Can you … Count flies with your iPhone ?

… The answer is YES !

I got this question from a reader of this blog a few month ago on a previous post. I thought I would share the answer I had given him over here as well. Just in case a poor student, somewhere, spends time counting manually and googles something like “isn’t there a better way to do this ?” …

If you recall, I wrote about this app called Fast Counter, developed by Shazino, and available on the App Store. It does a very decent job counting bacteria on petri dishes, as long as there are not too small and dense.

For a drosophilist, the connection from counting colonies on a plate to counting flies on a pad is not too difficult to make. So I tried it by myself (because, really this was a high priority ;)) and it worked very well.

Of course, flies should not be too dense, and not sticking to each other. By setting the detection threshold in the app, you will actually get an extremely decent accurate number.

Here is an example of the read-out you get:

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Pretty good stuff, huh ?

Maximal number of flies you can count would be around 200-300, accuracy of course is better if you put less.

Have you eve tried it ? If so, what are your impressions ?

 

 

 

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Ode to the Fruit Fly, by Curt Stern.

This week I was browsing trough this new book the Drosophila world is happy to place on the lab shelf, next the the red book*, blue book**, and fly pushing***. It’s the Atlas of Drosophila Morphology, written by Sylwester Chyb and Nicolas Gompel. It’s absolutely beautiful, and will be helpful to all fly pushers.(here is a  professional review)

At the beginning, there is this citation of Curt Stern I just love. I think this is a beautiful description of how every true fly pushers feels when looking at flies under the binocular microscope.

“For more than 25 years I have looked at the little fruit fly Drosophila and each time I find fresh delight. When I see Drosophila under moderate magnification of a binocular microscope I marvel at the clearcut form of the head with giant red eyes, the antennae, and elaborate mouth parts; at the arch of the sturdy thorax bearing a pair of beautifully iridescent, transparent wings and three pairs of legs; at the design of the simple abdomen composed of a series of ringlike segments. A shining, waxy armor of chitin entirely covers the body of the insect. In some regions this armor is bare, but in others regions there arise short or long outgrowths – the bristles – strong and wide at the base and gently tapering off to a fine point. Narrow grooves, as in fluted columns with a slightly baroque twist, extend along their lengths.” -Curt Stern, 1954. Two or three bistles, American Scientist, 42, p. 213.

Don’t you feel exactly the same way when looking at your flies ?

* The Genome of Drosophila melanogaster, by Dan L. Lindsley and Georgianna G. Zimm

** Drosophila: A Laboratory Handbook, by Michael Ashburner , Kent Golic and R. Scott Hawley

*** Fly Pushing, by R. J. Greenspan

Science pick: Nature PastCast

podcastNot sure I already mentioned this earlier, but I am a podcast junkie. The one I listen to every week is This week in Virology, and it’s “spin-offs”, This week in microbiology, and This week in Parasitism. I also listen to the Nature/Science podcast here and there, and discovered recently a new podcast made by Nature Publishing Group, the Nature PastCast.

The idea is to talk, once a month, about these old legendary papers published in Nature. The presenter and producer of these episodes gives more details about it here. The first episode is a tribute to the discovery of the structure of DNA which was 60 years ago. They feature Raymond Gosling, a 86 year-old men now, who was a PhD student in the lab of King’s college at the time of the discovery.

I thought this was a super good idea, and to come back to This week in Virology, some epidoes also consist of interviews of these “legends” of biology. One of the most amazing was the one with Pr. Marcus, the first scientist to clone HeLa cells. He talks about the whole process, and has crazy anecdotes, like his mentor calling Princeton one day and saying “I’d like to talk to Einstein, please.” I would really really recommend this podcast to everybody !

Here are the links to :

The first PastCast about DNA structure.

TVIW with Pr. Marcus 

-Many other nowadays/legend scientists guests on TVIW

And you, do you have any good podcasts to recommend ?

The iLab – A new Drosophila app !

Hey guys,

At first, I want to apologize for the long absence. I’ve been busy and lazy, the worst combination of all. But I had to share this little discovery I made a few weeks ago, a new app for Drosophilists ! (drum rolls …..)

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It is made by Genesee Sceintific, the FlyStuff.com division in particular. Weirdly, when it comes to the fly room, I’m a bit old-fashioned. I like scribbling crosses on pieces of papers, looking phenotypes up in these good old heavy fly books.

Nevertheless, this app has a undeniable advantage. I basically consist of pictures, description of the most current mutants and species. Comes in handy if you quickly need to check up what a Bar eye or a Curly wing looks like. (Ok, nobody would look up a curly wing) There are also quick links to FlyBase.

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Now, the best at last … There is little nerdy addition: A virtual fly pad. You can train your fly sorting skills, and even enter the competition with other geeks drosophilists by sharing your scores online. Ok, past the few minutes of excitement, it gets a bit boring, and has nothing to do with the real-life fly pad experience.

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An other excellent point is that the app is free, and soon available for the android users too. So guys, go to the App Store and download it, it’s definitely worth it !

Greetings from Strasbourg, France.

Bonjour,

This week I am back in Strasbourg, the city where I have been a student for 5 years. There are so many places, tastes, and people there who remind me of great times. On one hand, the undergrad times feel very far away; because being a PhD student is an entire another world. One the other hand, it still feels like one of my “homes”, and I could still walk over there to my old bench, and continue experimenting.

At the time I was 17 and started the Bachelor, the University was called “Louis Pasteur”, and not “Université de Strasbourg” yet. Louis Pasteur, the great scientist, was actually a professor in Strasbourg around 1850. So yesterday, I walked in front of one of the houses where he used to live, and took a little picture. It’s in a beautiful little small street near the cathedral. It’s these sort of things you don’t care for when you actually live there,and walk in front of it all the time; but that you really notice once you’re only an occasional visitor.

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Have a great week-end, people.

10 simple rules …

Just discovered this a few days ago … a little series of articles from Plos Computational Biology entitled “10 simple rules …

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Pretty interesting and nice to read, these articles are giving advice to people in science of all levels and areas. Among the ones I liked the best were:

Ten Simple Rules for Getting Grants

 Ten Simple Rules for Getting Published

 Ten Simple Rules for a Good Poster Presentation

 Ten Simple Rules for Making Good Oral Presentations

 Ten Simple Rules for Selecting a Postdoctoral Position (ahhhh)

 … and finally Ten Simple Rules for Graduate Students

In the latter, you will find the following recommendations:

Rule 1: Let Passion Be the Driving Force of Your Success

I could not agree more.

Rule 2: Select the Right Mentor, Project, and Laboratory

Essential, but also very very difficult to do. Often, it relies more on an impression, a gut feeling, a connection; then on a conscious or rational choice. Like Blaise Pascal once said, “Le coeur a ses raisons que la raison ignore”, which in english would translate as “The heart has its reasons which reason knows nothing of”.

Rule 4: Remember, Life Is All about Balance

True. True. True. We should not feel bad about it.

Rule 9: Build Confidence and a Thick Skin

For sure necessary to survive now and later on …

 

 

If you feel like reading more, all hyperlinks are already in the text. Ok, if you don’t feel like scrolling all the way up, here you go.