How Do You Create a Makerspace/Hackerspace?

Mirrored from Quora, since they require an account just to read articles.

The first of many classes at BioCurious, in this case making glowing cells with Green Fluorescent Protein!

5 bio-enthusiasts and I co-founded BioCurious, a biotech hackerspace in Sunnyvale, California. Eri Gentry had nurtured an awesome meetup group of 500+ people into biotech over about 2 years, and we felt that no one had lab space but a lot of newbs and experts wanted to experiment.

The best Hackerspaces are created when an existing community needs a physical nexus. Here’s what I think are the 4 core steps of starting a successful hackerspace.

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We’re Published In: Maker Pro – Are You BioCurious?

Maker Pro: Essays on Making a Living as a Maker

Maker Pro: Essays on Making a Living as a Maker

Maker Pro is out!  Eri Gentry and I wrote a chapter for Maker Pro called “Are You BioCurious?”, sharing perspectives on BioCurious, OpenPCR, and life. Other awesome contributors like bunnie Huang, Mitch Altman, and others. Also proud of my dad Theodore Jankowski for painting an illustration for the book http://jankowskiandbuck.com. And thank you to my friends who guided and reviewed my writing!

The Maker Pro book is written by 17 Makers, and you can order the Maker Pro book at Amazon now.

Are You BioCurious?

Written by Eri Gentry and Tito Jankowski

Biotech doesn’t have to be limited to labs anymore. There’s cool hardware and low cost hackerspaces springing up and being used by beginners and scientists. With this influx comes new ideas and new applications.

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Biology As Ideology

“Many people now believe that science is the religion of the twentieth century — that the authority of its clergy (scientists) is beyond question or challenge and that its recent findings can indisputably explain the past and predict the future of human existence and of our individual behaviors.

In this brief extraordinary work, RC Lewontin – – one the world’s most prominent geneticists – – takes to close and informed look at this tidy and showmanlike packaging of science as the panacea for global problems, persuasively demonstrating how science (and scientists) is molded by society and how the dominant social and economic forces in society determines for large extent what scientists do and how they do it.

Science and society in fact exist to symbiotically (hence the title of this book), and by admitting the shadings and limitations with in science we discover book the richness of human nature in the real value of science.”

Biology as Ideology, 1992
Quoted from the back cover
$10 on Amazon.com
 (not an affiliate link)

This New DNA Test Will Eat 23andme’s Lunch

 

Screenshot 2014-11-13 08.32.48

 

Yes, the website totally reeks of trying to sell work-out products. Look below the surface. This new “MuscleGenes” test shows the future of genetic testing — a narrow focus on solving a problem.  See how the underlying business of DNA sequencing is changing? I’m not even an athlete and this sounds way more valuable to me than the nebulous “DNA test” from 23andme.

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“LEGO Analogy Sucks”

hmm. According to a report by the Wilson Center on “Communicating Synthetic Biology”, the term “Legos” had a negative effect when applied to synthetic biology.

I use this analogy all the time. Seems to work well, but surprised their study says different. Maybe participants simply checked negative because they were irritated because the term is actually LEGO? I would know but I only skimmed the rest of the study.

Read the full study here

Figure 7: Focus group participants illustrate which words they find negative (red), positive (blue) or neutral (light blue and pink) when applied to synthetic biology

IMG_8910.PNG

How to find journal articles online

This post assumes you have a journal article you want to read, and you want to find it for free online.

Today I was researching the genetics of fast twitch and slow twitch muscle fibers. Here’s the journal article I wanted to read: Alpha-actinin-3 levels increase concomitantly with fast fibers in rat soleus muscle.

Thanks to the DIYbio list, I found 3 good options for getting journal articles and research studies.

Free – Reddit Scholar

Request the article on Reddit Scholar. Within about 20 minutes, a scholar responds with a link to download the PDF of your journal article.

1. Go to Reddit Scholar
2. Register if you’re not already.
3. Post the Title, Author, and a Link to the journal article

Alpha-actinin-3 levels increase concomitantly with fast fibers in rat soleus muscle
Yuji Ogura
http://www.sciencedirect.com/science/article/pii/S0006291X08009790

4. Wait for someone to post your paper. (Here’s the one I requested) Then do whatever you like with it!

In my experience it takes about 20 minutes for someone to respond with your journal article. Sometimes the wait is longer.

$4 – Read it on DeepDyve

Rent the article from DeepDyve, to read in your browser.

1. Go to DeepDyve
2. Search for your article (here’s mine)
3. Rent it for $4. “Rental” means you can read it for 30 days. No prints or downloads. $20 for 5 rental credits.

Rental isn’t an option for all articles. For instance, I can’t rent this ACTN3 journal paper.

A big mark down for Deepdyve: DeepDyve is horrible at telling you if an article is available for free somewhere else. I rented a copy of this paper (http://jap.physiology.org/content/99/1/154) from DeepDyve. When I clicked on their “Buy from Publisher” link, the paper was free online from JAP. In another case, DeepDyve said an article was “Buy only”, but was free to download on Nature’s website. I looked at 20+ results for ACTN3, and 80+% of them marked as “Rentable” were free from the publisher.

But I want to like DeepDyve. If DeepDyve was more reliable about tagging “Free” journal articles, it would be my first stop when doing research. If the article was free, read it; if it’s rentable, rent it; otherwise consider buying it. No more hunting around across so many websites! Would love to update this post in a few months and find that DeepDyve is much better.

$30 – From the Publisher

The final option is buying the article from the Publisher directly. Normally the first result of a Google search is a link to the NCBI Pubmed website, linking to the publisher’s site. My ACTN3 article costs $41.95. Yikes! In my experience prices range from $30 up to $60, depending on the Publisher.

 

That’s it! This post is in honor of Aaron Swartz who ran the GetArticles Google group. It was my favorite place to get real journal articles and research studies before it was shut down. I hope that finding journal articles online becomes easier and more people do it!

 

Heat sink dimensions

Getting dimensions after the fact..

So I ordered 2 heat sinks from Newegg, hoping that they will fit the 4×4 cm or 3x3cm block that we end up using. These heat sinks have an interesting approach to heat disposal, which lends itself to our desire for a horizontal fan setup.

http://www.newegg.com/Product/Product.aspx?Item=N82E16835233001 ($23)

  • This says it fits a various set of CPU sockets. Looking at the specs for the socket, they range from 3.75 cm to 4 cm, so I think we’re in good shape (I’m assuming this means that the heat sink contact surface is ~4 cm square).

http://www.newegg.com/Product/Product.aspx?Item=N82E16835103074 ($15)

  • hmm, might be cutting it close on this one. The intel sockets it’s design for are 3.75 cm square.