LavaAmp: cheapest pocket PCR thermocycler dreamed for DIY biologists

The LavaAmp is a portable PCR thermocycler that has the potential to become the default garage biology (home biology, bioDIY, DIYbio) tool once it hits the market. Think of Apple II for personal computing or MakerBot for 3D printing.

The 1st LavaAmp prototype was shipped this week from Biodesic to Gahaga Biosciences and the process is documented and engineering details uncovered in Rob Carlson’s post.

The people behind are mainly ex SciFoo Campers and open science advocates: Guido Nunez-Mujica, Joseph Jackson, Rob Carlson, Jim Hardy and a cool engineer Rik Wehbring.

Here’s the pic of the prototype:

lavaamp-thumb-500x375In the 2007 proof-of-concept paper, entitled A Pocket-Sized Convective PCR Thermocycler, authors Nitin Agrawal, Yassin A. Hassan, and Victor M. Ugaz wrote:

Herein, we introduce an innovative thermocycling system that
harnesses natural convection phenomena to amplify DNA rapidly by the PCR in a greatly simplified format. A key element of this design is an architecture that allows the entire thermocycling process to be actuated pseudo-isothermally by simply maintaining a single heater at a constant temperature, thereby enabling a pocket-sized battery-powered device to be constructed at a cost of about US$10.

PocketThermocyclerAgrawalpic

Realizing the potential of the device and thinking about how to build a digital thermocontroller for it with the Arduino I contacted Victor Ugaz this January and was informed that they only built the proof-of-the-concept  devices testing them in the lab interested mainly in ‘understanding the physics of the thermally driven flow and its effect on the reaction’. But it was obvious to me that somebody will produce those devices for the market and make them affordable to people as it seemed to me as the familiar case of the low(est)-hanging-fruit.

So when Joseph Jackson mentioned to me his grandiose open science plans and the groups’  ‘super affordable pcr’ project I became instantly interested. As Rob Carlson writes:

The intended initial customers are hobbyists and schools.  The price point for new LavaAmps should be well underneath the several thousand dollars charged for educational thermocyclers that use heater blocks powered by peltier chips.

Why the Dyna-Vision G1 Android Telemedicine App can only be used by licensed physicians???

Let us assume that you are a technological early adopter, a maker, a hacker, a geek. Your software/hardware skills and experiences are much better than the bulk of licensed physicians. You also have a G1.

Now imagine a mobile application/gadget-in-a-belt-pouch that is the most advanced telemedicine solution in the market. With this application/gadget you were able to non-invasively monitor vital signs of the people that matter you the most at anytime from anywhere around the world. You were able to quickly recognize life threatening heart and respiratory problems of the people you care about and maybe save their lives.

The problem is that such a product exists according to this press release (via androidguys) but you are not allowed to legally use it (no information on the details of purchase yet) unless you are a registered and licensed physician. The press release does not offer any reasonable (legal?) explanation on why this is the case.

The Dyna‐Vision© G1 Android Telemedicine Application by RS TechMedic B.V (“specialized in creating very easy-to-use user interfaces”) will be officially launched during the CeBIT starting today:

Dyna‐Vision© is a small light weight and portable device, with the dimensions of a PDA. The patient wears this device in a belt pouch. This reliable and sophisticated medical device monitors up‐to 10 clinical parameters through non‐invasive sensors attached to the skin. The measurements include 12‐lead ECG, Heart Rate, Heart Rate Variability, RR‐times, Respiration, Plethysmogram and Oxygen
Saturation.

Dyna‐Vision© automatically transmits cardiac events and even continuous real‐time ECG recordings to a secured server. Besides using a computer or laptop, physicians can now also monitor a patient’s real‐time vital signs on a G1 Android mobile phone. Physicians can use the application at anytime from anywhere around the world.

The Dyna-Vision G1 Telemedicine Application can only be used by licensed physicians after registration with RS TechMedic B.V.

Practical DNA: Hugh Rienhoff’s got a story to tell

After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details concerning how things were actually done. This is really a story that cannot be overemphasized by simply telling it again and again. 

By making inquiries with local surplus brokers, Rienhoff discovered he could buy a secondhand PCR machine for less than a MacBook. He ended up purchasing a full working model for just $750.
Obtaining additional supplies, like the PCR reagents, for his experiment was tougher. Some chemical companies didn’t want to ship to a private address, so Rienhoff pretended his house was the headquarters of the fictional Institute for Future Study.

While Rienhoff could spring for his own PCR machine, a used gene sequencer (assuming he could find one) would cost around $100,000. So he found a university lab (which he declines to identify) that would sequence the genes he had amplified, for $3.50 per 50-microliter sample. In spring 2007, Rienhoff mailed in more than 200 samples.

Rienhoff compared Beatrice’s DNA with the information on Ensembl, looking for any base-pair variants that hadn’t been previously recorded on Ensembl. Continue reading

1st UK Maker Faire, Newcastle, March 2009, makers wanted!

The first Euro Maker Faire in Brussels was an evening event but now with the first UK Maker Faire makers have a chance to hang around for 2 days and develop or deepen their DIY skills similar to the original US events (we enjoyed Austin Maker Faire in 2007). Let me know if you’re interested.

from my mailbox:

We are shortly to publicly announce the first UK Maker Faire but thought you would appreciate advanced notification.
The Make team forwarded me your names and email addresses as they believe you might be interested in the Newcastle upon Tyne Maker Fair on March 14th-15th 2009.

The first UK Maker Fair will take place in Newcastle 14-15 March as part
of Newcastle ScienceFest – a 10 day festival celebrating creativity and
innovation.

This two-day, family-friendly event celebrates the Do-It-Yourself (DIY) mindset and features interactive exhibits organized by individual enthusiasts, hobbyist groups and clubs as well as student groups. It’s for creative, resourceful folks who like to tinker and love to make things. Maker Faire is an opportunity to share what you do with others. Continue reading

Low budget, high tech: Microfluidics device out of a $50 plotter!

7550AplotterBuilding and using low budget but high tech devicesplotterink at home is a main motivation behind hacking. A Harvard Chemistry Research Group now created a microchannel producing device using a Hewlett Packard 7550A Graphics Plotter (see some eBay prices) to perform a diagnostic protein assay with it amongst others. /See my SciFoo microfluidics coverage./

According to the current Nature by Tim Lincoln:

“The system works like this. By replica moulding, the pens of the plotter are replaced with PDMS versions that can deliver various types of ‘ink’. The purpose of the ink, when cured, is to create channels in a filter-paper substrate, and after experimenting with the possibilities Bruzewicz et al. found that a syrupy mixture of 3:1 PDMS:hexane did just fine. Having chosen the appropriate paper, the trick then is to use the plotter to draw channel shapes, with the PDMS syrup penetrating the full depth of the paper to create water-tight chambers in various patterns.”

Hardware-Software Specs from the supporting information:

Computer.
• Computer: Dell Dimension 4100, Pentium III Processor (1 GHz)
• Plotter: Hewlett Packard 7550A Graphics Plotter
• Operating System: OpenSuSE Linux 10.1, Novell Corporation. Available for free download
• Additional Software:
1. Inkscape – vector drawing program, for design of channels. Included in OpenSuSE, also
available for free.

The HP Computer Museum highlights this particular plotter: Continue reading

Biotech DIY for aging/life extension research: the double future?

“The best way to predict the future is to invent it.” – said Alan Kay, computer legend in 1971.

Recently I had a comment dialogue with Chris on whether state-supported research or industrial business enterprises can (or should) lead to big progress in robust and healthy life extension technologies. Besides the government and corporation coin the research breakthrough could come from an aging focused foundation like the non-profit Methuselah Foundation behind the SENS approach, which supports research projects (like MitoSENS and LysoSENS) and scientists (like Mark and John) through cooperation with university labs. And finally, there is going to be another option to contribute:

agingbioDIYtoast

Imagine the following future scenario: biotech DIY is becoming an accepted home activity so geeks are setting up private labs and conduct basic in vitro (but not in vivo) research. Continue reading

First DIY RFID experience: Arduino controlled Parallax reader

RFIDParallaxArduinoiBookIn the last couple of weeks I became heavily interested in RFID (Radio Frequency Identification) technology probably because the dangerous idea of all pervasive computing and the opportunities to build sg from the bottom-up. So here is a how-to to my first installed low frequency, read-only RFID system hopefully followed by a more juicy stuff in the ultra high frequency range up to 9 meters.

Hardware:

Parallax RFID reader with 2 tags ($49.99+shipping, Radio Shack)

9-Position Female Crimp D-Sub Connector($1.99, Radio Shack)

4 hook-up wires

Arduino Diecimila microcontroller ($34.99)

Macbook, iBook

Software, code:

Code in C programming language for using the Arduino with the Parallax RFID reader but in order to upload it to the Arduino board and make it actually work I had to put the reader activator line:

 digitalWrite(2, LOW);                  // Activate the RFID reader

into the

 void loop()

function just like in the the sample Wiring tutorial

Arduino software: different packages for Intel based Macbook and PPC iBook

Here is a screenshot on the Serial Monitor reading the tags on iBook: Continue reading

Biotechies at O’Reilly ETech, March 3 – 6, San Diego

The O’Reilly Emerging Technology Conference (ETech) is on and this year they had a growing number of biotech related sessions. Fellow SciFoo Campers like Hugh Rienhoff and Timo Hannay, Makers like Phil Torrone and Limor Fried, Brain Hackers like Ed Boyden are visiting and many more.

ETechbiotech

science.TV joins the club but exactly which?

science.TV is one amongst the newest actors of the online video sharing marketplace, based in Bristol, UK.

scienceTV

As Matt Thurling, founder says:

“My vision for science.tv is simply to provide the best possible set of tools to enable interaction via video between the science community. My definition of the science community is probably broader than the other sites in that it includes hobbyists and school students as well as research scientists. The idea is that, given the right tools, everybody will find their level and their role in science.tv, be it creator, distributor, educator or consumer of niche content.”

With a domain name like this, I expected a lot more science content, but the emphasis at this early point is on entertaining Make-like tech and DIY videos (think of Instructables), many of them coming from YouTube. While I am in favor of merging science with tech and had a little role in popularizing tech sites like Make and O’Reilly Radar in the science blogosphere I do not think that science.TV is a good name choice for such type of combined content. However, in the long run, not the name that matters but the content. If science.TV can aggregate, share or produce quality content at the science-tech interface than it will be a colorful and appreciated member of the family of science video sites ranging from the research focused JoVE and SciVee to the less academic DNATube or Lab Action.

To achieve this aim science.TV is looking for contributors Continue reading

Everything you want to know about Make:TV on Videovoo

TVI am not watching to many videocasts, but the last 5 epizodes of the Make Weekend Projects with Bre Pettis are always on my iPhone and viewed every time. Now Anna over at Videovoo reports on the coming Make:TV featuring half-hour episodes that will be presented in High-Def TV and streamed on the web in as early as 2008. Anna made a detailed email Q&A with Philip Torrone, senior editor and alpha nerd on the emerging video and TV side of Make:

The first Make video was uploaded on YouTube in March 22, 2006 (if I’m not mistaken), while Make TV show started to run on Blip.TV in July 2006. As for Blip.TV, Phillip Torrone senior Make editor says “we like the player, the high quality playback and the team at blip”. However, YouTube still brings more eyeballs than Blip.TV – maybe more revenue too? Since December 2007 Make magazine has been in the YouTube Partner program, so they will get some revenue from the most popular video social networking site too. In 2008 they are also getting on air more ‘officially,’ harvesting more exposure on more screens, which is a nice example of an online success story spreading out on a national TV channel well-known for educational science programs. What can we expect in 2008? Continue reading

Tit in the webcam and lifecasting for animals

crowlifecastA lifecasting and human free video streaming channel for animals could easily be a lot more interesting than Justin.tv. An early video tracking system based on miniaturized, animal-borne video cameras was developed for studying the undisturbed behavior (capturing lizards, using tools, flying) of new Caledonian crows and published in Science. Of course the online supporting material in this case is obviously the main stage so enjoy the online birdwatching. Some technical details on the setup: We designed tail-mounted camera units that do not interfere with movement and ensure safe shedding of the tag with regular molt. Units transmit a color video signal with sound to custom-built receivers and incorporate very high frequency (VHF) radio tags for simultaneous positional tracking. We deployed cameras on 18 different crows (12 males) in our dry forest study site (21°33’50”S, 165°19’27”E), capturing 451 min of analyzable video footage from 12 subjects (38 ± 5 min per bird, mean ± SE; maximum of 60 min). Hey, Makers, it’s time to set up your homemade animal videocams and install them on the Rats in the front room, roaches in the back and the racoons at the backyard. The tit picture was made with a webcam in Szentgotthárd, Hungary.

cinke

My Arduino and home electronics starter kit

starterkithomeelectronicsAfter a hard experimental week (I have now around 55 T-75 or T-175 flasks with 6 different growing cell lines in the incubator) finally I have been able to turn a little weekend attention to move a step further with my home electronics “maker” plan. Instead of buying a complete Arduino starter pack ($65) I’ve just bought an Arduino diecimila open source microcontroller and a tiny breadboard on the Austin Maker Faire. But now I moved to the closest Radio Shack to get some capacitors, resistors and transistors. With all this investment so far I am still under $70. Bu I forgot to buy wires, hookup for the breadboard, stranded to panel-mounted components like LEDs, and I don’t have proper tools yet, like soldering iron and wire striper, multi-meter and loupe. Basic reference: MAKE The home electronics issue, particularly Charles Platt Your Electronics Workbench For programing an Arduino you need a PC, and my backup laptop, the iBook G4 is just perfect for that purpose. Next issue was to make the system work, and here is a step by step process, basically you download the programing environment and install it with the USB driver, then connect a LED (positive (longer) leg of the LED to pin 13 and the negative (shorter) leg to ground (marked “GND”), plug in the Arduino and upload the first trial Blinking LED code to the board and run it. Voila, you have the system.

blinkingLEDwith Arduino

Thoughts on Open Source Hardware at the Austin Maker Faire

For open source hardware you need open source software and a modular hardware design that makes building customized hardware just as easy as writing software or web apps. In order to make the idea mainstream you need to commercialize it and that’s what exactly Bug Labs is planning to do. (Again, my bioDIY brain says, that we should apply this concept to biological components too on different levels, just like nucleotide (DNA, RNA), protein, organellar, cellular, tissue level, and make them available to home tinkerers).

One interesting session at the Austin Maker Faire was the chat on Open Source Hardware with Limor Fried and Phil Torrone and Anna recorded it with her new camcorder, so please check Anna’s comments to learn more and see the talk:

Arduino Diecimila: my first microcontroller ever

arduinodiecim

The biggest impact of the Austin Maker Faire on me was that yesterday I bought an open source, CC licensed Arduino microcontroller and a breadboard for building prototype electronic circuits. I am a total rookie in home electronics but I thought it’s never too late to learn completely new things with the help of our extended memory, the web.

In the long run I’d like to utilize my microcontroller (or the acquired knowledge) for biological purposes in the lab and not just blinking LEDs.

Have you heard of any quality biotech-biology based community (blog, forum, network) specialized in electronics or coding for researchers, online?

Links: How to buy

Arduino Guide

MAKE Arduino Archives

Going to the Austin Maker Faire, October 20-21

At last a real family event for Anna and me: we are heading to Travis County Fairgrounds, Austin, Texas on October 19th to visit the MakerFaire. This will be the 3rd American MakerFaire, and the first outside the Bay Area. I am prepared to meet enthusiastic makers and mind-blowing DIY projects there, as well as to say hello to Phil Torrone, Dale Dougherty or Mike Hendrickson, the latter 2 I met at the Euro Maker Faire in Brussels (and Mike as an old Foo was at the SciFoo Camp too, offering me to laser etch my then-new and then-beloved iPhone).

AustinMakerFairetickets


Wired on the emerging science video websites: see one, do one, teach one

Wired has a nice piece on Video Sites Help Scientists Show Instead of Tell by Alexis Madrigal focusing on the high-end, non-youtubish, let’s-build-the-pro-network-of-video-geeks-in-the-labs-out-there approach of JoVE. Video players mentioned on the pop side: LabAction and PloS backed SciVee. The real question of this niche market is: In order to penetrate the mainstream science audience what is the proper mix of anti-Web 2.0 professional science rules and Web 2.0 techniques science video site builders should apply. Profit is not on the agenda yet.

“Highlighting little tricks in a video that might not be apparent in a paper can save an enormous amount of time,” said Dr. Arnold Kriegstein, whose University of California-San Francisco lab has posted a video about “cortical neurogenesis,” or the growth of neurons in the cerebral cortex. “There’s an old adage in medicine about learning: See one, do one, teach one. It carries over to the research lab, too.”

Sharing those little tricks with scientists everywhere is the idea behind the Journal of Visualized Experiments, an all-video scientific journal that launched its microfluidics-focused eighth issue in early October.

Dry, jargon-laden scientific papers can leave out what scientist and blogger Attila Csordas calls “the tacit dimension” on his blog.”

Mr. Madrigal has chosen a good post of mine to refer as that early post, Science: video protocols can help to share the tacit dimension was the starting point in 2 respects: a., in the comment section Moshe Pritsker introduced JoVE one month later to the blogosphere, so I could spend the same day to cover it instead of hanging around in Cambridge with my girlfriend b., at the same time the idea of LabAction was born.

I finish the post later, just let me get the breakfast and go to the lab first…. ok, I am here again. Continue reading

Second Annual Maker Faire this weekend and expecting the First BioMaker Faire…

partmakerposterBuilders, Hackers, Do-It-Yourselfers are gathering around this weekend at the most visible embodiment of the Maker spirit, the Maker Faire 2007 at San Mateo Fairgrounds, California. I remember the inquisitive and incredulous eyes of the traditional tech makers, coders, engineers while presenting my placental stem cell project at Euro Maker Faire last year. Now imagine a similar Faire for Biotech DIYers with open lab spaces… If you can imagine it, you can make it! Links: Make Blog, Phillip Torrone‘s Flickr Stream, Maker Social Network, Wired.


Life extension: body hack and/or life hack?

memento life hackIn recent culture, technological life extension is considered to be a form of hacking, as 2Dolphins says a “hacker is someone who enjoys the intellectual challenge of creatively overcoming or circumventing limitations — someone who makes things work beyond perceived limits through unconventional means or skills.” In hacking there is also a DIY element too.
There are now 2 broader hacking terms applied for physical life extension technologies: body hacking and life hacking. For first, see my previous post about Bodies in the Making book which handles a diverse range of practices that aren’t usually linked: tattooing, cosmetic surgery, body-building, life extension technologies, self-cutting as exemplars of the body hacking concept. Body hack in that context is something extreme, something very experimental. How extreme form it will take, that depends on the chosen technology. In the old school permalink-free blog Notes from Classy’s Kitchen it is said for instance in the November 26, 2005 post: “What Aubrey de Grey was proposing was the ultimate bodyhack, engineered immortality (or 1000 year life span at least).” Body hack also includes a form a DIY, for instance Nikolaj Nyholm of O’Reilly Radar blogged on the “protocol for “isolat[ing] stem cells from your baby’s placenta in a rent lab or at home” for the upcoming EuroOSCON Make Fest, which also plays well with one emerging theme at this year’s FOO Camp, body hacking — engineers and copper wire paired with doctors, psychologists and neurologists.”

On the other hand there is the emerging life hack movement popularized by blogs as Lifehacker or 43 Folders or Lifehack.org. According to Wikipedia “the term life hack refers to productivity tricks that programmers devise and employ to cut through information overload and organize their data.” And it is also Nikolaj Nyholm, who calls Aubrey de Grey an extraordinary life-hacker concerning his SENS-esque plan to defeat aging. Why life extension counts as a life hack? Long story short: it’s all about hacking time. The narrowest bottleneck of productivity is time, and indefinite life extension’s main ambition is to abandon this final limiting factor, to make time pressure out of time. But can indefinite or maximum life extension (and especially the here supported continuous regeneration treatment through systemic regenerative medicine called Pimm) really be interpreted as a life hack? I think yes. Indefinite life extension is the biggest scale life hack as it amplifies human capacities indefinitely, because it is the only possibility for a human and mortal individual to fully explore his/her own individuality, to develop his/her own abilities let it be mental, physical, or moral.

There is also the term biohacking, which refers mostly to synthetic biology or creating public awareness of human genetic information and in this context biohacker is a synonym for biopunk, and the term is not applied recently to life extension, although in the future it could considering the broad semantic field of the bio prefix.

To sum up: life extension is a form of extreme body hack which is the most extended life hack, although a body hack is rarely a life hack and vice versa. (In the movie Memento Guy Pearce (picture), who lacks short-term memory, uses tattoos on his body as fact memos, which is also a body and life hack, although most tattoos are just ornamental.)

Smart comments on the home placenta stem cell project

I collected some critical comments worth considering on the home placenta stem cell project from Make readers. Thanks for all.

“Um hello..how many people have a whole lab set up in their home?”20+ years ago — that sentiment would be — “How many people can afford a whole computing set up in their home? (and have space)” If there’s a demand — there will be a whole lot of companies explaining why their equipment is not only cost effective, but better than their competitors :P

Posted by: trebuchet03 on January 23, 2007 at 03:21 PM

Continue reading

What is bioDIY?

I republish here my “manifesto” like article on biotech DIY, which I wrote in April, 2006 on Newsvine in order to see the thoughts behind the placenta stem cell project.

Would you like to sequence your genome in your garage? To grow your stem cells in the kitchen-lab? To hunt for point mutations just for your own sake? Welcome to the coming world of personal biotech.
All you need is a short course in biotech basics, a few thousands of bucks, some tinkering capability, and enough spare time. The beautiful retro idea of tinkering with digital devices in a garage, conveyed by the Make magazine, can be extended to biotech too.
The know-how of hacking seemingly complicated electronic devices has been made accessible to non-pros. The needs were fuelled by the idea of personal fabrication. However, needs are constantly changing, and biotech is gaining more and more ground in everyday life.

Continue reading

How to isolate amniotic stem cells from the placenta, at home!

/Thanks for spreading the idea of biotech diy: Make, Pharyngula, kottke.org, Scientific American Blog, BoingBoing, Digital Bio, Clock among others…/

The placenta is a very valuable and scarce human tissue, although the proper recycling of it is not placentophagy, but the isolation of stem cells from its amnion layer, and storing them for later regenerative purposes for the whole family. Human amniotic epithelial cells (HAECs) from the placenta are alternative replacements of human embryonic stem cells, and have the potential to differentiate to all three germ layers in vitro. These cells are very close to those earlier and broadly multipotent amniotic fluid-derived stem cells, which made the big buzz lately on the web, published by De Coppi, Atala et al. in Nature Biotechnology. Here I would like to show, although I do not provide any warranty and can not give any guarantee, that isolating stem cells from the placenta is not more difficult than making a steak, and with proper preparation, investment and timing you can do it even at home or in a rent lab. The process is ethically non-controversial since the placenta is usually discarded after birth. Today, stem cell therapy is just a promising possibility, but in the not so distant future, self-aware citizens may manage their own stem cells, grow them in the garage, and store them in the fridge. If so, it could be a form of autonomous medical self-insurance. We are at the dawn of the bioDIY movement backed by open source science for anybody. I used Make magazine’s Backyard Biology issue as a reference, because it invented the basic language of bioDIY or home or garage biotech. Here is the algorithm at the cartoon and below are the detailed, although not self-including textual protocol. More details will come later, if asked.

isolatestem

Continue reading

Life Scientists: let us make video-articles for JoVE!

joveJournal of Visualized Experiments, or JoVE, the video focused science online journal was one of the most advanced and forward thinking newly launched website in 2006 in the field of life sciences. I am personally engaged in the topic of open source online protocol videos and JoVE is Pimm’s recurring theme. After the pioneer first issue, below is the Call for Submissions for the second issue by editor in chief and founder Moshe Pritsker. I would like to ask all the web-savvy and movie-able biologists to contribute. You do not have to make a strict narrative or perfect shots and cuts or publish complicated processes, just focus on the feasible and basic experimental procedures. A little DIY and a stable community makes web-based science and eventually offline science huge.

“Dear Scientist,

I invite you to submit a video-article on your experiments to the Journal of Visualized Experiments (JoVE).

JoVE is a newly founded journal devoted to visualized (video-based) publication of biological research. Continue reading

The image of science: Google-like Biomedical Image Search Engine for pros

hESCssearchbiomedCheck out the brand new BioMed Search, it is fantastic, currently over 1 million images have been indexed from peer-review journals in biomedical fields and more is on its way. BioMed Search has been created by Alex Ksikes, currently a Ph.D. candidate in Computer Science with focus in Computational Learning Theory at the University of Cambridge (good town, good to be here). The About says: “The goal of BioMed search is to organize figures, images or schema found in biomedical articles. BioMed Search indexes image captions along with the citations to these images. “ Pictures can be seen with full and thumbnail view. Recent Searches, my favourite, show terms recently searched for, with which you can catch research trends. If the number of users grew exponentially, a digg-like real-time spy could spectacularly dinamise the site.

With BioMed Search you can search for general terms like mitochondria, phrases like “proteomics”, searchrecent searches in the title of the articles only for “Mfn1″, get images from an article with a concrete PMID (PubMed Identifier), find images authored by “Nicholls”, limit results to content from a specific year date:1996 (actually just from 1996 presently), and limit search to a specific journal. And this is just by default.

Young science people with an entrepreneurial spirit full of diy hacker skills backed by current web technologies, like Alex Ksikes, who is a real coder, and Moshe Pritsker, biologist, founder of Journal of Visualized Experiments make filtered academic information instantly and easily accessible. And so academic scholar science becomes not just updated, but simply …cool.

via Google Blogoscoped, thanks Anna for the terrific tip.

Thanks Alex Ksikes to make this happen.

The Scientist on JoVE: Video makes the new science stars?

Thoughtful short piece on the new science video experiment site JoVE in The Scientist blog by Brendan Maher: “Videos like this could cut down troubleshooting time considerably. Moreover, there’s a great opportunity to create some new science stars. Who, after all, doesn’t have a running commentary going through their head as they run through the little tricks that make their experiments work sublimely? Now you can find an audience.” Link

Scientists, scholars in the lab: let us video bioDIY!

JoVE stats: blogosphere and Nature News traffic before official launch

The first official issue of the new biological video protocol site JoVE or Journal of Visualized Experiments will be available today 11 pm EST, November 30, 2006. The graph shows November traffic in term of unique visitors, first jovestats2.5 weeks mainly uploaders, authors, editors and editors’ friends used the page, from 17th there was a mild scientific blogosphere coverage, like Pimm, Blog around the clock and Easternblot, and from 24th, November, it was the Nature News article (no longer available, only to subscribers) aided by blogs, that generated the heaviest traffic, that led even to a server change.

Moshe Pritsker, founder and editor of JoVE says: “The first launch means more organized format (articles by categories), certain dates of issue. Later we plan to increase the qualities of the video-articles. The idea is to create a scientific publication with all the characteristics of publication, to avoid the Youtubish comparison, while remaining flexible. The site will have a different design and more video-articles, including ones from famous ES cell labs.”

Thanks Moshe for the data.

More on science video protocols: Science: video protocols can help to share the tacit dimension, Early science protocol video: OpenWetWare Drosophila CHiP

Nature News on JoVE: is JoVE really the YouTube for life scientists?

Nature News has an article of the new Journal of Visual Experiments website, whereof Pimm had a story one week ago with the help of Moshe Pritsker, founder of the site. The title of the Nature News post: YouTube for test tubes, which sounds good really, but is problematic a little bit. In a way the YouTube analogy is true, the biologists can now upload their protocol videos on the site, and can watch it freely, and there is the exciting DIY possibility, but on the other hand JoVE is not YouTube at all: there is a strict submission process with clear policies to go through, which excludes junk, and you cannot embed the videos freely. The first aim of JoVE is to be useful for people in the lab, which is a scientific purpose. Entertainment is just after that. Good luck for any bioDIYers.

Biological Video Protocols on JoVE: Online Journal of Visualized Experiments

At last there is an almost perfect solution for life scientists to share video protocols and insider tricks to learn techniques and repeat experiments properly. Journal of Visualized Experiments (JoVE) is a newly founded and FREE online research journal that publishes video-articles on biological experiments (video-protocols). It is an independent project by 2 people, Moshe Pritsker (postdoc at Harvard Medical School) and Nikita Bernstein (Web application developer). Moshe says: “As a biologist personally suffering from written “protocols”, I had this idea for some years, but couldn’t do it because was busy with my PhD studies at Princeton. Two months ago, Nikita and I have began implement it practically, as a research publication.” On JoVE Video-articles include step-by-step instructions actinjoveon experiments, and short discussions by experts describing possible technical problems and modifications. JoVE employs the OPEN-SOURCE model: Continue reading

John Cumbers’ DIY approach to life extension: personal genomics and synthetic biology

John Cumbers made the Drosophila CHiP protocol video. He is a graduate student at the Tatar lab in Brown University, USA. Below are his answers to the blogterview questions and through answer 5 you can take a fresh look at the bottom-up approach of synthetic biology. Continue reading

Early science protocol video: OpenWetWare Drosophila CHiP

One previous post of Pimm was about the advantages of online, open source-like science protocol videos. So thanks to Sri Kosuri, here is an early sample protocol movie (3 parts) made by John Cumbers on the preparation of fixed chromatin from Drosophila embryos to use the DNA in a genomic array technology, developed in Rob White’s Cambridge lab.

Science: video protocols can help to share the tacit dimension

Matias Pasquali has a short piece in recent Nature Magazine on the upcoming role of DIY videos in protocol sharing between scientists: “Probably the most feasible approach is to publish movies describing the methods, a service already offered by some publications and protocol websites, but which could become routine. Much more information on the essential steps of a new protocol, including audio commentary on the trickiest steps (from the position of the Petri dishes to the speed of dispensing), could be accessible using video format and published online with the paper. Such videos could transform the way in which methods are communicated.”

Pasquali has right. There are many possible advantages of the video-format. First, videos can show the insider tricks of a rigid lab science protocol, can reveal the tacit dimension behind the algorithm of mitochondrial DNA isolation from human fibroblasts for example. Second, short online protocol movies can resolve the ever-growing data amount problems ohelmetcamf original life science articles. Recent biology articles have deep disadvantages encoded in the Methods section, which are the most unnoticed parts of the papers. Materials and Methods sections became more and more ornamental, and you can hardly repeat the original experiment if you can lean only them. Third, videos show the way to an open source and publicly visible science, which is a good entrance into the DIY age.
Unfortunately not all scientists are geeks at the same time. One working solution for protocol documentation could be the Helmet Cam which is a head-mounted video camera that makes you capable of hands free protocol video production. Saul Griffith inventor of Helmet Cam says in current MAKE magazine Backyard Biology Issue that the aim is “to make how-tos a no-brainer.”
There are initiatives to share science protocols on the web, and wiki is obviously one good candidate to do that, just see OpenWetWare for example. So I can hardly wait the emergence of a YouTube-like science website. Unfortunately I did not find good sample science recipe videos on YouTube, Google or Yahoo Video, if you were lucky enough to find one, please do not hesitate to share it with all of us.

drosophilaUpdate: Thanks to Sri Kosuri, here is an early sample protocol (part of) movie on the preparation of fixed chromatin from Drosophila embryos to use the DNA in a genomic array technology, developed in Rob White’s Cambridge lab. Link

bioDIY on Euro Maker Faire: stem cells from the placenta

I am a big fan of bioDIY or home/garage biotech, the idea that tinkering could be extended to biological entities to. Just take a look at MAKE magazine current Backyard Biology Issue. I’ll be in Brussels at Wednesday at Maker Faire (list of Makers here) with the project: how to isolate stem cells from your baby’s placenta in a rent lab, or at home. Detailed instructions about the project will be published later so the information is restricted here.

From O’Reilly Radar:

radar1

There is plenty of room indeed for every biotech geek.

Bonus question for my stable readers: what can be the connection between private storage of placental derived stem cells and the continuous regeneration treatment called pimm?