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Posts from the ‘Biology’ Category

Jan 26

3 Comments

Videogames with paramecia players

Stanford University bioengineer Ingmar Riedel-Kruse and his colleagues are developing “biotic games” where players control paramecia and other living microorganisms. The PacMan-like video games are the first in which a player’s actions influence the behavior of living microorganisms while the game is being played.

Here we propose the concept of ‘biotic games’, i.e., games that operate on biological processes. Utilizing a variety of biological processes we designed and tested a collection of games: ‘Enlightenment’, ‘Ciliaball’, ‘PAC-mecium’, ‘Microbash’, ‘Biotic Pinball’, ‘POND PONG’, ‘PolymerRace’, and ‘The Prisoner’s Smellemma’. We found that biotic games exhibit unique features compared to existing game modalities, such as utilizing biological noise, providing a real-life experience rather than virtual reality, and integrating the chemical senses into play. Analogous to video games, biotic games could have significant conceptual and cost-reducing effects on biotechnology and eventually healthcare; enable volunteers to participate in crowd-sourcing to support medical research; and educate society at large to support personal medical decisions and the public discourse on bio-related issues.

Jan 11

1 Comment

OpenPCR – Open source, hackable PCR machine

I’ve recently come across an exciting project, OpenPCR that aims to build a PCR machine by using simple elements that you can buy anywhere. You can pre-order the machine for 512$.

We want to produce an open design for a PCR machine. Our goal is to start this project up quickly and get a working prototype made for Maker Faire. After that, add on applications such as SNPs or PCR kits or synthetic biology.

A DIY Xerox machine for DNA: A fast, computer controlled PCR machine that uses normal PCR tubes and may be built mostly with off the shelf components + free schematics. It does thermal cycling as well as boil, cool, and freeze (4C) samples.

Please help them!

You watch a presentation about the project here.

Oct 12

1 Comment

BioNumbers: Database of Biological Numbers

If you have ever tried to look up a number such as the volume of a cell, the outer membrane width of E. coli or the cellular concentration of ATP, you will like BioNumbers, a database of biological numbers.

It is often surprising how difficult it can be to find concrete biological numbers, even for properties that have been measured numerous times. To help solve this for one and all, BioNumbers (the database of key numbers in molecular biology) was created. Along with the numbers, you’ll find the relevant references to the original literature, useful comments, and related numbers.

Though we have made an honest first try at simplifying the process of finding useful biological numbers, there is still much work to be done. A key challenge is filling in the large number of missing items. Another challenge involves setting up a reliable and discriminating search engine which on a first try yields the numbers a user is actually interested in finding.

(Hat tip: Round the lab)

Sep 20

2 Comments

‘Dance Your Ph.D.’ Finalists Announced

Last year, I wrote about Science Magazine’s competition in which researchers could dance their research projects or PhDs. Now the finalists are announced. Check these highly creative scientists out:

That’s the idea behind “Dance Your Ph.D.” Over the past 3 years, scientists from around the world have teamed up to create dance videos based on their graduate research. This year’s contest, launched in June by Science, received 45 brave submissions.

Today, judges—including scientists, choreographers, and past winners—announced the finalists in four categories: physics, chemistry, biology, and social sciences. Each receives $500.

The judges will announce the winner next month at the Imagine Science Film Festival in New York City. But you can vote for your favorite now. We’ll reveal the victor—and our reader pick—on 19 October.

Winner of the Biology category: The influence of previous experiences on visual awareness

Runner-up: Genetic Diversity of Bacillus anthracis in North America

Jul 29

2 Comments

Serial Cloner: a Molecular Biology software

A short note about Serial Cloner, a free Molecular Biology software that is available for Windows and Mac as well. It has tons of features such as sequence alignment, vitual PCR, cloning, etc. A real diamond for molecular biologists.

Serial Cloner has been developed to provide a light molecular biology software to both Macintosh and Windows users. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format. Serial Cloner also import files saved in the Vector NTI, ApE, pDRAW32 and GenBank formats. Import from MacVector is also possible now.  Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Serial Cloner 2.0 now handles Annotations and Features both in the sequence and in the Graphic Map.

May 24

Self-Replicating Synthetic Life

When I started medical school in 2003, we heard rumours about Craig Venter who was working on some sort of synthetic life and now I just saw the recent reports. An excerpt from Wired:

In a feat that is the culmination of two and a half years of tests and adjustments, researchers at the J. Craig Venter Institute inserted artificial genetic material — chemically printed, synthesized and assembled — into cells that were then able to grow naturally.

On a Friday in March, scientists inserted over 1 million base pairs of synthetic DNA into Mycoplasma capricolum cells before leaving for the weekend. When they returned on Monday, their cells had bloomed into colonies.

Mar 14

4 Comments

Labtutorials in Biology: How to extract DNA?

A few days ago, I wrote about a new blog that focuses on tutorials about molecular biology. Labtutorials in Biology is going to be a unique blog providing step-by-step tutorials in molecular biology and descriptions that can be really useful for students.

The first posts:

Now the author, Bálint L. Bálint, posted new instructions:

Mar 7

4 Comments

Daily Fun: Biochemical Puzzles

Just a short post about a blog where you can find biochemical puzzles and quizzes. Let’s start with an amino acid crossword.

amino-acid-crossword

Further reading:

Feb 22

4 Comments

Labtutorials in Biology: A new blog on the horizon

I’m very happy and excited as the lab I’ve been working in for 2 years just launched a blog that focuses on tutorials about molecular biology. Labtutorials in Biology is going to be a unique blog providing step-by-step tutorials in molecular biology and descriptions that can be really useful for students. Bálint L. Bálint, junior lecturer, is behind the whole concept and he’s been making videos and writing descriptions for weeks.

Dear Colleagues!

I have decided to make an online collection of the basic (and not so basic) techiques we use in our lab. This is a (hopefully) classical molecular biology lab located in Europe, Hungary, more close in Debrecen. I will present you the lab and environment later.

The idea is to describe these techiques, make a pdf version of the protocols we are using and in some of the cases to upload videos about these techinques.

Any feed-back is welcome at:

image22

Please stay tuned,

Balint

The first posts:

3kep

Dec 1

1 Comment

Top 10 Amazing Biomedical Videos

Wired Blog published a list of 10 amazing biomedical videos featuring some really great animations, but they missed a few others:

And many more at MolecularMovies.org:

molecularmovies

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