DremelFuge at Shapeways

The Do-It-Yourself-Dremel-Centrifuge, DremelFuge, now nearly meets the capabilities of the best centrifuges!  As previously posted for DIYbio (in “Cathal has designed a simple centrifuge using open source hardware technology, and you can order one yourself!“), the DremelFuge is an adapter which turns a Dremel rotary-tool into a lab-quality centrifuge capable of use in various bioprotocols.

As Cathal states on the DIYbio mailing list:

“After a design revision which is now “official” and for sale on Shapeways, the Dremelfuge can hold tubes securely, with liquid load, up to the full speed of a Dremel 300. At a top speed of 33,000 RPM, this means the tubes experience about 52,000RCF (g).“

Read the previous story here:

DIY Centrifuge using Dremel Tool

Dremelfuge is a rotor designed to fit standard lab microcentrifuge tubes and miniprep/purification columns, to be spun by either a powerdrill or other chuck-loading machine or by a popular rotary tool. Dremelfuge features an easy click-in loading system which holds tubes parallel to the plane of rotation for optimum pelleting and delivery of force. Intended basic applications of Dremelfuge include column purification (tested to work with miniprep columns) and bacterial/cell debris pelleting (under testing). With standard microcentrifuge tubes, the average rotary distance is 4cms. Results (below) are shown with the Dremelfuge used to pellet E. Coli samples:

E. Coli sample pelleted with Dremelfuge

Dremelfuge is open-source hardware. Source files are available on Thingiverse, linked from the items on Shapeways. The Creative Commons license used entitles copying, sharing and remixing for any non commercial purpose. Please consider that professional printing services qualify as commercial use. Two editions of Dremelfuge are available for purchase at www.shapeways.com/shops/labsfromfabs

A Quick Guide to Teaching R Programming to Computational Biology Students

by Stephen J. Eglen^*, Cambridge Computational Biology Institute, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000482

The name “R” refers to the computational environment initially created by Robert Gentleman and 1 Robert Ihaka, similar in nature to the “S” statistical environment developed at Bell Laboratories (http://www.r-project.org/about.html) [1]. It has since been developed and maintained by a strong team of core developers (R-core), who are renowned researchers in computational disciplines. R has gained wide acceptance as a reliable and powerful modern computational environment for statistical computing and visualisation, and is now used in many areas of scientific computation. R is free software, released under the GNU General Public License; this means anyone can see all its source code, and there are no restrictive, costly licensing arrangements. One of the main reasons that computational biologists use R is the Bioconductor project (http://www.bioconductor.org), which is a set of packages for R to analyse genomic data. These packages have, in many cases, been provided by researchers to complement descriptions of algorithms in journal articles. Many computational biologists regard R and Bioconductor as fundamental tools for their research. R is a modern, functional programming language that allows for rapid development of ideas, together with object-oriented features for rigorous software development. The rich set of inbuilt functions makes it ideal for high-volume analysis or statistical simulations, and the packaging system means that code provided by others can easily be shared. Finally, it generates high-quality graphical output so that all stages of a study, from modelling/analysis to publication, can be undertaken within R. For detailed discussion of the merits of R in computational biology, see [2].

Projects

Bryan Bishop and others experiment with Sharpies and glass slides for making DIY microfluidics.

Why not sequence a genome? Sandra Porter suggests the idea and and Jason Bobe shares a writeup on a likely partner for this, Cofactor Genomics. No sooner does Jason suggest raising funds, and pledges $100 to kick-start the idea, than Tito Jankowski mentions the fact that Cofactor is running a contest for a free ~700Mb sequencing project for education. Follow along on the “Why not sequence a genome?” thread.

Equipment

Lots of people ask about the best way to get started with a DIY lab setup for doing amateur biology. It turns out that now is a great time to shop for your lab on eBay! Aaron Hicks shares his experience on in the “DIY Lab Setup” discussion thread.

Dan Heidel posts a review of a nice (and affordable) $100 pipetter set.

Cheap CCDs might enable building spectrophotometers and using dynamic light-scattering to probe the sizes of molecules in a solution in the “DIY biophysical setups?” thread.

Regulation and perception

An article from GenomeWeb gets us thinking about the perception by the public and the larger scientific establishment. A prolific discussion ensues.

Bryan Bishop brings up a new report out of U. Virginia “New Life, Old Bottles: Regulating First Generation Products of Synthetic Biology“, with video.

This week: Gel electrophoresis in a straw

Hi everyone — Thoughts and discussions took a backseat to projects and results. This week we had everything from starting DIY iGEM Teams to sharing results of straw electrophoresis. Check it out!

Projects:

• iGEM Team – Mac Cowell invited everyone to start a DIY iGEM team in 2009. (thread)
• Gel electrophoresis –  Tito Jankowski ran gel electrophoresis in a straw. The instructions are on OpenWetWare. (thread)
• DIY PCR – Bryan Bishop wants a cheap PCR machine. (thread)
• DIY Spectrophotometer – “Let’s not concentrate on making duplicates of old technology; let’s make something better.” – Tom Knight (thread)
• The Toothbrush Genome Project – Andrew Hessel invites us to know more about the bacteria in our mouths (thread)
• DIYbio Educational Outreach – Julie Norville starts the DIYoutreach group (thread)

Links and Discussion:

• Defining and shaping DIYbio culture (Security, Safety, and Responsibility) is discussed by Roger Brent and others (thread)
• Do-it-yourself PCR by Scientific American is brought to attention by Reshma Shetty (thread)
• Can ‘open peer review’ work for biologists? Jason Morrison and others discuss an article from Nature (thread)
• Flu biology: Lora wonders if we can sequence different strains of flu (thread)

The Weekly DIYbio link fountain of science for children

The DIYbio google group is fast approaching 2000 unique posts.  To highlight some of the more interesting conversations and links, we’ll post a weekly summary on Friday.  We’re hooking up a drinking fountain to the firehose.  So, without further ado – the Week of 30 Jan 2009 in review:

• Doug Ridgway brought some attention to Invitrogen’s 3-step Clonewell Electrophoresis system (thread)

• Kay Aull and Mac Cowell told New Hampshire Public Radio about DIYbio (thread)

• Kay Aull, Jason Morrison, Mac Cowell, and Ben Peterson experimented with Gel Electrophoresis at Willoughby & Baltic

• Bryan Bishop shared a website with a comprehensive (200+) list of Hacker Spaces around the world (thread)

• John Cumbers pointed out some great biochemistry tutorials, particularly J Chris Anderson’s Bare Bones Biochemistry. (thread)

• Professor George Church had an article in SEED about Safeguarding Biology, which Jason Bobe mentioned in response to a Post for Reactions by Roger Brent (topics: BioSafety, BioSecurity, and Responsibility).  (thread)

• Members of the community recapped their interviews with the Monitor 360 consultants, and have a long discussion about the pros and cons of “Biohacking” as an adjective. (Tito, Marnia, Meredith, Andrew, Kay

• Jonathan Cline found a video of a biology + electronics hacking project that measures the health parameters of beehives and reports it to the web. (thread)