Installing JabRef in spite of Windows Protection

This week, I was setting up my new work computer (with Windows). As part of it, I wanted to install my favorite reference manager: JabRef. Unfortunately, the normal installation (i.e., downloading the .msi file) didn’t work, since Windows Protection was blocking it:

I found this weird since I did have admin rights to install stuff. After digging around, I learned that this is because the installer needs to have an electronic certificate. Sadly, this is very expensive, which is a big problem for (Open Source) projects like JabRef which depend mostly on donations. However, there are alternatives. In this post I would like to share a few of them and which one worked for me. Hopefully this will save you a headache.

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Troubleshooting Deploying Documentation Using MkDocs

Recently, I was developing a package for my job. One of the requirements was to make sure that it was properly documented. Being a big fan of Markdown, MkDocs was a natural choice. Not only is it easy to pick up and customize, but Material for MkDocs offers some fantastic functionality on top of it. With very little effort, you can add admonitions (the nice colorful boxes with handy information), tables , site search , and many others.

After spending time and effort in writing the documentation per se, it was finally time to go live and deploy it. You can do this manually using GitHub Pages. However, in my case it was much handier to automate the documentation deployment after every push. GitHub Actions allow you to do this very easily. Unfortunately, this solution didn’t really work out of the box for me. In this post, I will share the problems I ran into and how I fixed them. Maybe this will be useful for someone else.

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Using the .github directory in Enterprise Accounts

Among GitHub’s many cool features, you can create default “community health files” (e.g.,, FUNDING.yml, etc.) for all your repositories.

If you are working on repositories from your personal account, you can create a .github repository where you can place the corresponding files. Then, new repositories that you create will use these same files (unless you create community health files for each of them, in which case these will override the defaults). However, when working on an enterprise organization, there are a couple of considerations that you need to take into account to get this up and running.

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New Paper - A Federated Approach to Identify Women with Early-stage Cervical Cancer

After more than two years of work, I am happy to share that our latest paper is out! Here, we used federated learning (more specifically, the logistic regression flavor of our previously published GLM model) to identify women at low risk of pN+ cervical cancer. This work has the potential to be used as a guide in shared decision-making process when considering the extent of lymph node dissection.

The abstract is as follows:

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Estimating Breathing Rate from Respiratory Sinus Arrhythmia

As a Biomedical Engineer, I’ve always been fascinated by working with physiological signals. It amazes much how much stuff we can measure on the human body and what we can learn from it. Lately, I’ve been missing working with such data. To scratch that itch, I have been busy with a side project focused on estimating the respiratory rate from the heart rate variability signal (measured from single-lead ECG), as shown in the work by Schäfer and Kratky (2008).

GIF for display purposes only. Original lung GIF by PresenterMedia

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