Create a conda environment with the Python ISA-API
The ISA (Investigation, Study, Assay) metadata framework (https://isa-tools.org/) can be used to describe experimental metadata readable for both humans and machines (using ontologies). ISA-Tab and ISA-JSON files can be created, read and edited using
Install R/Bioconductor packages in RStudio using renv package manager (Windows)
The `renv` package (https://rstudio.github.io/renv/articles/renv.html) allows project-wise package management in R. This is useful when working on multiple R projects with different dependencies, and sharing these environment across users or VMs. In order
Whitelisting Github/Bitbucket IPs
I would like to whitelist either Github or Bitbucket in order to pull/push/commit etc. On the following page I found information on a couple of IPs. Do I have to whitelist all of these? https://support.atlassian.com/bitbucket-cloud/docs/what-are-the-bitbucket-cloud-ip-addresses-i-should-use-to-configure-my-corporate-firewall/
myDRE and Git
Setting Some workloads require the versioning of scripts/code. Git is an industry solution that is widely used. Questions Can Git be used within myDRE? Yes, applications like SmartGit can work in a Workspace with both the 'remote' and 'local' repo lives
Teams & myDRE
Introduction myDRE Workspaces are good to store, process, and analyse data. However, it is not that uncommon that a lot more is needed; especially in a collaboration setting. Things like: storing documents and agreements, collaborating on articles/documents,
Add in the email who added the new member
Recently I added and directly removed a colleague to demo how easy this is. Stupid, never ever invite somebody into a Workspace who has no business. The good thing is that the other Owners got an email that this user was added. However, it was not clear
Jupyter Lab - open files in external applications directly (e.g. .xlsx)
I find it very useful to combine Jupyter Lab with spreadsheets (Excel, Calc). This I do to store mappings, configuration, etc. This works very nicely, but the annoying thing is when working in Jupyter Lab and you need to open the Excel for editing. This
Scrambling Datasets
Introduction For testing purposes, or for demonstration purposes, it is good to have a representative but very fake dataset. A dataset that doesn't even allow basic statistics to be similar to the actual datasets. Solution If you are familiar with Jupyter
Remapping Datasets
Background I've been involved in COVID-19 related data gathering. Data was capured in CASTOR, but needed to be remapped to WHO standard. This meant mapping variables, remapping values (e.g. NO: 2 in the one NO: 0 in the other), adding missing units, substituting
Is it helpful to differentiate between Personal Data and Data of Persons?
Introduction According the the GDPR Art. 4 (1). Personal data are any information which are related to an identified or identifiable natural person. When dealing with personal data, measurements must be in-place that comply to Confidentiality = High.
Does DRE keep running when computer shuts down or internet connection is disrupted?
I am currently running an analysis on DRE and it will probably continue to run for another 14 hours. If my connection with the virtual desktop is disrupted because the internet stops or I shut down my laptop, will the VM continue or will the analysis
No username received after migration
Who would we email if we were not sent a username for the migrated system?
Improved / New Features
New & Improved Features TAB: Virtual Machines The VM can be quickly accessed in portal.azure.com. For trouble shooting, looking at performance metrics, etc. For example: when your VM is stuck in Unknown status, you can quickly access your VM in the Aure
Collaborate!
This forum is to have general discussions, announcements, a place to ask questions, to an answer questions. Give your opinion and ideas. To keep track of certain issues. We love to learn from your input and do hope we can build together a nice eco-system.
Important announcements
This forum is reserved for announcing issues, new features, etc. Subscribing to this forum will keep you informed. Please only post reactions or add topics to this forum if you believe it is of utmost important for everybody. Their are other forums that
Announcements
Remapping Datasets
Background I've been involved in COVID-19 related data gathering. Data was capured in CASTOR, but needed to be remapped to WHO standard. This meant mapping variables, remapping values (e.g. NO: 2 in the one NO: 0 in the other), adding missing units, substituting
Improved / New Features
New & Improved Features TAB: Virtual Machines The VM can be quickly accessed in portal.azure.com. For trouble shooting, looking at performance metrics, etc. For example: when your VM is stuck in Unknown status, you can quickly access your VM in the Aure
Collaborate!
This forum is to have general discussions, announcements, a place to ask questions, to an answer questions. Give your opinion and ideas. To keep track of certain issues. We love to learn from your input and do hope we can build together a nice eco-system.
Important announcements
This forum is reserved for announcing issues, new features, etc. Subscribing to this forum will keep you informed. Please only post reactions or add topics to this forum if you believe it is of utmost important for everybody. Their are other forums that