One year of desktop Linux


If you consider switching to Linux from a Windows or OS X machine, you will find some of my experience in this post, one year after starting to use Linux exclusively for my professional life as a scientist. With the ubiquity of web applications, the desktop environment might seem less important than a few years ago. Still, there are plenty of things that are better done on a desktop, including computation-heavy or specialized analyses. This post assumes you have some knowledge of Linux, specifically how to install applications and how to edit configuration files.

I first tested Linux on my laptop in 2001 and 2002 but was only convinced to permanently switch to using it for my personal use with the arrival of Ubuntu Dapper Drake in 2006. Using Ubuntu at home had an impact on my daily professional life. For example, our collection of reagents is maintained on a LabKey server on Ubuntu in a virtual machine. Experience with the command line definitely helped for the administration of our laboratory backup server, a Sinology network disk station. Last, but not least, the extensive experience with shell and shell scripts, was crucial for data analysis projects both for research and in teaching.

Before going further, I would like to share with you a desktop screenshot, showing my current theme in Gnome, OneStepBack. The easiest way to install the theme is to download and unzip the corresponding file in a .themes folder in your home directory. The theme can be applied with the Gnome Tweaks application.


An important choice when switching to Linux is the distribution, as it affects several aspects of the linuxian life . Based on my previous experience with Ubuntu, I chose it, because “it just works”. The size of the Ubuntu users community is very important, since many questions that I might have had were already asked and answered by someone. Many thanks to those which asked and answered questions, as well as to those sharing their experience with specific issues of application install or configuration. In addition to generic Linux documentation, one of the best sources of information on arcane Linux configuration options is the ArchWiki, a documentation portal for ArchLinux (which you can try in a user-friendly version called Manjaro).

Installation and basic configuration

It was not an easy choice to change after 18 years of Mac use. I still like the way Macs work and how the desktop looks, but the lack of a Pro solution in latest years, as well as the steady development of user-friendliness in Linux, settled the decision. Ubuntu 17.04 was thus installed on a Dell machine with plenty of RAM, an SSD disk for the system (more on this later) and two 2 Tb data disks.

Initial installation required endless updates for the preinstalled Windows system, reducing the size of the Windows partition and installation of Ubuntu. The most difficult part was the assignment of the two data disk to a zfs pool in a ‘mirrored’ configuration. The data, which are also mirrored daily to an external network disk, are thus duplicated among the two disks, without any need for further configuration. The use of ZFS is probably a headache for most users, and unfortunately I did not have enough time to do more than basic configuration.

While it might seem a minor issue for most of the system administrators who use Linux  servers mostly through a command line interface, the desktop environment has a major impact on Linux used through a graphical user interface. It has been my pleasure to test and work for some time with most of the major desktop environments and, strangely enough, I like them all. So, no, you won’t find here any of the “The 5 best desktop environments for Linux” non-sense. The current blog post is written under a Gnome Shell environment, which, with extensions, works mostly as I want it to work. KDE Plasma is probably my “go to” distribution if I take my laptop on a journey, since I am sure that external monitors, for example, are correctly recognized. On the workstation, Cinnamon, a GTK3-based DE from the Linux Mint creators, works flawlessly. I spent some time as well with XFCE, my distribution of choice for my 12 year old laptop, and with MATE.

Advantages and annoyances of using Linux

My major problem since using Linux has been the death of the system SSD in December last year, 8 months after buying the workstation. Maybe it was not Linux’s fault, but I tend to believe that somehow, the very frequent writing of logs and other information to the disk had a catastrophic effect. I am not a specialist, but I prefer to use now a 7200 rpm hard disk for the system. So, be cautious on what type of media your operating system lives. You might want to follow some advice from Pjotr, a Linux user from Holland.

A clear advantage in using Linux is anything linked with development, from scripting in R or Python, to installing software that you need for mapping reads to DNA sequences (where Conda and Bioconda are fantastic tools). Many available text editors are fantastic, and I have a personal preference for Kate, both for its multiple customization options, speed, and overall usability.


A major advantage in using Linux daily is the existence of excellent open-source tools and their ease of installation, mostly with a apt install program command. For Python, I’m using Spyder and for R, RStudio. The manuscript figures benefit from editing in Inkscape and the manuscripts, as well as other documents are written with LibreOffice. Bibliography is handled gracefully by Zotero and its extensions, together with Firefox. For any kind of ideas, for collecting figures from papers, and general notes, CherryTree is a fantastic open-source program. PDF reading benefits from Okular. Image analysis and editing are the realm of ImageJ (and FIJI) and Gimp. For file searches, CatFish is fantastic. For a knowledge database with indexed pdf files, Recoll is my tool of choice. Handling pdf files can be done with an extremely flexible Java tool, jPdftweak.

Switching to Linux is not easy and you have to be ready to invest some time in customizing your experience with the system. Some very strange bugs manifested themselves with the printing system, for example. From time to time, the pages printed on a local network printer have a “Top secret” watermark :-(. Fonts can also be a problem, especially when exchanging files with your colleagues, who use Macs or Windows machines. Establishing a file share server is not painless either (the best solution I found was to install and configure a Samba server on my machine).

In view of the time and effort spent with setting up and customizing my Linux machines, it would be impossible for me to say that I regret my decision. Having invested in this installation, places me between the post-purchase rationalization and IKEA effect cognitive biases. I’ll be back with experience at two years post-switch, probably in April 2019….

Conclusion: if you are already a ‘power user’ for Linux and you don’t need proprietary applications for your work, switching to Linux is a lot of work coupled with a lot of fun.

If you have any specific question or want to share your positive or negative experience, please go to the comments section. Thank you.


Twitter archive for 2016

A collection of my tweets in the past two years (only a very limited number of retweets), recovered from Twitter, with the option to be found in everyone’s profile. Chronologically reversed order.

Will probably edit later to highlight what looks most important for me.


A ‘get things done’ file manager for any Java-enabled platform, recently revived is muCommander (with pretty ghosts)
Teachers need to use a historical perspective when teaching mathematics, but who will teach the teachers ?
Sad how Twitter thinks that the most *popular* tweets are the *best* tweets. No, they are the most *popular* and should be labeled as such.
If politicians do not understand the language of science, scientists should learn the language of politics and translate for them.
If interested in science, mostly physics, its history and science-fiction, a blog to follow is Greg Gbur’s
Creating a Python3 environment is painless: >conda create -n py3k python=3 anaconda …wait >source activate py3k…
Maybe I know myself less than the #Google+ algorithm knows me, but no, I’m not interested that much in the Bitcoin G+ community. Thank you.
Music streaming services, like subscribing to ‘unlimited books’ offers have the side-effect that *no* sharing of music or books can occur.
#Spyder is the #Python equivalent of #RStudio, easy to configure, with completions, block comments and #iPython console. Slow on OSX though.
The fact that tweets most retweeted contain a higher proportion of images does not mean that adding an irrelevant image will increase impact
I like the #StarWars saga because its broad context is the struggle of democratic Rebels to replace a dictatorship, the Empire.
@ToKTeacher Naive questions: are there testable predictions the multiverse model makes that other theories do not ? Has it more reach ?
Realistic human face rendering in movies still not there in 2016. #RogueOne
@Elysee @fhollande @najatvb Le numerique, oui, mais mettre l’accent sur la methode scientifique aurait plus d’impact à long terme.
To manage strains, plasmids or reagents, an open and mature solution is @LabKey . Used every day in our laboratory…
Wondering what is the ratio bot/human in my Twitter #followers. Is this ratio variable, in general ?
Some people spend tremendous amounts of energy to share knowledge, without any obvious immediate benefit for themselves. Why ?
A nice explanation about the hard to grasp concept of wave-particle duality:
Open source success: lots of scientific presentations use the open source mouse image by @Lemmling on @openclipart…
When nothing else works, or you just want to select columns in a text file, try #jEdit, a great text editor:
Have questions about globalization ? Interesting answers and predictions:
Some tweets should be retweeted twice: Ten rules for structuring papers @biorxivpreprint
‘In 2016, lies, the whole lies and nothing but the lies’ Joel Stein’s title of ‘The awesome column’, Time December 2016
@TIME – sad to see your #CRISPR story failing to mention that the discovery was the result of many years of publicly funded research.
Deep learning and expert systems are not artificial intelligence but sophisticated and useful tools for complex data.
My best teachers helped me understand the value of well crafted books for learning chemistry, physics or mathematics.
Going slightly mad with GFFs, GTFs, #gffutils, #Salmon, #bedtools, etc. So many tools, so short the time …
Calling coding sequences “cDNA” is misleading in the #Ensemblgenomes, please correct README files (e.g.…)
«Tweeting is teaching, for better or for worse.» Anonymous
Sur BFM – les ‘experts’ pensent qu’apprendre une langue etrangere à l’ecole diminue le temps pour le francais… En fait, c’est le contraire
Will not click on links in tweets that begin with “Scientists have discovered a causal link between something and else.” Just #correlations.
@TIME – please refrain from using axes with arbitrary starting values for percentages. It distords the message.
Learnt today one of my long time interests is called epistemiology – a scary word designating the study of ways to gain knowledge.
Sun Tzu’s 2500 years old ‘The Art of War’ is probably famous because it reads like a scientific report. Concise, precise and pragmatic.
Wondering how much equivalent of Random Access Memory, #RAM, humans have. Most efficient ways to increase it ?
The innate desire of humans to teach others was probably selected during evolution. *What* we teach is a deliberate choice.
Video tutorials in which a guy explains his slides are a waste of time compared with an equivalent written document.
When you can’t see the top of the head for men in cropped pictures on the net, probability is high that they are bald.Apprendre l’anglais à l’école permettrait l’accès à des superbes livres, non-traduits, comme celui de John Stillwell: Maths and its history.


Fantastic open-source Android note taking application: OmniNotes.…
Read 16 out of the 17 science fiction ‘classics’ listed by lifehacker:… . But why 17 ?
After lots of phylosophy today, pragmatic observations on how to touch-type on an Android device with Multiling O:…
Looked yesterday into a book about happiness through meditation. Scientists should all be cheerful because they never stop meditating.
People think economic progress depends on making more and better ‘products’, when in reality all progress depends on advancing ‘knowledge’.
Est-ce-que c’est normal d’aller voter pour soi-même quand on est candidat ? Surtout quand le seul enjeux est de choisir une personne ?
About impact: even the most influential books, like those by Darwin or Popper, needed people, active proponents, to spread the word.
‘Refocus journal club discussion from findings to methods and approaches.’ Great advice.
“It is easy to obtain confirmations, or verifications, for nearly every theory – if we look for confirmations.”…
Converting one font format to another works beautifully with #FontForge, a complex program for font design (
Philosophers are to science what critics are to art. Good ones are true scientists, just like good art critics are great writers.
Bizarre comment je suis content de voir une place de parking libre même si je suis à pied…


The historical origins of ‘seconds’ and ‘minutes’ explained by a reddit user:…
Human intervention *still* required for #Sanger DNA #sequencing. There are only two “T” bases there.
“Science is what we have learned about how to keep from fooling ourselves.” Richard Feynman
Dommage qu’avec #Bayard et #jaimelirestore les e-book pour enfants sont disponibles seulement sur une app iPad. ePub sans DRM resoudrait ça.
Not satisfied by an #eBay seller, I tend to leave no evaluation. A lack of evaluations might be a robust indicator of not that great sellers
Great to see how yeast genetic screens with fungal viruses led to insights into mRNA degradation in humans (#SKIcomplex) #EESmRNA
Removing those annoying newsletters does not require any special program to assist you in clicking on the ‘unsubscribe’ link at msg end.
Many kids today believe that #Amazon is a kind of god that answers prayers done on your home computer. Next day delivery.
The person most likely to re-read this tweet some day is my future self. The same with blog entries.
The smartwatch of 1981, with perpetual calendar until … 2019. Pricely #Citizen at that time. 8940 movement.
Batch renaming files is done in OS X #Finder through right click on a list of selected files. Should be a default option in other OSes.
Cut-throat academia leads to ‘natural selection of bad science’, claims study…
Wondering if everyone stops dreaming about flying, with age.
Learning to program by making a game is like trying to get a driving licence with a 2 inch replica car.
Most annoying error in simple #bash scripts so far: COMMA not used in array variables.
Instead of dealing with with GEO sra files, search for the equivalent fastq files in the European Nucleotide Archive
Why not allow comments on #GooglePlay for apps without having to give “stars” ? Constructive criticism could be done without a rating change
Un exemple des limites des methodes de “deep-learning”, completer l’information manquante deforme trop l’image.


BBC News – How to be mediocre and be happy with yourself…
If only R could warn stupid/ignorant/beginner users when they push “Enter” on a command that risks to run forever …
I dream of smarter command line interfaces. Imagine a shell that can correct typing mistakes and gives usage hints when things go wrong.
Only 85.5% of viewers will like this cartoon #smbc #hiveworks…
#PokemonGo illustrates in the real what Vernor Vinge described as widespread in the Hugo awarded Rainbows end book.…
“The Feynman Lectures on Physics,” The Most Popular Physics Book Ever Written, Now Online
A beautiful large-scale study of the impact of combinations of codons on gene expression in yeast.…


Ca fait plaisir de voir #Musnet en vitrine. Superbe bande déssinée de #Kickliy.
CRISPR-directed mitotic recombination enables genetic mapping without crosses…
Switching the Linux kernel from 4.4.8 to 4.6 in #Ubuntu is easy and dramatically affected idle energy load from 15 to 9W.
L”application #Android #OrangeRadio est excellente pour les radios FM par Internet.
If #Gimp or #Inkscape look fuzzy on a high resolution screen in Windows 10, inactivate scaling in the “compatibility” tab of properties.
Switching back to #Windows after 10 years of Linux desktop use. 5 hours of battery life for Windows 10 vs 1.5 hours on #Ubuntu 16.04.
Translation dynamics of single mRNAs in live cells and neurons (Singer lab)…


#DoubleCommander can rename a bunch of files with or without regular expressions. Works well and replaces other batch file renamers.
Trouver un trèfle à quatre feuilles n’est pas une question de chance mais de persévérance.
UpSetR, our #rstats based alternative to venn diagrams has now more than 5k downloads!
App stores should have separate ratings for buginess, annoyance and ergonomy of apps.
Most scientific, ‘expert’, reviews repeat the conclusions of published papers instead of discussing actual data and potential pitfalls.
Feather: A Fast On-Disk Format for Data Frames for R and Python. This may interest you @biocs.… #rstats #python
Comment #SFR va garder ses clients tout en augmentant leur tarifs? En proposant des services dont on n’a pas besoin?
Upgrading to the latest version of the #TiddlyWiki is simple like drag and drop:
PIN digits distribution, math puzzles and more:
Authentic mail excerpt: “X salutes you for your compendium of writings which immensely help the global society and their #descendants…”
“[Scientific] work is not done for the sake of an application. It is done for the excitement of what is found out.” R. Feynman
#SQL on delim #textfiles as databases. Ex: $ cat some.txt | q -H -t “select * from – where Type like ‘%pattrn%'”
There is a choice between Tree Style Tab and Tab Tree for tab handling in #Firefox on a wide screen.
#Inkscape and #Sozi work well together for presentations nicely rendered by any web browser:…
One of the reasons why using #TeX is more cumbersome that it could be. We should not need tips to write “32°F”.…
Essential #genes might be essential because there was no need to duplicate them in evolution. “Essential” is different from “Important”.
After Ubuntu’s cloud storage, goes extinct. I hope #Hubic and #SpiderOak will continue to operate.
“The X journal invites you to view your publication performance” – I didn’t know my poor publication was in a competition for “performance”.
This is when you know you are followed by #bots.
Testing #Sozi for an #Inkscape based presentation shown in a web browser. Looks promising so far.
Thank you #PlayOnLinux and #wine for the easy install of #AdobeReader on a #Ubuntu machine. Sad that #Adobe dropped support for Linux.
A useful dock in #XFCE is #DockBarX, in its panel integrated version. Install on #Ubuntu:…
All JS libraries should be authored in TypeScript… via @andrestaltz
/Soft drop shadows/ is a feature that would greatly improve the aspect of #LibreOffice presentations
Scientists tend to discover beautiful equations in maths and physics because the brain is rewarded by “beauty”…
If a 7 yo kid asks about what fractions are, tell them they were invented. #Mathematics is a mind construct and should be taught as such.
Another highly readable #font for #ebooks mobile devices is #Fontin:
Font preferences in #Thunderbird may need the “Other Writing Systems” option to be modified (not only Latin).
Recovered my tweets from #Twitter and found that none of the uploaded images were present in the archive, just links to them. Frustrating…
Quick list of customizations that can be done on a laptop after installing #Ubuntu 14.04. #selfpromotion…
You never know for how long you can read your bought #DRMed books. Sadly, #Nook #ebooks and tablets cease operation.
#wordpressdotcom seems to have a technical bug with two-factor authentication. Sending messages to phones all over the world might be hard..
Once well implemented, #Ubuntu #Unity features are time and screen space-saving: the launcher, integrated menus and the dock.
The comment for the article about how basic maths are known and used are very interesting too.…


#Zootopie est l’equivalent moderne de #Monstresetcie. Drole, positif et bourré de blagues visuelles et textuelles. #films
Non-Long Term Support versions of #Ubuntu should be called Experimental. Best tested in a virtual environment of an LTS version.
Back to #Ubuntu after a year of using a Mac. Waiting for the next Unity release, to be able to adjust global menus.
Funny how Windows needs installation of a dozen of drivers when Linux mostly just works. Unless you happen to have an M.2 SSD drive :-((
#Acer built into the #Z630 phone a perfect set of endurance and expandabiliy for 200€. Crop of a ISO 280 image, f/2.
Taking notes on #Android is made easy with #ColorNote.…. Plenty of nice ergonomy features.
Savoir les dates des vacances scolaires par zone, c’est plus facile avec des calendriers officiels:…
Hard to decide if the home (and work) laptop should run an #ArchLinux-based (#Manjaro) or a #Debian-based distribution (#Ubuntu, #Mint).
The only thing I learnt from lousy lectures delivered by boring teachers was that I should not inflict the same treatment to my students.
Code: “Good style is important because while your code only has one author, it will usually have multiple readers.”
The #Outlook web app asks users to wait until the attachments are uploaded. Much less elegant than #Gmail.
Making interactive plots with #ggiraph and #ggplot2:…. Other extensions here: (
@TiddlyWiki is wonderful as a note-keeper – sync on any platform (e.g. Hubic) and easy to use with #TiddlyFox.
The system font of the old Nokia #Symbian S60 phones is one of the most readable for #ebooks.
Update on my blog post about sharing folders between host and #VirtualBox machines (important -o gid=1000,uid=1000)…
#Doublecommander, a file manager that can synchronize the content of two folders #LinMacWin.
Bravo pour l’enseignant qui montre aux enfants de CE1 l’edition des documents avec #LibreOffice. Ce n’est pas une initiative du ministere…
Wondering if there is any dual pane file manager that can do folder content synchronization #rsync-like.
“The criterion /upon which we base our decision to reject/ the hypothesis” -> The criterion /used to reject/ the hypothesis. #Gopen/writing
Stable #Debian that plays nice in virtualbox and allows easy install of recent versions of many apps: MX15 Linux.
The worse error of an aspiring statistician is to look at models instead of visualizing the data.
#opensuse is the first distribution tested in the last monhs that would not install on a virtualbox architecture
Qui a dit que #windowsxp est périmé? Toujours en vie et vaillant sur des machines ouvertes au public… en 2016.
One day, regular users might use #containers on their operating systems, to test new features without adding bloat.…
Visualize how different means vary together; one of the gems in “Street-fighting maths”…
“Quotidiennitude” – une perle entendue à la radio #OMGlangue
‘Trying is the first step towards failure.’ — Homer Simpson
“…updating a blog post with new content makes more sense than creating a new post that continues the discussion.”…
“[…]Much of an expert’s competence stems from having learned to avoid the most common bugs.[…]” – Marvin Minsky…
#Conversations add-on for @mozthunderbird allows easy finding of mails and replies, better than Gmail’s thread view…
“Never use a complex word when a simple word will do.”…
At last the Apple FR keyboard behaving on #Linux: setxkbmap -layout fr -model macintosh. Make it persistent by adding to .profile.
Efficient data #backup in #Linux is easier from a specific disk partition than from a /home directory overcrowded by hidden files.
Un excellent investissement pour 10 euros – “Les clés de l’#orthographe” par André Porquet. Petit livre, excellentes explications.
Not checking mail for a few work hours could be effective. Doing this is not likely to require a special service.…
A post about how I move columns of a text file or do small but global changes fast in text files with #awk and #sed:…
“Improving the quality of writing actually improves the quality of thought.” Not only in science.,… Gopen, Swan 1990
Keeping offline copies of my #GoogleCalendar and #gmail is pretty easy (…).
For an #Xfce panel that overlays windows (…) use and add a False ‘disable-struts’ to panel.
#Geany is a cross-platform alternative to #TextWrangler for editing or source code print (
#Thunderbird is a more reliable IMAP mail client than #Outlook, on Mac. N=3, but still…
If you like the no-nonsense approach of #Xfce, #Manjaro is an alternative to #Xubuntu. Derived and user-friendlier than #ArchLinux.
#Archlinux is an interesting choice when you need #Linux in a virtual env. Very reasonable minimal install size.
‘With four parameters I can fit an elephant, and with five I can make him wiggle his trunk.’ — John von Neumann


What’s the secret of good writing?
En verlan, le “iPhone” devient “Phonei” (phoney = “imposteur” en anglais).
Using +scale+ when saving #ggplots, and other tips…
Slide changed before I could manage to understand a #Venn diagram. Images with 3 or more Venn regions are utterly unreadable.
Un “sociologue” sur Fr info: “Les classes pop votent moins malgré le fait qu’ils ont plus de temps libre le weekend.” #abstention (????)
Programmer un bon outil en #bioinfo, et en général en #informatique, n’est possible que si le developpeur veut cet outil pour soi-même.
Trying #Rodeo, a #Python IDE that makes an #RStudio – like interface with #Electron/#Jupyter. Promising but freezes at first tab key press.
Just like a redditor said: reading tweets and reddit front page in the morning replaced the daily newspaper.
“This is a sickness in Europe,” Galbraith says: “The past is valued more than the future.”
Humor: “Users can be very dumb but it’s still the developer’s fault for not making something easy enough.” from…
#Coding for one hour provides about 0.01% of a programmer’s knowledge. “Teach Yourself Programming in Ten Years”
#TiddlyWiki ( became more user-friendly with the #TiddlyFox extension (…). Personal or shared.
#Zotero is used by one third of scientists who answered an online survey (N=882).…
A cheap way to promote clicks is to hide essential content of a tweet by truncation. This is why
Dismissed #plotly as a commercial tool in the past, but it recently became open source, seems very promising…
Mail clients should focus on standards and very long term support and compatibility instead of ‘revolutionary’ user interfaces.

Reading ‘Tom Sawyer’ for my son is like rediscovering a beautiful landscape filled with delightful details.
#IGV, #ImageJ, #JavaTreeView, #LabKey – some of the most used programs for research are written in #Java. Should reconsider attitude on J.
Défi: expliquer à un enfant de 7 ans ce que c’est un “groupe nominal” et surtout à quoi ça sert de connaitre ça… #écoleprimaire
Well written and thorough explanations on the benefits of SVG for animated graphs or icons.…
@mozilla developers – please read and take into account the users. @zotero is a major tool for science.…
Excellent explanations on stat overinterpretations.…
#ElCapitan makes the pointer larger if you wiggle the mouse fast enough. No mouse pointer lost anymore!
I thought I knew English from reading on the Internet, but then I started reading a #book.
Moins d’éducation corrélé à une méfiance envers la vaccination parmi les participants à l’etude @GrippeNet.
Are people more likely to attend a talk knowing that sweets and coffee is offered afterwards ? An experiment to test this would be fun.
#ElCapitan – slight lack of attention to the detail even before installing it. Polished and nice otherwise.
Videos and postcasts should not be used as replacements of good old written articles.
How nice would it be if #Zotero could tell me if the article I’m viewing right now is already in the database or not…
Seeing the pixels of the glorious qHD 534 ppi screen of the #LGG3. Because water droplets work as lenses.
Identical size selection in #Gimp is easy by writing the size in the tool option dialog. Handy with #scientific figs
Invitations to ‘guest edit’ an issue of an obscure journal are like ‘free lunch, bring your food’.
The #Nexus5X is available but, at 479€, too expensive for the number of compromises they made (no FM, no SD card, no user-replaceble batt).

How git works? No idea!…
There is a need for an #antitweet – to cancel tweets or blog posts that are notoriously made just to go viral and for that, distord reality.
For an avid #reader, replacing a #smartphone with one with a bigger screen is like changing from the paperback to #hardcover edition.
#Themartian me: ‘Nobody will like this movie, there are no fights, no action’ 7 yo: ‘But dad, he’s fighting with the entire planet’ me: …
“Motivation: It’s Not the Carrot or the Stick” by @callmemrmorris…
Current reading font: #Andada – beautiful and highly lisible.…
Apparently #DavMail can be used to access goodies from an Exchange server. Good do know but setup seems cplx:…
Scored an estimated 43 wpm writing speed with #MessagEase #keyboard on #Android. Without predictive mode!
Entering the second phase of #twittership: ‘blasé’
“Great products happen when people build a product for themselves.” Eric Schmidt…
Did not really feel like a hacker when copy-pasting commands from a forum in a terminal to gain root access to a phone. But it worked.
A few simple and not that simple data analysis tasks done with #R AND #Python and various packages.…
It would make sense to have Twitter as a #publicservice rather than a private company.
Wondering if there is some weekly periodicity when loosing weight (with the help of #R and #ggplot2).
Elephants: Large, Long-Living and Less Prone to Cancer
Understand why there is no FM radio in so many new devices including #GalaxyS6, #iPhone6s or #Nexus phones:…
L’information des affiches électorales frôle le zéro car 99% de leur surface n’est qu’un grand #sourirevotepourmoi. Et ca marche?
Laziness must correlate pretty well with the retweets to tweets ratio. Or is is lack of self-confidence?
The advanced search dialog in #Thunderbird should be promoted as the only search system, easily accesible from the toolbar.
Fast shoe lace tying – works with reasonably long laces:…
Funny online tool to see what a short script does: Learning programming at scale… via @radar
Realized today that I was following a prolific Twitter bot (#YCombinator). Impressed.
Just discovered that the Google #keyboard can assist in orthograph corrections on a previously written text.…
Le campus de Stanford a commencé à utiliser #WordPress il y a 8 ans, maintenant ils ont un accès privilegié à #Overleaf. A réfléchir.
Potentially a way to use a single image file and load various resolutions of it on a web page or on screen.…
The #nexus5x has a nice camera but non-removable #battery, no #SD card an no #FM radio. Too expensive in Europe too.

Nice discussion and study on the ergonomy of screens while driving, for lovers of #typography and #design :
Great advice for faster weight loss: Don’t.
My post about, the library that serves as the basis of Lens viewer in the #eLife journal and others…
CEO who raised price of old pill more than $700 calls journalist a ‘moron’ for asking why
Eating less without knowing it: smaller portions in smaller plates.…
Nobody looks smart when driving a Ferarri in a traffic jam.
Reseautage – moche mot ‘moderne’ pour ‘se creer des relations’ – entendu à la radio.
Reminder: a tweet a day keeps the bad doctor away.
@Science_Open Thank you. So, the term ‘peer review’ is recent, not the process in itself. It is an entirely different perspective.
Admiring scientists who seem to know what questions are worth exploring.
Me: Have you heard of Ebola ? Someone: Oh, yes! Me: It’s an RNA virus and I’m working on RNA. (better intro to my research?)
Still far from the time when the smartphone would automatically search for the bus schedule when you walk towards the bus station.
The humble #Nikon E 50mm f/1.8 is compact light and perfectly usable in low light for a scientific meeting.
Introducing computers in schools does not lead to improved performance for pupils, probably the opposite.…
Wondering why online sellers would still send untracked parcels. Cheaper is definitely bad for the bussiness.
Bourré de trouvailles et d’images surprenantes, “Le tout nouveau testament”. Effectivement iconoclaste.
Possible solution pour inclure les annotations et descriptions des données dans un fichier #csv… via @mfenner
Amusant – kibi, mébi, et autres unités de mesures des multiples des octets ……
“Humans desire certainty, and science infrequently provides it.”…
Ediacarans extinction was probably due to ‘new kids on the block’ organisms, currently known as animals.
There is a reason why 12, 60 or 360 are very much in use – they are all “collosally abundant numbers”.…

Interesting analogy between automatic elevators and Google cars – @NPR:
Messy HTML that cannot be removed in a #gmail “Reply”, can be avoided by highlighting some text before clicking Reply…
“Before the introduction of laboratory mice, scientists endured many difficult years with lab bears”.
Would love to see pre-defined shapes like arrows and Pacmans in #Inkscape.
Bioinformatics is about extracting meaning from data. Software engineering principles do not apply, mostly (…)
Shouldn’t have invested any money in an e-book reader. An Android smartphone is a better reading device. #FBReader, #AlReader or #ZXReader.
#Unity interface of #Ubuntu fails completely for several colleague scientists. Their conclusion: “#Linux is hard to use and unfriendly”.
Diets are harmful both physically and emotionally. Slight mods of lifestyle are not.…
Maigrir durablement c’est maigrir lentement – le propos bien documenté de “L’Anti-régime” de Michel #Desmurget (…).
“Pour un sommeil reparateur … dormez sur un drap de cuivre.” Pub pour les fakirs embetes par les clous en fer..
“A key accomplishment of evolution is … piling up endless new ways of doing the same old thing”. Amazon wisdom:…
#Ubuntu 14.04 with default Unity does not have a way to easily set up a time for programmed shutdown on non-laptops. Pretty annoying.

Et si MongoDB et NodeJS n’étaient pas le bon choix … Une présentation:…
Le prince de Motordu est un grand plastique de la litterature francaise pour enfants. A deguster à partir de 6-7 ans.
For those scared of the flood of data in science, excellent reference.…
Retweeting a link gives credit to the one who found it but means more clicks for those who are interested in the original story.
For those who want a glimpse into the world of drug addiction : Junk de Burgess…
Comparing versions of text with #Meld ( is both cool and efficient. Complements LaTeX and git.
Comments with examples about efficiency of numpy use and difficulties in using an alternative like Pypy or Cython (
Pocket spectrophotometer paper – parallel intensity measurements of ligh filtered through an array of quantum dots:
“need a change of institutional culture so that, instead of being rewarded, unfeasibly lengthy CVs are discouraged.”…

The #ReaderView, switched on with the book icon in #Firefox’s address bar helps with diminishing eye strain.
With ggvis and other web based solutions interactive visualizations might come at last to R (#rstudio).…
Lars Arvestad @arvestad: I worry more about natural stupidity than artificial intelligence.
A colleague with prior #LaTeX experience is enthusiastic about #overleaf. Others prefer #GoogleDocs. Having choices is good.
Interesting documentary, showing that some scientists do not make much use of the scientific method.…
“Data analysis is an easy, relaxing and wasteful part of research, especially if compared with true bench work giving true results” – yeah.
Struggling for quite some time with hard to understand and remember syntax in R – could #dplyr solve that ?
Correlations, correlations.…
Basics of operations on data frames in R, including how to initialize an empty one with named columns and types:…
Strange that major e-ink #ebook readers do not use an #Android-based OS, since #CoolReader, #FBReader are such great reading apps. #DRM?
#RStudio knows now about code snippets: writing the dreadful *stringsAsFactors=F* becomes so much easier.…
Learn how to obtain best estimate for the length of the nose of the China’s emperor, from Feynman’s autobiography (
RNA degradation intermediates give post-mortem details about how many ribosomes had once travelled along an mRNA.…
Carefully crafted tweets with no links are like advice being given without being asked. Makes one think. Pocket literature.

Funny how RSS feeds become redundant after setting up a Twitter account.
Including Python results in a LaTeX document – did not know about Pweave.…
Graphics from code – optical illusion images made with LaTeX and TikZ/PSTricks –…
Promising tool ( for shared document editing. Helps students to see how nice reports can be generated with LaTeX.
Science article data analysis suggests fraud and will likely lead to retraction.…
Explaining p value misuse, doing stats in science, also in book form (found on O’Reilly)
Managing and recruiting advice from Google (2013)

Pervasiveness of quantitative data in biology raises questions about abusing statistical significance.…
Showing more data and using better plots. Yes!…
Brilliant, even for the most reluctant students.…

Tweeting more to do better science ?
“Do the best experiments you can, and always tell the truth. That’s all.” -Sydney Brenner –…

Android apps list for busy people

Comments on several Android applications that transform a smartphone in an entertainment and work tool. Updated in December 2016.

Lightning Launcher and apps
Lightning Launcher and apps (1 screen and a half)

I hate pages with titles like: the ten best music players for Android! Best is a “superlative” and should be used for a single app, not ten, even if I will contradict myself in the e-book reader section of this guide. I’m relatively new to the Android platform since it has only been two years that I first struggled with the interface of a phone with the modern, at that time, Gingerbread, or 2.3 version. Earlier exposure to Android, on an Archos tablet, was really getting me into the prehistory of the operating system (version 1.5). I have also experienced the earlier, almost smart, interfaces provided by Nokia in the form of the modest Symbian S40 (Nokia 6600 slide) and the very capable S60 (Nokia N97 mini).

What did I learn from two years of intensive use of Android apps on a Sony Ericsson Xperia Pro device?

First: there are too many apps available on the PlayStore and, unfortunately, their quality varies wildly. Testing all of them is impossible, so I stayed with those having reasonable marks from a large number of users. The number of open source apps is relatively small, which takes us back to the ’90s when small programs were most often of the freeware or shareware type. Let’s hope developers will come to reason if they hope to give birth to long term projects. Most freeware/shareware that I know of have been replaced over time with open source equivalents. Or changed to different business models, like Opera software did with their browser.

The following apps are useful and either open source or free of advertising (I really appreciate developers that accept donations for their work or state clearly in the app description if it is ad supported). They are classified by type of activity in which the apps play a role.

Basic or fundamental utilities


MessagEase keyboard: the only virtual keyboard that allows the typing without looking and with no need for a dictionary. The letters are formed on a 9 cell matrix by typing or swiping in one direction or another.I type faster now with MessagEase than with the physical keyboard of the Xperia Pro. As proof, I had actually typed most of this guide on my phone with MessagEase. This keyboard needs some training, which can be quite enjoyable when playing the MessagEase game. Once you reach 20 wpm in the game, you will find that going back to traditional virtual keyboards is next to impossible. Accessing capital letters requires some special gestures, circle the main letters or do a double swipe on others. Numbers are also entered directly from the main keyboard or on can switch to a phonepad like layout. Countless ways of customization are available, one of the most useful being that one can keep visible a series of characters that are most useful (“%”, “-“, for example). One can add to the main screen the most used characters or hide some of the least used ones, adjust the size and colors and back and forward delete characters or words.

An alternative, that I recently described in another blog post, is MultiLingO, that allows infinite customization of the keyboard, including a copy of most of the functionality of MessagEase (edit Dec 2016)


GestureSearch by Google: absolutely fantastic way to find contacts or apps on the phone by simply drawing the first few letters. Should be installed by default on all smartphones.

Edit 2016 – Not using it much any more. Draweroid is enough to find the apps quickly. It has also the advantage of usability with any launcher.


X-plore: a great dual pane file manager that gets things done®. It also incorporates efficient viewers for pictures, videos or text files and operates well with compressed archives. The different operation are done on a selection of files or folders through a row of icons for copy or move, share, create new folder, create zip. Fullfills all my file manager needs on Android (I confess on using Krusader on the PC).

Update 2016: I like and use in paralllel another dual-pane file manager, called Total Commander. Works very well.


J4velin apps: these are extremely impressive and useful apps from the same developer: Notification toggle and Simple Calendar widget. The widget is scrollable and easy to customize and just extremely useful. Simple Calendar allows very nice customization options for text color, background and font size. Beautiful.

Update 2016: I still use Notification toggle, but replaced Simple Calendar with the widget that comes with aCalendar+. The situation is better nowadays, with Google Agenda also providing a reasonable widget.


Atom launcher and its widgets. For quite a long time I was a fan of Lightning Launcher, then reverted to the Sony original one and re-reverted to a lightweight launcher called Nemus. What was impressive with Nemus was the gain in battery life from one day to one and a half. Nemus has not been updated in a while, so I searched for the team that developed it. I thus found Atom, presumably an evolution of Nemus, a launcher that has a few nice features: a calendar widget that shows the current month or the previous and next ones, an app drawer in which you can hide all the apps that you don’t use but cannot uninstall (thus unnecessary poluting the list) and other small features that ease the user’s life.

Update 2016: Lightning Launcher has only a paid version, which is annoying for people who would like to try it out. Surprisingly, the ZenUI launcher from Asus is very good, but my current preference goes to the exceptional TSF Launcher 3D. Smooth, easy to customize to any liking, the TSF Launcher replaced all the others for my use.

Lightning Launcher was in the end the best choice for the type of customization I prefer – extreme. Very convenient, it allows me to have just one single screen with all the information I need and easy access to my most important apps and contacts. Actually, the screen is longer than the physical screen, so it should me more accuractely described as a 1.3 screens long.


Notepad by plattom: There are many notepad application in smartphoneworld but none is such well thought as this one. It does only text but it does it extremely well. You don’t need to save any note you take, it is saved automatically. Notes backup is very easy either as text or as an sqlite file. The search function works very well and the aesthetics of the app is perfect. Note sharing is also very straightforward. Altogether, Notepad strikes the perfect balance between being simple, nice and having the whole set of features you would expect from such an app.

Update 2016: Two updates in the last 2 years. For some time I used ColorNote, a great note-taking alternative to Notepad. One day, I wanted to export all the notes in a single text file and understood that it is not possible. Thus, since that day, I changed for a great open-source alternative called OmniNotes.


QuickPic: small, fast and extremely useful picture and video viewer. It can be configured to ignore some folders and look for pictures in others.

Update 2016: I’m using a lot Piktures, as an alternative.


PhoneSchedule: helps keep the battery for up to two days under moderate use by switching off WiFi and data access automatically. One can program many different phone actions at a given time of the day or the week. Well done scheduler with minimal memory footprint.


Jorte and aCalendar/aCalendar+: I was a long term user of Jorte despite the awful French translation (‘Fixer’, par exemple, used instead of ‘Enregistrer’) and the rather strange nature of the Jorte Store – where you can buy colorful, hello kitty like pictures and icon sets. Recently, the ‘add event’ plus sign disappeared from the agenda view and I switched to aCalendar+. While I liked the possibility of adding icons to events and using various colors and fonts for calendar display in Jorte, these are only minor features missing from aCalendar. The most important dialog, to add an event, is well done in aCalendar and swiping to week, month or day view works well. In both cases, free, feature limited version of these calendar applications exist.

Reading DRM-free books and news

As my phone is also my ebook reader (or the other way around), I’m using several readers at the same time, each one with its own strengths and weaknesses. A special mention goes to CoolReader and FBReader, two readers that are not only free but also open source. Other great book reading applications are: ALReader, ZXReader and Google PlayBooks.

I refuse to read books with DRM protection and I’m very glad that some publishers, like O’Reilly (for technical ones) or Baen (for science-fiction) are providing uncrippled files for their ebooks. So, most of the readers reviewed here are not suitable for DRM protected files. Fortunately, tools exist to remove the protection, if so you wish but, in most of the cases, you will need a working Windows or MacOSX environment.

The best reader for complex epub files is the one from Google. However, getting to read your own books with this reader is pretty convoluted: first you need to upload your files to Google Drive. Next, you import the file back to Play Books and pay attention to make the book available offline. This will allow book reading without a network connection. For some reason, the offline reading does not work all the time and sometimes the application keeps a black screen until Internet connection comes up. Aside some epub files that are beautifully rendered by Play Books, there is no other major reason to use it.


CoolReader has been for some time my main and only book reader. Since the main features are the same with other good ebook readers, I will only write here some of the annoyances when using one or the other of the apps presented here. For CoolReader, complex epub files may be hard to handle. It is buggy on very old Androids. Apart that, it is a really cool e-book reader.


FBReader is a fast reader that I’m not using often during the night since its backlight control does not go down enough on my phone. Works very well on old Android (v 1.5). Like CoolReader, the developers are very active in making it better and better.


ZXreader is a minimalist reader that has a Symbian S60 ascendance. Very pleasant and fast, it has also the smaller size in terms of sd card occupied space. No reason not to use it apart its close source origin. Some users complained about the character set that has sometime to be manually reset to UTF-8. Not a major problem, though.


AlReader is the most customizable of the five mentioned. One funny feature that puts it apart is the ability to change the appearance of the first letter of each paragraph. In addition, the ability to add weight to the font used for reading is a big plus. Looks beautiful and works flawlessly.


Document Viewer is not for epub but for pdf files. Fast and reliable.


Most of these readers can be used with offline dictionaries and a nice one is Aard. I’m using it with a local copy of the WordNet dictionary.


Pulse: news aggregator – I was using Taptu but the arrogant answer of a person from Taptu’s team to my suggestion that long articles should have an option to be read page by page, like it is always the case with ebooks, made me change. In the last year I almost exclusively used FeedEx, a fantastic open-source RSS reader. Simple, beautiful, fast.

Music and sound


Mort Player – a very nice music player that uses the folder strucutre to let you explore and play the music you want the way you want. It also offers an equalizer and, most importantly a Quit menu entry. Replaced by the more recent and minimalistic FPlayer. Open source and a great developer.


Voice Record for good quality recordings that can be easily encoded as mp3s by the app itself.

DaTuner or DaTuner Pro for sound analysis and guitar tuning, for example.

vlcNothing beats VLC for playing audio and video files “in style”.

Edit 2016: Also, VLC can play many kinds of streamable content, including online radio stations, as long as you know their address.

Communication and navigation


Opera Mini – the only browser working great on low speed networks. Sometimes, I need to change to the default Web Browser for complex pages.


GPS navigation: MapFactor Navigator and Google Maps and Nokia. I used to use the older Nokia for GPS navigation and it worked and still works great. Google Maps is good to have and, in the absence of a network connection, Navigator’s offline capabilities is a plus. Sometimes the open maps are mors deailed than what Google provides.

solmail profimailgo

Yahoomail, Gmail and the integrated Mail client are kind of standard. I appreciate YMail for its ability to send any kind of attached file (Gmail and Mail were restricted to images). SolMail and ProfiMailGo (restricted to a single account) are excellent mail clients for IMAP or POP3 protocols.

Local utilities: RATP was essential if you take the bus in Paris. Gave time schedules in real time and plans for all the public transports around Paris. The major revision during May 2014 made it useless on my phone because it require services that I cannot install (Google Play things). Abandoned.

Other useful apps


Mathdroid for a complex scientific calculator that understands expressions like log2(26). Simpler, and with a nice interface is Calc Etc.

Search Light – for finding your path in the dark.


Swiss army knife – of useful utilities including a very useful multiple timer, compass, calculator and unit converter.


A weather Life – for a clean weather forecast widget and app.


Egg Timer – for easy count-down with alarm and eStopWatch for measuring elapsed time (very small utilities that do one thing but do it well).

wualaWuala – the Android client for the corresponding cloud storage offer. Really useful if you are a little bit paranoid about your data being read by someone else. Encryption at device level ensures some data privacy and minimizes the possibility of private data becoming public. Wuala is no longer a free option. Great replacement is SpiderOak and a generally useful and generous free cloud space can be found in Hubic’s offer.

advancedclockwidgetAdvanced Clock Widget and its Pro version offer a configurable clock with supplementary information. Great working and does not drain battery.

Zeiss Ikon Contessa S310 – heavy, metallic and toyish

One of the compact cameras I bought to see how they work and if I like them was a camera that I waited for a few weeks until finding one at a decent price on the german eBay: Zeiss Ikon Contessa S310 (you may find another opinion on this camera from Mike Elek’s page):

Contessa S310 – an aperture priority electronic shutter camera

I like compact cameras that are solidly built to last decades and I was hoping to be able to use this Voigtländer designed Zeiss Ikon camera for casual shooting. From the first moment I took it in my hands, I did not like it: there is something strange about its design and square geometry that just does not feel right.

I had to read the manual to be able to understand why the rewinding arm blocks when adding film. The back is difficult to take off and put on, the little lens’s controls are not very easy on the fingers. The viewfinder is indeed informative about the chosen aperture and very approximate shutter speed that the camera choses. Moreover, the approximate focusing distance is painted with symbols:

Full with information but somewhat “toyish” viewfinder of the S310

As you can see, when I say “approximate” speed, that really is approximate. Unfortunately, on my camera, even if the meter was working, for some unclear reasons, all the pictures of the first roll came out highly underexposed. Maybe the fact that I replaced the original batteries with a CR123a was not on the liking of the camera ?

Focusing is by guessing the distances and using smaller apertures for more depth of field. The S312 version of the same camera has a range finder.

Conclusion (influenced by the faulty camera I own): even if it would work, the ergonomics of this camera are pretty awful. For a compact one, it is pretty heavy. I much prefer the Olympus XA which, as long as it works, really fits much better its use of a compact film camera.

Kind of update: Agfa Selectronic or its rangefinder version Agfa Selectronic S are aperture priority cameras of the same era as the Zeiss Ikon. I grabbed a Selectronic to see how it works. The beast is very sensitive to the kind of batteries one puts inside. It would not work with zinc air replacements, only with LR44 equivalents (in the otherwise too large space provided for mercury 625 batteries). From time to time, the lamp that illuminates during shutter actuation would remain on forever, unless removing the batteries. I could not even test it and must conclude that there is a curse of old german compact cameras. Never had such problems with their old japanese cousins.

Tamron 500 mm f/8 and the magic of mirror lenses


The Tamron 500 mm f/8 Adaptall model 55B is an interesting beast. At 600 g, it is very light and can be used without a tripod at 1/300-1/500s. Being an f/8, one and only aperture, the lens requires high ISO values to be used even on sunny days, which is less of a problem with a current dSLR than once was with film photography. These mirror lenses are not for everyone and everything but are a compact alternative to “normal” long lenses for moon shots or birds and animals. Using it for portraits is hard and not very convenient, despite the close focusing capabilities of the lens (1.7 meters, a record).

What’s nice about the Tamron is that it can be used either on Nikon or Pentax dSLRs bodies with the original Adaptall rings. Additional adapters are required to fit the Adaptall lenses on Canon or Sony dSLRs.


My experience with the lens is shallow. I don’t use a tripod most of the time, and with such focal lenght and aperture it is a must. The out of focus area mirror the central part of the lens to give some pictural effects:


In terms of sharpness, I would most likely use a faster shorter lens for a given subject. In real life use, I remember about a year ago taking pictures of the 14th of July fireworks. First, the overall setting (135mm Tokina f/2.8 lens, at f/4):


The center of the same scene, as seen by the Tamron 500 mm lens (on an APS-C size sensor). Motion blur is obvious even at web site size of the picture:



I have sold this lens for the same price that I bought it. It was an interesting experience well worth the money :-). The mirror had some slight fungi growth but was very easy to clean (the tricky part was to unscrew the ring retaining the front element). The lens built is excellent.

If interested, you can also look at the photozone review.

Tamron Adaptall 28mm

Why another lens ?

Finding an Olympus OM-30 camera on a garage sale a few weeks ago rekindled my interest in film photography.
Olympus OM-30 SLR camera (OM-F)

Now, the Olympus camera only came with the standard 50mm f/1.8 compact lens and I thought it would be fun to see how film works with a 28 or 24mm wide angle without the crop factor that applies to APS-C size digital cameras. The only widely known group of lenses that are interchangeable between different cameras, if provided with the right adapter, is the Tamron’s Adaptall series (see for more information).

From the different Tamrons I had the occasion to use, with one exception, the late plastic version of a 28-70mm f/3.5-4.5 zoom, they were all optically good to excellent. One special mention goes to the famous Tamron 90mm f/2.5 (or f/2.8, there are several models) macro lens. A compact, fast zoom is the 35-80mm f/2.8-3.8 which delivers excellent image quality and is a pleasure to use. Let me show it to you, mounted on a Nikon D40 dSLR:

Tamron zoom model 01A

Tamron 28mm f/2.8, cheap, heavy, good

The lens shown in the following images is not the typical Tamron 28mm f/2.8 only because it is not painted black. I did not like the look of the black ones, that’s why the sample I have is brushed aluminium:

Tamron 28mm f/2.8 white, front

The characteristics of the lens, as borrowed from the Tamron official site (in Japanese, thank you Google Translate) are:

Model: CW-28
Lens configuration: 7 lenses in 7 groups
Minimum Aperture: 16
Minimum focusing distance: 0.25m
Filter Diameter: 52mm
Weight: 240g
Maximum Overall Length X Diameter: 65mmx42mm
Produced between 1976 and 1979

Not mentioned – aperture has 5 blades.

The lens was replaced by a more compact version that is also lighter but, alas, takes 49mm filters. On Nikon I’m used with 52mm filter diameters.It’s much easier if all the lenses have interchangeable caps. Mounted on a D40, the lens looks impressive, due in part to the perspective distortion of the Fuji E900 lens when taking the picture:

Nikon D40 with Tamron 28mm f/2.8 adaptall lens

In fact the lens is pretty compact even if it cannot compete with the Nikon series E 28mm, which has a lot more plastic and a simpler optical formula (so there is a difference of 5 cm in the minimal focusing distance – 25 cm for the Tamron and 30 cm for the Nikon):

Tamron 28mm vs Nikon 28mm

A  few more images of the lens before jumping to conclusions about handling and optical quality:

Tamron 28mm f/2.8 front

Tamron 28mm f/2.8 side view

Tolo Toys and Tamron

Handling is excellent, the lens has the right size and bulk (for my hands in any case). Manual focusing is very pleasant though not always easy (an f/2 lens would have been better, but that’s a lot more expensive and does not exist in the Tamron’s adaptall line).

Depth of field preview on a D40 ?

The Tamron was built in the 70s and intended for use on many different cameras. Some of these, I imagine, were not able to allow focusing and metering with the lens wide-open and to stop down “automatically” only at the very moment the picture was taken. For those cameras, the Tamron has a switch on the side (marked A, for Automatic, I imagine). The A gets covered by the switch when moved and the lens aperture closes to the value set on the aperture ring:

Tamron 28mm f/2.8 depth of field preview switch

Now I have a depth of field preview on my Nikon D40!

Even if the camera had such a function it would be close to useless due to the size of the image in the viewfinder. On a full frame camera the situation would be different. Anyway, while the depth of field preview is extremely useful on film, when you cannot see the result immediately the lack of such a function became much less problematic on digital SLRs.

Image quality (on APS-C sensor)

Excellent! That sums up a few hours of tests and comparisons. At f/2.8 there is some loss of contrast and I would not use the lens wide open. However, from f/4 the images are crisp with good contrast and with plenty detail showing everywhere. Take this opinion cautiously because I am no expert and, for me, the series E Nikon, generally badly rated (see for example this evaluation, in French, of several Nikon lenses or another one on Bjørn Rørslett’s site), has a lot to offer. I just don’t like its handling as much as I like the handling of the Tamron.

Quick 100% crop from images taken with the Tamron vs the excellent 18-55mm Nikkor kit lens:

Tamron vs Nikon kit lens

At left, there is no much difference at f/4 between the center resolution and contrast (kit at left, Tamron at right). Extreme left side of the image (right image) shows that the Tamron keeps more resolution, which would be expected from a prime vs a consumer zoom lens. Color rendition is different. The Tamron lets in less light at the same aperture too.

In conclusion, by taking pictures with the Tamron, one “benefits” from a marvelous mechanical device and gets similar or better results than with the kit lens. That’s all that I needed to know. Some other test and sample images follow.

Sample images with the Tamron 28mm f/2.8

Flowers at f/5.6 without or with camera flash

Evening place de Catalogne, f/4

Night on rue d'Alesia, long exposure

f/4 vs f/2.8 Tamron 28mm

Flare Tamron 28mm

Flare 2, Tamron 28mm f/2.8 at f/4

Pretty funny internal reflexions and ‘rainbows’ when the sun is in frame. However, contrast is preserved to a good extent in the shadows and that’s important. The BBAR (Broad-Band Anti Reflection) coating seems efficient.

Summary and conclusion

There are several good points about the Tamron 28mm f/2.8:

  • Excellent mechanical construction and a pleasure to handle
  • Very good image quality from f/4
  • Depth-of-field preview integrated in the lens (not really useful but funny to use)
  • Adaptall system that allows the use of the lens on other brand film or digital cameras
  • Takes Nikon-type 52mm filters, unlike its descendant, the 28mm f/2.5, which takes 49mm filters

And of course, there are downsides:

  • Aperture with “only” 5 blades. But I did not see any adverse effect to that. It’s not only the number of blades that determines the out of focus areas appearance. It is true that the macro Tamrons have 9 blades and the zoom I was mentioning before has 8.
  • Quite heavy and bulky – the more compact Tamron that followed (28mm f/2.5) may have a more convenient size.
  • Not that good at f/2.8

In conclusion: a pretty/ugly lens that’s a pleasure to use.

If you have any comments or negative or positive experience with Tamrons, it would be great to share our opinions.

Toshiba P300-156, a Linux-friendly 17″ laptop

As for the Ricoh camera, I could only find very little information on the Linux compatibility of the new P300 series of Toshiba laptops. One discussion on a forum (sorry I forgot where…) mentioned that the A300 series had good compatibility with Linux and that the P300 was not that compatible. However, I took the risk and I’m very happy to report that the Toshiba P300-156 european model is very Linux (Ubuntu) friendly.

Most of the things work out of the box, without any special intervention. My distribution of choice is Kiwi, a version of Ubuntu 8.04 that was tailored for ease of use and oriented towards Romanian and Hungarian users.

I had some difficulties in understanding how to shrink the Windows Vista partitions and allocate space to the Ubuntu distribution but finally it worked without any problem (by first using Vista to decrease the occupied disk size).

LXDE, Gnome, OpenBox

In addition, I had to install the ATI Radeon HD 3470 driver and, for convenience, Wicd, an excellent manager of network (especially wifi) connections.

To my surprise, the included webcam and microphone worked without any problem (tested with Skype and Kopete). Everything worked like a charm with two exceptions:

1. The integrated Ethernet card is not recognized and I was too lazy to search if any driver is available to make it work. I’m using wifi connnections right now so this is not critical.

2. The disk was parking heads very often and I applied the uggly fix described by ubuntu_demon. It solved the problem.


I’m a very happy Ubuntu user on a great Toshiba laptop 🙂


June 9, 2008 – first disappointment – the incorporated DVD player did not accept to play a DVD that had light scratches. No problem to read the DVD on another computer…

August 11, 2008 – maybe it was only the lens of the player that was dirty – cleaned it lightly with a piece of cloth and no problems since.

December 2, 2009 – after upgrading to Ubuntu 9.10, the computer fans were continuously working at full speed. Installing the proprietary ATI driver for the graphics card seems to have solved the problem. One annoying problem though: upgrading the kernel will remove the module and it has to be reinstalled…

December, 2012 – the laptop is still working fine with Xubuntu 12.10. I don’t like Unity and Gnome Shell. XFCE is a great desktop environment and Ubuntu remains one of the most friendliest distributions.