 can be found ([here](http://www.molgenis.org/wiki/Molgenis-connect)). The source code is avaiable on ([GitHub](https://github.com/chaopang/molgenis/tree/feature/biobankuniverse)). + +--- + +## Discover biobanks + +The circle represents a biobank and the larger a biobank, the larger the circle. The line represents the distance between the biobanks, the longer the line, the less similar the connected biobanks are to each other. There are two types of universes, one is generated based on the overall similarity of the automatically tagged ontology terms, the other one is generated based on the number of candidate matches. + +![Example 1](images/retired/biobank_universe/example_1.png) + +For example, see image below. When clicked on the button 'Number of matches', typed in 'Beer' in the search box and selected 'C0004922:Beer' and then hit the 'Search' button, only the candidate matches related to 'Beer' are retrieved and universe will reduce in size. The search box was configured with typeahead function to provide ontology terms. See the image 'Example 2' below. + +![Example 2](images/retired/biobank_universe/example_2.png) + +--- + +## Curate attribute matches + +We had pre-generated the candidate attribute matches between the biobanks including Finrisk2002, Finrisk2007, Lifelines, Prevend, Mitchelstown and HOP. The matches generated where pairwise so users needed to choose a leading 'target' data schema to generate the match table, in which they can curate the candidate matches. An example can be seen in 'Example 3' with the term 'hop'. + +![Example 3](images/retired/biobank_universe/example_3.png) + +--- + +## Technical design + +![Technical design](images/retired/biobank_universe/Figure1_overall.jpg) + +--- + +# If you want to use molgenis with new features, visit [molgenis.org](https://molgenis.org) diff --git a/retired_server_molgenis_connect.md b/retired_server_molgenis_connect.md new file mode 100644 index 0000000..df89061 --- /dev/null +++ b/retired_server_molgenis_connect.md @@ -0,0 +1,85 @@ +--- +title: MOLGENIS/connect +intro: MOLGENIS/connect is archived on the 22th of September 2021. +layout: blue +--- + + +# **Project is archived** - Welcome to MOLGENIS/connect + + +## Background + +MOLGENIS/connect was a semi-automatic data integration system built in ([MOLGENIS](https://github.com/molgenis/molgenis)) that can assist researchers in finding, matching and pooling data from different biobanks. During the data integration process, Molgenis/connect not only can suggest relevant data elements from biobanks for the given interest of research variables but also is capable of generating data tranformation algorithms for data integration. In addition, users can easily interact with the system to improve upon the suggested mappings and algorithms. + +The instruction on how to deploy it in tomcat 7 can be found ([here](http://www.molgenis.org/wiki/Molgenis-connect)). The source code is avaiable on ([GitHub](https://github.com/molgenis/molgenis/tree/1.15)). + +--- + +## Demo + +The demo is no longer available because the project is archived. There is however still a live demo on ([YouTube](https://www.youtube.com/watch?v=Gc1VKRCmTWU)). + +The demo was created using data from the BioSHARE project. The target schema consists of approximiately 90 core data elements e.g. Body Mass Index, History of Hypertension representing the research question. Three biobanks (LifeLines, Prevend and Mitchelstown) are selected in this demo as the source datasets for which we have the data. The task is to harmonize the 90 core data elements in the three biobanks separately and then pool the harmonized results into one dataset. + + +## Demo data + +Although the demo version did not have full functionality, it allowed you to view all the mappings and algorithms in the demo mapping project that have been generated in advance. You are not able anymore to try out the semantic search and the algorithm generator functions in the demo. The examples are no longer available. + + +The first image is of 'Example 2'. Here you can see an example of the mapping + algorithm auto-generated for the target data element Body Mass Index kg/m2 (BMI) in the biobank lifelines. + +![Example 2](images/retired/molgenis_connect/example_2.png) + +### The explanation of generating the algorithm for BMI in lifelines + +> The semantic search is applied to find all the relevant data elements in lifelines for BMI. +> 1. BMI: Body Mass Index +> 2. HEIGHT: Height in cm +> 3. WEIGHT: Weight in kg +> 4. ..... +> +> The algorithm generator checks if there are any pre-defined templates associated with BMI and the template is detecetd in the database shown below. +> +> ``` +> $('weight').div($('height').pow(2)).value() +> ```` +> +> The algorithm generator implements the BMI template with the data elements found in lifelines. Units of mapped data elements are adjusted accordingly e.g. HEIGHT is divided by 100. +> +> ``` +> $('WEIGHT').div($('HEIGHT').div(100.0).pow(2)).value() +> ``` + +--- + +In 'Example 3' image you can see the mapping + algorithm auto-generated for the target data element History of Hypertension in the biobank lifelines. In the example, you will find that: + +> * the first suggested data element is 'Do you ever have high blood pressure' because 'high blood pressure' is a synonym of 'Hypertension'. +> * the target categories and source categories are automatically matched based on the lexical similarity. + +![Example 3](images/retired/molgenis_connect/example_3.png) + +--- + +In the image of 'Example 4' you can see the mapping + algorithm auto-generated for the target data element Current Consumption Frequency of Potatoes in the biobank lifelines. In the example, target and source categories are automatically matched following a strategry, where + +> * both of the target and source categories are first converted to quantifiable amounts. +> .. The source amounts are matched to the closest target amounts. + +You will see that only the first source data element is used in the algorithm. However the second element is also related to Potatoes, therefore + +> * you need to select the checkbox of the second data element. +> * you will see that the algorithm is updated based on the new selection of data elements. + +![Example 4](images/retired/molgenis_connect/example_4.png) + +--- + +## Technical design +First, we developed the semantic search that uses ontology-based query expansion to find relevant data elements from biobanks, irrespective of variations in the terminologies used. Second, we created the algorithm generator that can automatically generate data transformation algorithms to convert these data elements to the target schema, including unit conversion, category mapping, and more complex recurring conversion patterns e.g. calculation of BMI. + +--- + +# If you want to use molgenis with new features, visit [molgenis.org](https://molgenis.org) \ No newline at end of file diff --git a/team.md b/team.md index 8f3da03..b636cd1 100644 --- a/team.md +++ b/team.md @@ -41,16 +41,13 @@ MOLGENIS development is strategically guided by an independent international Str In addition to strategic advice MOLGENIS also has several user communities guiding its development. These groups are managed by the respective communities, and often change dynamically following changes in funded project. For example, there is a Dutch biobank user group and a European directory user forum. We plan to expand these user engagement activities to ensure optimal allocation of the limited development resources. ## Hosting and support -MOLGENIS is free to download and install yourself. You can also get MOLGENIS ready for use from two support providers. They can also provide support with entering and managing your data. Please contact one of the support groups below for details and costs. +MOLGENIS is free to download and install yourself. You can also get a MOLGENIS instance ready for use from us. We can also provide support with entering and managing your data. Please contact us for details and costs. -**Genomics Coordination Center** +**Genomics Coordination Center (GCC)** University Medical Center Groningen email: conditions: [Acceptable Use Conditions(AUP)](/attachments/MOLGENIS_AUP.pdf), [Example service agreement](/attachments/MOLGENIS_DVO_annex4_20201120.pdf) -**TraIT service desk, TraIT foundation** -Lygature, Utrecht -website: ## Partners