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fix: links to go to emx2 instead of old molgenis and other updates #140

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fix: links to go to emx2 instead of old molgenis and other updates #140

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1515c03
fix links to go to emx2 instead of old molgenis
mswertz Feb 28, 2024
2027b4b
Update get.md
mswertz Feb 28, 2024
5169150
Update index.md
mswertz Feb 28, 2024
9bbef9d
Update communities.md
mswertz Feb 28, 2024
7816824
Update learn.md
mswertz Feb 28, 2024
e608d57
add https
mswertz Aug 5, 2024
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8 changes: 5 additions & 3 deletions communities.md
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Expand Up @@ -8,12 +8,13 @@ layout: black
<h1>FAIR Catalogues</h1>
Make data and samples from biobanks, registries and research collections findable to ensure maximum (re)use for research and improve patients and citizens lives. Examples:
<ul>
<li><a href="data-catalogue.molgeniscloud.org">EU health data networks and harmonization catalogue</a></li>
<li><a href="http://directory.bbmri-eric.eu">European directory of biobank collections (BBMRI-ERIC)</a></li>
<li><a href="http://catalogue.bbmri.nl">Dutch catalogue of human data and sample collections (BBMRI-NL)</a></li>
<li><a href="http://catalogue.lifecycle-project.eu/">EU child network for multi-center cohort harmonisation</a></li>
<li><a href="https://umcgresearchdatacatalogue.nl/">University Medical Center Groningen Cohorts and Data Catalogue (UMCG)</a></li>
<li><a href="http://samples.rd-connect.eu">Catalogue of rare disease samples (RD-Connect)</a></li>
<li><a href="http://www.palgaopenbaredatabank.nl/">Dutch catalogue of pathology samples (PALGA)</a></li>
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I came here out of curiousity, but since I'm here I might as well be bold enough to place a comment:

It's probably only documentation, but I think it's better to change these links to HTTPS, as these also seem to work, same for the ones above.

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yes, this is pretty old stuff

<li><a href="https://catalogue.lifelines.nl">LifeLines request portal of data and materials</a></li>
<li><a href="https://datacatalogue.lifelines.nl">LifeLines request portal of data and materials</a></li>
</ul>
</div>
<div class="feature_image_box">
Expand Down Expand Up @@ -60,7 +61,8 @@ Capture, manage, analyse and share complete datasets with biomedical researchers
<h1>Pipelines</h1>
MOLGENIS compute based reusable bioinformatics protocols to process molecular profiles that can now be produced at unbelievable rates demanding bespoke bioinformatics protocols and high performance computing to process. Examples:
<ul>
<li><a href="https://github.com/molgenis/NGS_DNA">[NGS DNA pipeline</a></li>
<li><a href="https://github.com/molgenis/vip">Variant interpretation pipeline</a></li>
<li><a href="https://github.com/molgenis/NGS_DNA">NGS DNA pipeline</a></li>
<li><a href="https://github.com/molgenis/NGS_RNA">NGS RNA pipeline</a></li>
<li><a href="https://github.com/molgenis/NGS_ScRNA">NGS scRNA pipelin</a></li>
<li><a href="https://github.com/molgenis/NGS_Microbiome">NGS Microbiome</a></li>
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8 changes: 3 additions & 5 deletions get.md
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Expand Up @@ -4,7 +4,7 @@ intro: MOLGENIS is open source and free to download, install and use. There are
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:
You can freely copy and install MOLGENIS on your own machines (Licence: LGPLv3). See [Releases](https://github.com/molgenis/molgenis-emx2/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:

# Hosting and support
Our team provide MOLGENIS hosting as a service. Please contact us for details and costs regarding tailored support:
Expand All @@ -20,11 +20,9 @@ If our hosting solution is not suitable and you want to host your own molgenis i

# Install locally for single user testing with Docker (experimental)

For local testing purposes we provide a Docker image. Get [Docker Images](https://github.com/molgenis/docker)
For local testing purposes we provide a Docker image. Get [Docker Images](https://molgenis.github.io/molgenis-emx2/#/molgenis/run_docker)

# For programmers
The complete source code of MOLGENIS is open source available at [Github](http://github.com/molgenis/molgenis)

You can find developer documentation as part of the [Manual](https://molgenis.gitbook.io/molgenis/)
The latest incarnation of MOLGENIS is codenamed 'emx2'. The complete documentation and source code of MOLGENIS is open source available at [Github](http://github.com/molgenis/molgenis-emx2)

We are always happy to hear about your experience with MOLGENIS and suggestions for improvement. Please, help us to improve MOLGENIS and send your feedback and ideas to our 'product owner': <a href="mailto:[email protected]">[email protected]</a>
8 changes: 6 additions & 2 deletions index.md
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Expand Up @@ -25,12 +25,16 @@ MOLGENIS was born from molecular genetics research and is now a broadly applicab

# Get molgenis

MOLGENIS data platform: [docs](https://molgenis.gitbook.io/molgenis/), [deploy](https://molgenis.gitbook.io/molgenis/guide-deploy-molgenis), [code](https://github.com/molgenis/molgenis), [releases](https://github.com/molgenis/molgenis/releases)
MOLGENIS data platform: [docs](https://molgenis.github.io/molgenis-emx2/#/molgenis/), [deploy](https://molgenis.github.io/molgenis-emx2/#/molgenis/run_java), [code](https://github.com/molgenis/molgenis-emx2), [releases](https://github.com/molgenis/molgenis-emx2/releases)

MOLGENIS compute platform: [docs](https://rawgit.com/molgenis/molgenis-compute/master/molgenis-compute-core/README.html),[releases](https://github.com/molgenis/molgenis-compute/releases), [code](https://github.com/molgenis/molgenis-compute).
MOLGENIS datashield armadillo: [docs](https://molgenis.github.io/molgenis-service-armadillo),[releases](https://github.com/molgenis/molgenis-service-armadillo/releases), [code](https://github.com/molgenis/molgenis-service-armadillo).

MOLGENIS variant interpretation pipeline (VIP): [docs](https://molgenis.github.io/vip/),[releases](https://github.com/molgenis/vip/releases), [code](https://github.com/molgenis/vip).

MOLGENIS Pipelines: [DNA pipeline](https://github.com/molgenis/NGS_DNA) [docs](https://molgenis.gitbooks.io/ngs_dna/), [code](https://github.com/molgenis/NGS_DNA), [RNA pipeline](https://github.com/molgenis/NGS_RNA), [easybuild for automatic installation](https://github.com/molgenis/easybuild-easyconfigs)

MOLGENIS compute platform: [docs](https://rawgit.com/molgenis/molgenis-compute/master/molgenis-compute-core/README.html),[releases](https://github.com/molgenis/molgenis-compute/releases), [code](https://github.com/molgenis/molgenis-compute).

<div style="text-align: center">
<a href="/get.html" class="bluebutton">Discover more resources</a>
</div>
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7 changes: 6 additions & 1 deletion learn.md
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# Documentation
Here you can find documentation:

* [MOLGENIS Data Platform manual](https://molgenis.gitbook.io/molgenis/)
* [MOLGENIS Data Platform manual](https://molgenis.github.io/molgenis-emx2/#/molgenis/)
* [MOLGENIS Datashield Armadillo Platform manual](https://molgenis.github.io/molgenis-service-armadillo/#/)
* [MOLGENIS Variant Interpretation Pipeline (VIP) manual](https://molgenis.github.io/vip/)
* [MOLGENIS Catalogue manual](https://molgenis.github.io/molgenis-emx2/#/catalogue/)
* [MOLGENIS Compute Platform manual](https://molgenis.gitbook.io/molgenis-pipelines/)

# News archive
Expand All @@ -22,10 +25,12 @@ Here you can find all news items:
Relevant publications by MOLGENIS community members:

## Sample and data catalogues:
* Swertz et al (2022) Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies. [Yearb Med Inform](https://pubmed.ncbi.nlm.nih.gov/36463884/)
* Holub et al (2016) BBMRI-ERIC Directory: 515 Biobanks with Over 60 Million Biological Samples. [Biopreservation and Biobanking](https://www.ncbi.nlm.nih.gov/pubmed/27936342)
* Roxana Merino-Martinez et al (2016) Toward Global Biobank Integration by Implementation of the Minimum Information About BIobank Data Sharing (MIABIS 2.0 Core). [Biopreservation and Biobanking](https://www.ncbi.nlm.nih.gov/pubmed/26977825)

## Harmonization / FAIRification:
* Van der velde et al (2022) FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. [Sci Data](https://pubmed.ncbi.nlm.nih.gov/35418585/)
* Pang et al (2017) BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration. [Bioinformatics](https://www.ncbi.nlm.nih.gov/pubmed/29036577)
* Wilkinson et al (2016) The FAIR Guiding Principles for scientific data management and stewardship. [Scientific Data](https://www.ncbi.nlm.nih.gov/pubmed/26978244)
* Pang et al (2016) MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks. [Bioinformatics](https://www.ncbi.nlm.nih.gov/pubmed/27153686)
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