The latest news from The Hyve on Open Source solutions for bioinformatics

Downloading data from the cBioportal Oncoprint view

March 09, 2018 | By Dionne Zaal 0
The OncoPrint view in cBioPortal is a user friendly visualization for genetic alterations. All types of data from a cancer genomic study are integrated in the OncoPrint view: in one overview you can see mutations, expression levels and copy number[…]
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Python and R client: data retrieval for analysis made easier

March 05, 2018 | By Irina Pulyakhina 0
To simplify extraction of a specific data subset from a tranSMART data warehouse for analysis with Python or R, The Hyve developed both a tranSMART Python and a R client.
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Identifying real-world security needs: user management in context of real world data and RADAR platform

February 22, 2018 | By Irina Pulyakhina 0
Data, especially real-world medical data, is eminently sensitive. What would happen if all the GPS tracking data of a research project would become public, along with identifiable information? Can data that has been polluted by a hacker still be[…]
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Adding your own annotations to mutations in cBioPortal

February 09, 2018 | By Sjoerd van Hagen 0
One of the key challenges in cancer research is to find patients that will respond well to targeted drug therapy. Specific mutations in a patient’s tumor can be an indication of the patient’s potential responsiveness to such therapy. Recently we[…]
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Six quick tips to start making your data FAIR

February 01, 2018 | By Jarno van Erp 0
This is an update of a previous blog post which listed four quick and easy tips. We have updated the old tips and added 2 new tips at the end of the post.  Making your data “FAIR” is something you hear more and more. In the age of creating large[…]
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Glowing Bear: the new tranSMART UI is almost here!

January 19, 2018 | By Irina Pulyakhina 0
Update: Glowing Bear is now publicly available! Read the blog post here.   Why tranSMART needed a new UI tranSMART is a data warehouse which enables sharing, storing and analyzing various types of biomedical data. It was originally developed by[…]
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Expanding analytical power with JupyterHub and HPC

January 10, 2018 | By Jarno van Erp 0
These days, computers need to be able to cope with the vast amounts of data that the Life Science sector is constantly generating. I am not talking about storing the data but about having the ability to perform computationally intensive analysis on[…]
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Using wearables in daily medical practice and research: the future is here

January 08, 2018 | By Irina Pulyakhina 0
Wearable devices and wearable sensors have recently become very popular, especially in the areas of fitnessand sports. An important feature of wearable devices and smartwatches is that they provide a continuous, non-stop recording of your activity[…]
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Simple data loading into cBioPortal with Docker

December 28, 2017 | By Sander Tan 3
In our recent blogpost we discussed an easy solution to set up a local instance of cBioPortal using Docker. The next step is to load a study into the database.
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Health-RI conference 2017: building on a strong foundation

December 21, 2017 | By Maxim Moinat 0
The aim of the third Health-RI (Research Infrastructure) conference, held on 8 December 2017, was to highlight the challenges in bridging the gap between research and medical practice.  Although many challenges still lay ahead, we are delighted to[…]
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