Taking advantage of a trip to Canada and a very favourable CAN$:€ exchange rate, I bought a Dell XPS13 (9350 or “late 2015”), following excellent reviews from around the web. Dell sold a ‘developer edition‘ of this laptop (shipping with Ubuntu Linux) but unfortunately it was out of stock on Dell US and I couldn’t find the item on the Dell Canada website. So I bought the Windows version with a touchscreen (it was Black Friday :-)).
Here is how to install Fedora 23 on it (and probably most other Linux distribution) … I will focus on three aspects (in brief: everything works out of the box, except the wireless card that needed some additional action):
How to boot and install Fedora Workstation
What works and what doesn’t work out of the box
Some things to do after installation (additional software)
I wrote earlier that I really liked Zotero, a reference management software. However, there is one thing that was missing, imho: the capability to import PDFs (individually or in bulk) and correctly fill in the various fields of the reference.
But in fact, this already exists in Zotero! Just drag a PDF in the middle section (the reference list) then right-click on it and choose “Retrieve Metadata from PDF” (*). Retrieval of the title, the authors, the journal, etc. everything goes very fast and they are stored as a normal reference, now on the right.
Now, it works for most papers I tested yesterday and today. Most major editors are supported (it seems Zotero doesn’t actually extract metadata from the PDF but finds these metadata by comparing the PDF content with Google Scholar). As hinted in the Zotero support page for this function, please re-check the imported reference in case something went wrong (I imported something like 20 references since yesterday with this function and I didn’t spot any error for the moment).
Bulk import and metadata retrieval works too: just import several PDFs at the same time and, while all of them are selected in Zotero, right-click on them and choose “Retrieve Metadata for PDF”.
As mentioned earlier, “it’s just plain efficiency, without bells and whistles“. It just works 🙂
(*) On MS-Windows, on the first use, you might see a dialog box warning you that you must first install the “PDF tools”.
If you see it, just choose the “Open preferences” button and follow the very intuitive procedure. The installation takes 30 seconds maximum, download included.
The first paper describes how the web started as something static, became all dynamic and is progressively coming back to something more static, at least for some specific tasks. The interesting thing is that the author also describes pros and cons of each stage and why the web jumped to the next level.
While reading this, I couldn’t help thinking of Jadoo, a pet project I started in 2007. Its goal was to get rid of the complexity and number of resources required to run a dynamic blog system. Following some notes from Alexandre Dulaunoy, it was written in Python and already used concepts now hidden under buzzwords 😉 like templating and a rudimentary meta-data organization. At that time, there was nothing like Markdown, assets management, caching, Github, … (not as widespread as today at least). There is an initial post and an update – then I gave up (reasons inside). Note drawbacks I wrote at that time are still drawbacks of current static website generators (manual update and local edition only). All these ideas in 2007, one year before Jekyll … 😉
P.S. The irony is that posts about Jadoo were later transferred to WordPress – and this blog is also npw currently hosted on WordPress!
Marketing is a powerful persuasion tool and you sometimes need a few early applications to create the impression that something radically new came and is changing an area.
I like to listen to podcast while doing repetitive activities that don’t require my brain too much. One of the podcasts I listen to is the Clinical Air from the Pharma Talk serie. A few weeks ago, I listened to episode #14 about consumer electronics in clinical research. It was all about the Apple HealthKit. In a sense it was very interesting to hear about it as it contained more details than its Wikipedia page for the moment ; another top-level summary of its capabilities is found in this Rahlyn Gossen’s blog post (Rahlyn was one of the guests of this episode). Episode #14 was published on July 21, 2015.
Tonight I listen to episode #12 about digital startups and applications for clinical research. It struck me that the discussion was more serious, more focused on actual startups and apps, what they try to solve, how they would/should evolve in the future, etc. Apple was mentioned only once, as part of provocative titles of articles in the press at that time. Because “that time” was August 29, 2014 (when episode #12 was published), one month before Apple announcement.
For some things, we’ll have to dig for information before big marketing campaign, in order to find out interesting content that explore various areas instead of being funneled in the same direction …
Photo credit: Birds: a tragedy by Shannon Kokoska on Flickr (licence CC-by-nc-nd).
For my work I need to reference a lot of statements, mainly with papers and books in the biological / medical literature. Usually “professionals” use two proprietary software, Reference Manager or EndNote (both owned by Thomson Reuters). But there are a few very interesting free alternatives (see this comparison of reference management software).
Mid last year, Gartner mentioned “medical applications [of 3D printing] will have the biggest impact in the next two to five years“. With 3D printing you can already create a lot of physical artifacts and medical applications go from building medical equipments to prosthetic parts, but also blood vessels, bone, heart valve, cartilage, etc. Complete organs are not too far, with companies like Organovo already printing functional liver assays, prospects to restore a body by replacing or consolidating personalized parts seem interesting.
On the other side, restoring a body function by providing personalized molecules was a dream so far. Preventing body malfunction via similar systems is too.
I recently watched and read about Lee Cronin’s laboratory work and these dreams may come true, one of these days. In a TEDxGateway video in 2013, Prof. Cronin explained briefly how he did it. Last December, they published their method with a basic application in Nature Communications. What I also liked is that, beyond the technical capabilities, this research is based on common components (right) and free software that are available for everyone. And Cronin also insisted on compatibility between “recipes” and the possibilities to exchange them as well as source code – one day, will their software be released on Github like some of their 3D models as STL files?
Cronin also talks about pharmaceutical companies releasing blueprints for drugs that could save plenty of lives in emerging economies, for instance. In my opinion, this is however where the technology goes much faster than the ideological framework we live in: pharma companies will not likely suddenly release recipes for drugs that bring them money (no for-profit company in any other sector would, by the way) and the regulatory framework for healthcare is far from ready to accommodate these advances.
Prevention could also benefit from these advances. Synthetic vaccines are in production since two decades at least. If safety is the first argument often put forward in their favor, rapid prototyping and versatile production could one day become possible. It seems it was already tested for flu vaccines. Now imagine to move the “engineering” part in a computer, sending the recipe for the best-adapted vaccine directly to “vaccine printers” in regions where health hazards are likely to occur or as early as they occur … We would also face many corporate and regulatory hurdles. But it wouldn’t be the first field where technology would push broader changes …
With more than 2,400€ collected, our team – Bordet’s angels – can be proud, for a first participation! We are 12th of more than 100 Belgian teams. One key learning is that the gold, old paper display still works better than anything else to raise money.
And it was fun for me, a bit itchy in the end. But with the right trimming tools, this goes away very quickly. Thanks for all my supporters 😉 – your support is worth a thousand thank-you!
We’re nearly halfway through Movember, the month we grow our moustache in order to raise awareness about men’s health. I am in Amsterdam, for a congress and this was the hardest day of the month so far: since 8am, nearly every single person I met said it didn’t look good. And this can be harsh when you talk with (potential) business partners! However, practically, when you have time, this is an unique opportunity to initiate discussions with others about prostate cancer.
So this is a plea to make it worth! Please donate to prostate cancer research via my profile page: http://mobro.co/jepoirrier. Belgian men lives on average 5 years less than Belgian women. Belgium has the 4th highest cancer rate for men diagnosed in 2012 worldwide. Survival rates are however good but together we can do better!
Still want to see how it looks like so far? Here you see I will soon need to use wax, scissors and all sorts of precision instruments to tame it 😉
A contact matrix is a representation of contacts between individuals. For instance, in order to model the spread of rumors on social media, you ideally have to rely on contact matrices to compute the strength of bonds between types of individual agents. In the infectious disease world, a contact matrix is used to approximate contacts between individuals, e.g. between grand-parents and grand-children.
In this blog post, after a short explanation of POLYMOD contact matrices, I will show how to get the data, process it and 3D print these matrices. Ready?
1. Finding contact matrices
The most used contact matrices in epidemiological modelling are coming from the POLYMOD study, published by Mossong et al. in 2008. The study is a population-based prospective survey of mixing patterns in eight European countries (Belgium, Germany, Finland, Great Britain, Italy, Luxembourg, The Netherlands, and Poland). For that purpose their method consisted in common paper-diaries used by individuals to record information about their daily contacts (you might think this is so old fashion but nobody reproduced this study or did better so far!).
So what does it look like (I’ll take Belgium as an example here)?
Smoothed weighted physical contact matrix (Fig. 3 from Mossong et al.)
You can see above a heatmap of physical contacts between participants and their contacts. The more towards the blue indicates fewer contacts. The more towards white indicates more contacts. Therefore the diagonal towards the top right shows that most Belgian participants have contacts with people of the same age. And this diagonal has two “wings”, representing interactions between parents in their 30s and their children. There are also two “bumps”, representing interactions between grand-parents and their grand-children.
So these heatmaps are already something pleasant to the eye. But what if you could actually touch them? Can you actually physically play with them? This was made possible thanks to 3D printing, a manufacturing process that transform practically any custom 3D model created on a computed into a physical artifact.
We’ll first need to get the data, process it in a suitable format and finally print it …
Here is how to install Fedora 23 on it (and probably most other Linux distribution) … I will focus on three aspects (in brief: everything works out of the box, except the wireless card that needed some additional action):
Jean-Etienne's blog 