Bastian Greshake Tzovaras is an open/citizen science activist and researcher with a background in biology and bioinformatics. He worked as a senior researcher at The Alan Turing Institute and Inserm. In 2011, he founded openSNP. He was awarded a PhD in Bioinformatics in 2018. In 2017 he joined the Open Humans Foundation as the Director of Research.

Bastian Greshake Tzovaras

In October 2022, Eugenia and I spent a few weeks in Laos both in Vientiane and Luang Prabang. A big reason for going was that Eugenia gave some workshops in Vientiane, but we also gave some school lectures through Lecturers Without Borders while there.

Laos

What the output of a personal API can look like.

 Open Humans

has been expanding thanks to lots of new data sources that have gone live in the last couple of months. Thanks to our Outreachy interns we already have added support for sharing your Google Location History and your Spotify Listening History.

A personal API

President Bartlet of

 The West Wing

is calling his famous “What’s next” to his secretary after managing a task. I just defended my PhD last week, and one question from virtually every person who attended and stayed for the after-party:

 What’s Next?

Which initially felt a bit weird. After all, I already took my next step three months ago when I joined

 Open Humans

as the Director of Research.

Open Humans, what’s next?

Socrates I’m a huge fan of the

 Quantified Self

and

 Personal Science

movement in which one uses empirical methods to answer personal questions. Related to that, I try to collect and mine as many personal data sources as possible. And visualizing the data to learn from this is the part I really enjoy.

Quantified Self

Ever since a certain

 someone

bought Twitter, I’ve been quite invested into using the Fediverse as my main social web efforts. My Mastodon timeline does a good job for short-form text updates. And Pixelfed is a great nascent Instagram-replacement. One thing I particularly enjoy about both of them is the fact that they bring back the simple, chronological timeline.

Turning popular links from your Mastodon timeline into an RSS feed

I am more than delighted to announce that I will join

 Open Humans

. Supported by a fellowship I will assume the role of

 Director of Research

in November.

 Open Humans

as a platform connects individuals who want to participate in research with research studies and projects that can be run by academic and “

 citizen

” scientists alike.

Joining Open Humans

tl;dr: You can turn your Puck.js into a
 
 one-button tracker
 
 with this open source website I made


 Open Humans

community member James Littlejohn highlighted the

 Espruino

family of open source hardware boards and devices during one of our community calls some weeks ago.

Turning a Puck.js into an open source one-button tracker

Exactly 5 years ago

 Twitter

started offering the option for users to download their full archive of personal tweets. The archive gives you a change to quickly browse through your personal history and find those funny cat pictures you once posted. But there is additional value in the archive, transcending the trips down to memory lane.

Meet the TwArχiv

If you pick dates close to each other, they also make for a great “find the differences”-puzzle.

 tl;dr: One can now create before/after maps of OpenStreetMap with osm-mapping-party-before-after right in the browser, thanks to MyBinder. Just click here to launch it.

For a good 6 months now, I’ve been contributing to OpenStreetMap virtually every day.

Making the creation of before/after comparisons for OpenStreetMap more accessible

On the weekend of September 17/18, 2022 the annual European Heritage Days took place again. During this weekend many monuments which typically aren’t openly accessible open their doors for the general public. Amongst the buildings that are open to the public during these days is the

 Palais du Luxembourg

, which was built in the 17th century and has been housing parts of the French legislature since the 19th century.

Journées européennes du patrimoine

A video of Panoramax in action. Starting out with a map view which has small orange lines for where images are available. Then going into the actual 360 degree images and moving around. Above: a video showcasing the panoramax viewer, with a map to see where (most

 [1]

) images are, and the 360º views.

Openly licensed streetview with Panoramax

Download PDF of the slides directly. Yesterday I presented what I learned from all of my passive data collection as a

 Show &amp; Tell

at the first European

 online

Quantified Self meet-up. I already showed some of my insights here on the blog, but I added some more data analyses for the presentation, including my movement patterns from the GPS data and details on phone usage.

Quantified Self Show &amp; Tell: Lockdown Life

This website has included a little

 personal API

in the footer for quite a while. But in recent-(ish) months I’ve expanded a bit on it, as you can see in the screenshot above. It now also makes an informed guess on whether I’m likely doing okay on a given day or whether I might be under the weather – for example because of falling sick, having slept poorly or other factors.

A heuristic for feeling fine

Happening just a week after the

 London Pride

event/parade, the

 London Trans Pride

gathered more than 25,000 people for a march from Trafalgar Square to Wellington Arch at Hyde Park Corner – despite a rainy start. The more mainstream crowds attending the

 London Pride

have turned the event into a party-like spectacle. In contrast, the

 London Trans Pride

consciously sticks to being a political protest march.

London Trans Pride

I have recently started to move my personal code repositories away from GitHub, in favor of hosting them with a smaller, independent and collectively managed alternative - including for this static website. In the same spirit, I was also interested in whether I could be doing my small part to diversify my overall web hosting approach.

Self-deploying more of my own small web

La Grande-Motte is a comparatively new commune in the Hérault département in Occitanie in southern France that was built in the 60s and 70s in what used to be a marsh. The city was planned by a single architect – Jean Balladur – who was inspired by the works of Oscar Niemeyer and pre-Columbian, Aztec pyramids.

La Grande-Motte

Photo: VOICES festival

Last week I attended the

 The European Festival of Journalism and Media Literacy

, to join a panel on

 Artificial intelligence – Which skills do I need?

. Moderated by Lee Hibbard, the panel consisted of writer Maria Farrell, computational linguist &amp;

‘AI’ at The European Festival of Journalism and Media Literacy

Flickr

as one of the old school photo sharing communities celebrated it 20th birthday on February 10th, 2024. To celebrate, there were photo walks in many different places around the globe, including in London. Beyond lots of

 Flickr

themed swag, our photo walk also took us into the

 British Museum

. The

 London

Flickr group has a thread where you can find links and images of a lot of the other attendees.

Flickr Turns 20

Having recently moved from Paris to London, it was time to get a new nametag for our dog Ohana – as the old one still displayed Eugenia’s old, French phone number. This wasn’t great as many folks don’t have phone contracts that allow calling abroad (thanks Brexit?).  Ohana’s old name tag was custom-made with a laser cutter – for both cutting the shape and adding her name and the phone number.

On the internet, everyone knows you’re a dog

Participating in the

 Mozilla Global Sprint

is somewhat of an annual ritual for me. This year’s installment took place on May 10/11. As

 Open Humans

hadn’t ever participated in a Sprint before, I spent some time in getting up a clean list of ways to contribute on a small micro-site.

The 2018 #mozsprint

“

 Algorithm

” is a word that has become more and more meaningless in our day and age – given how it is thrown around everywhere. If you bring it up with people who didn’t undergo some form of tech initiation – be that formal education or self-learning - it’s easy for them to conjure a picture like the one above: A colourful mess of things, too complex to understand if you don’t have some advanced degree in computer science.

Demystifying Algorithms by Doing

How can we make it easy to add data to

 Open Humans

?

 Open Humans

lives through its community of members and the projects they design.

Get your own Open Humans project up in 5-10 minutes

Mozfest is

 Mozilla

’s annual festival that brings together technologists, activists, scientists, artists and many more for a weekend in London’s Ravensbourne College. Unlike schedules of many other events, time for passive consumption of talks can barely be found. Instead, workshops make up the bulk of the schedule. And even the science fair &amp; demo parts consist largely of lively discussions between participants.

Mozfest 2018

{""=““} Image: Apple As is custom,

 Apple

gave a sneak peek into the new features that will come with the new versions of their operating systems later this year at the WWDC.

Interpreting the quantified self

The

 Wassail

or

 orchard-visiting wassail

is an English tradition in which people bless their fruit trees to ensure a good harvest come autumn. Typically, these celebrations and blessings are accompanied by song and dance – including Morris dancing – and bring the local community together.

East Greenwich Wassail

Or: Why 2024 is my personal

 year of Linux on the desktop

According to Doctorow,

 enshittification

might be coming

 for absolutely everything

. I’ve more and more felt this was for my own digital devices and means of digital production: Be that Apple’s just increasing love for walled gardens - especially since having the opaque app review processes (c.f. cpython’s --with-app-store-compliance), Microsoft’s (successful?)

Seizing my means of computation

The first month in Berkeley – and with that also with

 Open Humans

– is slowly coming to an end. And while much of this time was spent wrangling various forms of organisational and bureaucratic ordeals (finding an apartment; making sure all visa stuff is in order; getting a Social Security Number;

Getting started at Open Humans

The COVID-19 confinement in Paris and France at large lasted from March 17th to May 11th, with comparatively strict measures on when you could leave your house, where you could go and for how long &amp; when you could be outside. As a result a lot of folks, including me were forced to drastically change their daily routines, shifting to a home office approach.

The effects the COVID-19 lockdown had on me

{"=““}

 
 tl;dr
 
 : metrics-obsessed capitalism is the reason why we can’t have nice things – and watch @tante’s talk

Back in Paris, I was semi-joking with friends about how the rate of technological innovations seem to have slowed down or come to a halt. The last “big” innovation that we could think about were smartphones, as carrying the internet permanently in our pockets was quite a change.

Emptying Innovation - one metric at a time

On November 8, 2018 the Camp Fire in Butte County started and wasn’t contained until November 25, 2018. With at least 88 dead, 62,053 ha covered by the fire and over 18,000 destroyed structures it was the deadliest and most destructive wildfire in California so far. Over 52,000 people had to evacuate their homes. Soon, the smoke of the fires reached down to the Bay Area, leading to an increase in air pollution.

Wildfire Season

In the process of doing research for a snarky tweet I was looking for the yearly subscription costs of

 Nature

. In itself not an easy task, as the corresponding page one finds via Google is devoid of content.

When Nature pushes Malvertising

If you have spent any time on Mastodon and are intested in data visualisations, geography, RStats, or any of the intersections thereof, you are likely to have seen the stunningly beautiful 3D map visualisations that @terence has been creating with the rayshader package. I have been itching to get an excuse to play around more with this myself, and finally found a lovely one within the context of another little project.

Rayshading Argentina in R

In April 2023, I went to Argentina with the main reason being attending the 7th CSVconf in Buenos Aires. But of course we also went to visit Eugenia’s family over Easter. And we also managed to squeeze in some Lecturers Without Borders while there, even one in German for myself! Between all of these things we also found some time off for sightseeing.

Santa Fe &amp; Corrientes

US Senator Kamala Harris held the launch rally of her campaign for US Presidential election in Oakland on Sunday, January 27th in Downtown Oakland. A crowd of around 20,000 people showed up, filling the streets around city hall at Frank H. Ogawa Plaza. People (and animals) of all ages spent hours in line, waiting to gain entrance to the plaza itself, blocking off a whole city block in a snaking queue.

Kamala Harris Presidential Campaign Kickoff

tl;dr: I handed in my resignation back in early July and will be leaving my job - and the UK - at the end of October to go on a sabbatical.

This could have been a long and rambling post about all the problems with academia and/or the tech industry, but at the end of the day Lucidity’s

 Quitting My Job For The Way Of Pain

already made most of the aspects in a more fun way than I could hope to deliver them, so I’ll try to

Time to move on

{"=““}  The dynamic footer of my website has been powered by a little aggregation of some of my personal data for about 5 1/2 years by now. Until recently, all the data related to my activity and physiology (steps, heart rate, sleep, body) came from an Oura Ring.

Automating data exports from Apple Health

{nothing=““ about=““ us=““ without=““ us""=““} Last week, I attended

 “AI” UK

– which was organised by

 The Alan Turing Institute

and where I served in a minor role on the program advisory committee – and a workshop on

 Responsible “AI”

, co-organised by some fellow fellows of the Software Sustainability Institute.

‘AI’ from below

Today I finally submitted my PhD thesis (🎉) and what better way to celebrate that day than doing some data analysis and visualization, right? So, let’s get some idea on how much time the actual write-up took after all and how I spent my time during these weeks. Luckily, I’m running

 RescueTime

on my machines. The service allows you to monitor how, when and how long you’re using your computer.

Writing up a PhD: some numbers

Philipp and I again participated in the

 Mozilla Global Sprint

, which took place on 1st and 2nd of July.

openSNP at the #mozsprint

In the last blog post, I had mentioned that I was looking to move away some of my personal code hosting away from GitHub (GH), to avoid being locked in into yet another tech giant. Instead, I wanted to move to a proper free alternative. On Mastodon, lots of folks recommended checking out Codeberg as a potential alternative that is based on forgejo and provides static page hosting.

Code from some mountaintop

After having had some time to reflect on my writing process I’d like to share some of the things that I found useful during the writing of my PhD thesis. There’s probably already a million of these articles out there, but this also means that one more shouldn’t make much of a difference, so here we go. In principle this should all be applicable for other thesis writings as well.

A PhD writing survival guide

The pews of the

 Internet Archive

back in 2018.

 tl;dr: Posts on this blog are now automatically archived, indexed and full-text searchable through
 
 The Rogue Scholar
 

. The jury might still be out on whether the

 small

or

 indie

web will make a comeback, but I’ve personally enjoyed posting more on my blog here in recent months.

Archiving scholarly blogs with Rogue Scholar

Get a copy of the first zine of the project


 As if the sand were made of stone

is an ongoing documentary photography project that we (that is Eugenia and I) are working on. The project covers how small villages &amp; hamlets across rural Argentina – in particular the Argentinean Pampa – are changing and adapting in response to transport shifting from rail to road.

as if the sand were stone

Enoch’s Hammer

of Luddite fame, at the Tolson Memorial Museum.

 I gave a talk at the

Pint of Science Festival

 – an international science festival that takes places at local pubs and cafes across the world – this evening.

Imagined Future: Data democracy at Pint of Science 2074

Eugenia and I made our first zine,

 available here

, for our ongoing documentary photography project

 as if the sand were stone

. The project focuses on how small villages &amp; hamlets across the Argentinean Pampa are adapting in response to a shift in urbanism and transport – from rail to road. For our first zine, we selected 24 images, all made on black &amp;

As if the sand… – volume 1

tl;dr: Differences in my heart rate depending on the applications I use are small

With France being back in a second lockdown (though the rules are a bit less strict this time around), I thought it would be interesting to look at the impact of different habits a bit more.

Measuring app-related stress

Paris came out on 2020-06-06 for local #blacklivesmatter protests today. A part of it took place in front of the US embassy at Place de la Concorde, with the police fencing off the area widely. Another group gathered at the Champs de Mars facing the Eiffel Tower.      The full image set can be found on Flickr.

#BLM 2020 in Paris

Being more of a dog-person (or to stay in

 OkCupid

lingo

 likes dogs, has cats

) I was sad when I saw that the

 CatterPlots

made their rounds on Twitter again this week, as there’s still no dog-centric alternative if you’re an

 R

-faring data visualizer. In order to dry my tears I went over to dog_rates for some binge dog-watching. And then I wondered, aren’t these puppers all getting cuter and cuter?

They are Good Dogs, Indeed

In August 2022 I went to visit Wetzlar and the Leitz-Park together with Vinh. Beyond checking out the old city, we were particular interested in going to the Leitz-Park as it is the birth place of Leica cameras and 35mm photography more broadly.

Wetzlar &amp; Leitz-Park

Geotagging photos in

 Adobe Lightroom

. After semi-accidentally ending up at SantaCon in San Francisco last weekend, I was wondering how I could geo-tag my photos more easily. If you’re only taking pictures with your smartphone, that’s not much of an issue as the internal GPS applies the metadata automatically. But lots of modern cameras still don’t come with an internal GPS or require some ridiculous add-ons.

Using Overland to Geotag Photos with Lightroom

Santa Con: What started out as anti-capitalist performance art in San Francisco (hanging Santa included), has turned into a ‘reviled bar crawl’, across the US.  So also in San Francisco in 2018 where hordes of Santas took over Union Square on Saturday, 2018-12-08. And it wouldn’t be San Francisco if a group of naked Santa was missing.

SantaCon

Last week the

 The Royal Society

issued a joint statement about the importance of the international nature of research along with national academies across the UK and Europe. At the same time they started the hashtag

 #ScienceIsGlobal

on

 Twitter

, where individuals reported what nationalities are collaborating in their labs. I, and many others, reported their lab’s composition using the emoji flags.

#ScienceIsGlobal

[![a split map, with an older view with less items on the left and a
more current one with more items on the
right](/assets/images/2024-12-15-osm-comp.png)](/assets/images/2024-12-15-osm-comp.png)
[If you pick dates close to each other, they also make for a great "find
the differences"-puzzle.]{.small}

**tl;dr: One can now create before/after maps of OpenStreetMap with
`osm-mapping-party-before-after`{.language-plaintext .highlighter-rouge}
right in the browser, thanks to MyBinder. Just [click here to launch
it](https://mybinder.org/v2/gh/gedankenstuecke/osm-mapping-party-before-after/binderrize?labpath=make-images.ipynb).**

For a good 6 months now, I've been contributing to
[OpenStreetMap](https://www.openstreetmap.org) virtually [every
day](https://hdyc.neis-one.org/?Bastian%20Greshake%20Tzovaras). One of
the things that is very addictive about it is the rapid feedback, as one
can immediately see the effect of an edit show up on the map. And of
course, in regular intervals those changes find their ways into great
apps such as [OrganicMaps](https://organicmaps.app/).

What can be a bit harder to see is the cumulative effect made of edits
over a longer distance of time. Of course, not just based on one's own
edits, but the joint edits by all contributors that are active in a
place. For a very long-term view, [*OSM: Then &
Now*](https://2008.osm.lol) provides a comparison between a point in
2008 to *now* for the whole world, while [*baato*'s
before/after](https://beforeafter.baato.io/) allows to make comparisons
for small slices of the world (think city-level) for a user-chosen year
to *now*.

If one wants to make more targeted comparison, down to the second-level
for the before *and* after date, [Amanda McCann wrote a very
comprehensive, bash-based
pipeline](https://github.com/amandasaurus/osm-mapping-party-before-after/).
It takes an OSM history file, the before/after timestamps, the bounding
box one wants to have displayed in a (static) map, as well as the zoom
levels of interest. With this it creates both png-based, side-by-side
comparisons as above, as well as animated gifs.

![an animated gif that switches between the before & after
view](/assets/images/2024-12-15-before-after.gif)

Unfortunately, being able to create such comparisons locally means
needing to have all the prerequisites for rendering your own map tiles
installed. And as for any complex software project, this means
installing a ton of dependencies, which in turn come with their own
dependencies, which in turn... ...you get the idea. Trying to get all of
those set up, and avoiding to run into incompatibilities, isn't for the
faint of heart (or at least that's how it feels to me).

So when I started to try setting it up for myself, I [decided to do so
in a Docker
container](https://github.com/amandasaurus/osm-mapping-party-before-after/pull/5).
On the one hand, to avoid me accidentally breaking my operating system.
And on the other hand, to make it a bit more predictable and reusable
for others. Thanks to lots of feedback by [Máté
Gyöngyösi](https://github.com/gy-mate), that approach now works quite
well. I also made a ready-to-use image under
[`gedankenstuecke/osm-mapping-party-before-after:v1`{.language-plaintext
.highlighter-rouge}](https://hub.docker.com/r/gedankenstuecke/osm-mapping-party-before-after/tags).

While this approach side-steps the trouble of having to locally install
the whole tile generation pipeline, it replaces it with the need to
install Docker, having to connect into the container, get the files out,
... In other words, it's maybe easier but still far from easy.

Which is why I tried to package this approach up into a Docker container
that can run on [*MyBinder*](https://mybinder.org/), which allows
running containers in *'the cloud'*, without having to install anything
locally. The way MyBinder works is that it launches an ephemeral
container for the user, based on a GitHub repository that is build into
the container. The container then launches a web-interface that the user
is being forwarded to, to interact with the custom-build environment
right through the web browser.

I decided to use the standard *[JupyterLab](https://jupyter.org/)*
interface as the web-entrypoint for making this work. To do so I
[expanded the
image](https://github.com/gedankenstuecke/osm-mapping-party-before-after/blob/binderrize/Dockerfile)
I had already used as a starting point (the
[`postgis`{.language-plaintext .highlighter-rouge}
image](https://github.com/postgis/docker-postgis)), added *JupyterLab*
to it, and modified the entrypoint to launch both the needed *Postgres*
database & the *JupyterLab* server. Once that worked, I wrote a [little
*Python*-based
notebook](https://github.com/gedankenstuecke/osm-mapping-party-before-after/blob/binderrize/make-images.ipynb)
that makes use of the `ipywidgets`{.language-plaintext
.highlighter-rouge} to allow people to pass the necessary parameters
before creating the actual images.

Combined, all of this means that [one can now click this
link](https://mybinder.org/v2/gh/gedankenstuecke/osm-mapping-party-before-after/binderrize?labpath=make-images.ipynb)
and it will automatically launch the container through MyBinder, and
even open up the notebook. All that's left is first uploading the right
[*OSM history* file from
*Geofabrik*](https://osm-internal.download.geofabrik.de/), and then one
can enter the parameters and create the comparison images.

## When to use which approach?

Compared to my prior, local *Docker* solution there's some benefits and
some drawbacks: The most obvious benefit is that the *MyBinder* solution
doesn't require installing anything locally, as it all happens in a
browser. So there's not even a need to install Docker.

The main drawback of using the *Binder* approach comes from the fact
that the virtual machines that *MyBinder* provides are ephemeral. I.e.
None of the files that are uploaded into it or created within it are
stored long-term, as the virtual machines are being shut down if not
used for some time. As a result, creating a new comparison image after
starting a new *Binder* will take a while. This is, because it first
downloads a lot of external data which *openstreetmap-carto* needs.
Similarly, the *OSM history file* that needs to be uploaded as the basis
for creating the images will have to be re-uploaded.

In contrast, the local container is made to store the external data, how
it has been processed, as well as the history file for the long-term,
making it easier to return to creating more images later on.

So, when to use which approach? I'd say if you don't want to install
anything and/or don't plan on returning to creating maps regularly,
using MyBinder is a great way to get started. But if you'll regularly
create updated images, then figuring out the local *Docker* setup might
be worth it, to avoid waiting every time.

Lastly, I'm sure there's still potential to improve both approaches, as
I'm extremely far from being an expert in any of these technologies. 🙈
So, if you have ideas for that, please have a look and maybe even leave
a pull request.

------------------------------------------------------------------------

**ps:** Thanks to an invite by [Daniel
Bellomo](https://social.coop/@dbellomo), I gave a talk about *citizen
science* and ways of creating community knowledge (including
OpenStreetMap & [Panoramax](/open-source-streetview) at *Universidad
Nacional de Río Cuarto* last week. You can [find my slides
online](https://tzovar.as/cs-mapping-talk-unrc/).
