Genomikon kit - BioBytes 2.0

I would really want to get my hands on the Genomikon kit to build my own plasmids. It is an educational self-contained kit. Read more here :http://2010.igem.org/Team:Alberta/biobyte2

"Synthetic Life?" The New Industrial Revolution? (Bioethics Seminar)

From Youtube : Will biological engineering usher in a new industrial revolution? Gregory Kaebnick, a research scholar at The Hastings Center, leads a bioethics seminar on synthetic biology. What is it? Where might it lead? What ethical questions does it raise?

Synthetic biology will bring us a slimy, moist future

The first post i put up on this blog was a quote from Freeman Dyson in 'Many colored glass' and descibed for me where we are heading with biology.  This wired UK article is an excellent article quoting the same source :


.....But those might be the aesthetics we'll have to get used to if Freeman Dyson was right when he wrote this a couple of years ago: "I predict that the domestication of biotechnology will dominate our lives during the next 50 years at least as much as the domestication of computers has dominated our lives during the previous 50 years."....


Read more : http://www.wired.co.uk/magazine/archive/2009/09/start/synthetic-biology-will-bring-us-a-slimy-moist-future

Synthetic Biology Open Language

I guess these kinds of develeopments are the equivalent of a programming language and standardisation with respect to biological parts :

Synthetic Biology Open Language (SBOL) is a community effort involving University of Washington, BIOFAB, and VirginiaTech (Jean Peccoud). The purpose of the project is to develop computational representations for synthetic biology parts so that they can be efficiently exchanged between research labs. SBOL presently consist of semantics for describing parts and visual styles for visually displaying parts.

The insides of Openpcr

A nice photo of the isides of the openpcr machine. When i find some time i Will construct one myself.

Space Travel and Synthetic Biology

The article gives a hint of applications to come as a result of Synthetic Biology. In this case with respect to space travel. However, I suspect that here on earth we could very well benefit from most of these developments as well :

• microbial community could add cells to produce certain vitamins and proteins needed for long-term space missions.
• eliminate future infections, tooth decay

Read more on arsbiologica : http://www.arsbiologica.org/2010/11/synthetic-biology-and-space-travel.html

The map of the genome of the first synthetic cell

On edge.org the map of the genome of the first synthetic organism : http://www.edge.org/documents/Edge-Serpentine-MapsGallery/high-res/venter.png

George M. Church in Rotterdam received the 4th Steven Hoogendijk Award

Last Thursday (23rd September) I attended an impressive lecture by George Church at the Erasmusiaans Gymnasium near the Erasmus Medical Centre in Rotterdam. His talk was among other things about the PGP-10 (personal genome) project. See video here :




The following Friday George M. Church was officially awarded the 4th International Steven Hoogendijk award instated by the Bataafsch genootschap. See a partial google translate of their announcement here :

"On Friday September 24, 2010 George M. Church will receive in the Citizens of the City Hall of Rotterdam from the Mayor Ahmed Aboutaleb ing by the Batavian Society of Experimental Philosophy in Rotterdam granted International Steven Hoogendijk Award. This prize is awarded this year in the medical-technical field "minimal invasive diagnosis and consists of a silver medal and a sum of 15,000 euros. "

Computational genomics - where to start my diybio journey?

As an electrical engineer, with an ever growing interest and curiousity into DIY biology, synthetic biology and genomics, i wondered where to jumpstart this journey. So i figured it would be a good thing to start there where i understand the tools and language best. After searching for a while i stumbled upon the field of computational genomics. In particular i found the site http://www.computational-genomics.net/ which is part of course taught at the university of Bristol.

Currently, I  am working my way through the book (Introduction to Computational Genomics: A Case Studies Approach) and exercises. Already some familiar statistical techniques, i have been working with in other fields, passed by. In addition, it is very pleasing to see that so many of the basic software to analyse a genetic sequence are open source tools.

So hopefully my journey into the field of computational genomics is a little step forward and I am wondering where to go next. Any suggestions?

Bètabrede docentendag Synthetische Biologie, een synthese van verschillende bèta-vakken

De 'synthetische biologie' staat sinds kort in de belangstelling sinds het gelukt is een cel te verkrijgen met een volledig synthetisch genoom. Welke chemische processen spelen hierbij een rol, wat is het belang van het maken van een dergelijke cel. Kan dit een rol spelen in productietechnologie?

Lees verder : http://www.rug.nl/fwn/informatieVoor/VWOdocenten/BetabredeDocentendag

Crappy Google translate :

Teacher's day : Synthetic Biology, a synthesis of several beta-courses

The "synthetic biology" is in the spotlight recently since it has been possible to obtain a cell with a completely synthetic genome.Chemical processes which play a role, what is the importance of making such a cell. Could this play a role in production technology?

Synthetic biology research on biofuels has a mathematical angle

Qing Lin and colleagues are using a common mathematical concept to develop 'nano-reactors' designed to generate much higher yields of biofuels. Read more here : http://www.physorg.com/news203267252.html

Danish bio hack space : BiologiGaragen

BiologiGaragen is a laboratory and open creative space where anybody with an interest in biological science can meet, play, and share their ideas and thoughts.  We will encourage citizen science in biology and make knowledge, tools and software available for people to develop solutions based on their personal, local and specific needs.


Read more here : http://biologigaragen.org/

Neither models nor miracles: a look at synthetic biology

The 20th century broke open both the atom and the human genome. Physics deftly imposed mathematical order on the upwelling of particles. Now, in the 21^st century, systems biology aims to fit equations to living matter, creating mathematical models that promise new insight into disease and cures. But, after a decade of effort and growth in computing power, models of cells and organs remain crude. Researchers are retreating from complexity towards simpler systems. And, perversely, ever-expanding data are making models more complicated instead of accurate. To an extent, systems biology, rather than climbing upwards to sparkling mathematical vistas, is stuck in a mire of its own deepening details.

Read more : Neither models nor miracles: a look at synthetic biology

Biotech Revolution must start with Education

Popular media coverage of biotechnology is saturated with talk of “revolution” — the time when genetic engineering, synthetic biology, and personalized medicine will change our lives in more ways than we can imagine.  These technologies, we are assured, are right around the corner.  But having heard such promises for well over a decade, I find myself asking:  http://www.hplusmagazine.com/editors-blog/biotech-revolution-must-start-education

IGEM Team Helps Prevent Rogue Use Of Synthetic Biology

A team of students from ENSIMAG, an engineering school in Grenoble, France, and Virginia Tech is using bioinformatics to implement federal guidance on synthetic genomics. The students' work will help gene synthesis companies and their customers better detect the possible use of manufactured DNA as harmful agents for bioterrorism.

Read more here : http://www.medicalnewstoday.com/articles/195304.php

Opmars van synthetische biologie

Synthetische biologie is een nieuwe technologie met als hoofdthema de ontwerpbenadering van biologische systemen. Vanwege het grote aantal mogelijkheden wordt er verwacht dat synthetische biologie veel uiteenlopende toepassingen zal krijgen. Japan profileert zich met R&D op verschillende onderwerpen. Veel aandacht is er voor onderzoek naar het van de grond af opbouwen van celachtige systemen (protocel). Ook strategiebepalende organisaties in Japan zijn overtuigd van het feit dat synthetische biologie een belangrijk R&D-thema wordt.


Lees meer hier : http://www.twanetwerk.nl/default.ashx?DocumentID=14241

Do-It-Yourself Bioengineers Bedeviled by Society's Paranoia

Gather up a few thousand people and you will find, without fail, that several of them have some very impressive hobbies.

Read more here : http://www.genengnews.com/gen-articles/do-it-yourself-bioengineers-bedeviled-by-society-s-paranoia/3383/

Biohackers – the geneticists in the garage

If you are living outside America, chances are you have not yet heard of DIYbio, a new approach to biotechnology that is already generating great interest across the Atlantic, and is now gathering pace in Europe.

Read more : http://euroscientist.com/2010/08/157/

Biotechniques.com : Cheap PCR: new low cost machines challenge traditional designs

Although PCR is a fundamental tool for many biologists, thermal cyclers—essential to driving PCR reactions—have not yet become easily affordable or widely accessible. An instrument’s expense, which is between $4000 and $10,000, has essentially confined its usage to university laboratories, and excluded entities like public schools or field-based health initiatives, which could benefit from easy access to DNA amplification technologies.

Read more : http://www.biotechniques.com/news/Cheap-PCR-new-low-cost-machines-challenge-traditional-designs/biotechniques-301745.html

Global Synthetic Biology Market to Exceed $4.5 Billion by 2015, According to New Report by Global Industry Analysts, Inc.

Global Synthetic Biology Market to Exceed $4.5 Billion by 2015, According to New Report by Global Industry Analysts, Inc. GIA announces the release of a global market report on Synthetic Biology. Global Synthetic biology market is projected to exceed $4.5 billion by the year 2015. Synthetic biology is expected to provide major advances in the areas of biomedicine, biopharmaceuticals synthesis, biosecurity, energy and environment, sustainable chemical segment, and biomaterials/smart materials production. Significant investments are expected in the synthetic biology field.

Global Synthetic Biology Market to Exceed $4.5 Billion by 2015, According to New Report by Global Industry Analysts, Inc.

Gel Electrophoresis Virtual Lab

Have you ever wondered how scientists work with tiny molecules that they can't see? Here's your chance to try it yourself! Sort and measure DNA strands by running your own gel electrophoresis experiment.

Find out here how gel electrophoresis works : http://learn.genetics.utah.edu/content/labs/gel/

IFTF - Curing Cancer in a Garage?

This is the first time I've seen someone happily exclaim, "I'm curing cancer in my garage!"

Biocurious, a new hackerspace for biotech based in Mountain View, CA, has just been born. Founders Eri Gentry and Joseph Jackson started this community lab space for citizen science, expanding the trend of hackerspaces like Noisebridge and HackerDojo into biology. They are crowd-raising $30,000 to help get their garage lab off the ground.

Read more : http://www.iftf.org/node/3526?utm_source=twitterfeed&utm_medium=twitter

Synthetic biology, ethics and the hacker culture

 by ANDREW MAYNARD on AUGUST 17, 2010

While the DIY Biotechnology community has grown considerably since this post, the piece still captures something of what is still a young movement, and one that challenges assumptions about top-down technology innovation.

Read more: http://2020science.org/2010/08/17/synthetic-biology-ethics-and-the-hacker-culture/#ixzz0x9hpkhn3

On Cunningprojects.com : An Analysis of What #DIYbio Has and What It Needs

DIYbio and its more professionally oriented cousin, Garage Biotech, are undergoing a revolution at present. Essential equipment that used to cost thousands is now available at affordable prices, in many cases under open licensing schemes and open to community development. Knowledge of biology, genetics and the procedures underlying it all is being disseminated in ever-more-abstracted forms to make it easier to get started. And soon, even the biological components: strains, enzymes and substrates, will likely become mass-marketable.

It’s an exciting time to be involved in the development of tomorrow’s technology, and sometimes I find myself stepping back to consider what we have, and what we still need. I may as well share these musings with others to spare them the time, and perhaps to inspire someone with the know-how to fill in the gaps and help make this happen.

Prepare for a long, long post. Read more here : http://letters.cunningprojects.com/?p=132

Opinion on Synthetic Biology

Like Tom Wakeford and Jackie Haq (26 June, p 26), we were part of the group overseeing the preliminary dialogue between scientists and members of the public, discussing breakthroughs in synthetic biology with a view to gauging their response to the new technologies......

Read more on the New Scientist website : http://www.newscientist.com/article/mg20727720.200-synthetic-biology.html

BioCurious: A Hackerspace for Biotech. The Community Lab for Citizen Science

What ideas would you come up with if you hung out with a molecular biologist, a mechanical engineer, a computer programmer and an artist - and happened to be sitting next to a lab?





Read more and make your pledge : http://www.kickstarter.com/projects/1040581998/biocurious-a-hackerspace-for-biotech-the-community

DIYbio in Singapore

DiyBio is everywhere .....

http://diybiosingapore.wordpress.com/

The state of DIY Biology

Makezine is running a piece on the amateur biotech movement

http://blog.makezine.com/archive/2010/07/the_state_of_diy_biology.html

DIYBio meet-up - Folk Microbiology

It was a night of culture - yoghurt cultures. Vaughn Tan shared his passion for yoghurt with about two dozen captivated future yoghurt makers. He spoke about the biochemistry and microbial ecology of the process - ways to optimize the proteins in the milk, effects of inoculation temperatures, the activities of the different bacterial populations in the culture.

read more : DIYBio meet-up - Folk Microbiology

Responsible Science for Do-It-Yourself Biologists

..... The Synthetic Biology Project at the Woodrow Wilson Center is partnering with DIYbio.org, on a project to ensure safety within the rapidly expanding community of amateur biologists.....

Read more : http://www.earthtimes.org/articles/press/responsible-science-do-it-yourself-biologists,1363363.html

The Risks and Rewards of Synthetic Biology

When scientist cross the moral Rubicon its time for debate:

The Risks and Rewards of Synthetic Biology

What is DIYbio in 4 minutes?

Watch this clip to get a sense of what DIYbio is all about. Source : http://bmlabs-mag.posterous.com/what-is-diybio-in-4-minutes via : diybio.org

Embedded video :

The DIYbio Community - Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

Will Synthetic Biology Change How We Value Human Life

Will Synthetic Biology Change How We Value Human Life

Synthetic Biology Curriculum Expands with New Courses

The NSF-funded Synthetic Biology Engineering Research Center (SynBERC) has made exceptional inroads this year in the effort to train a new generation of synthetic biologists by developing and launching a series of courses at the graduate, undergraduate, and high school levels. The courses reflect not just the scientific and engineering goals of the field, but also its social and ethical dimensions. Some of these courses are available outside the host university through online modules at openwetware.org, and a course on the Fundamentals of Synthetic Biology was taught at the Korea Advanced Institute of Science and Technology (KAIST) in Daejeon, Korea. SynBERC is headquartered at the University of California, Berkeley.

Read more : http://showcase.erc-assoc.org/accomplishments/2010/2010-SynBERC10-L-curriculum_BH.html

Open Science Summit 2010 : Enlightenment 2.0: Unleashing the Open Science Revolution

Renowned physicist Freeman Dyson identifies two kinds of scientific revolutions, those driven by new concepts (theoretical), and those driven by new tools (technological).

Read more : http://opensciencesummit.com/2010/05/12/enlightenment-2-0-unleashing-the-open-science-revolution-2/

100 Ideas : Keegotech microbial fuel cell voltage

An arduino is hooked up to measure the voltage created inside a Keegotech microbial fuel cell. Some of the soil microbes in the MFC become electrogenic in anaerobic conditions, and the MFC collects electrons from them.


http://www.pachube.com/feeds/8254

Will Synthetic Biology Lead to Truly Living Buildings? | Buildings | GreenBiz.com

Will Synthetic Biology Lead to Truly Living Buildings? | Buildings | GreenBiz.com

UK Workshops on Synthetic Biology Reveal Fascination, Worries | GenomeWeb Daily News | GenomeWeb

UK Workshops on Synthetic Biology Reveal Fascination, Worries | GenomeWeb Daily News | GenomeWeb

Wired :U.S. Leading Charge on Synthetic Biology Funding

Synthetic biology received about $430 million in U.S. government funding from 2005 to 2010, far outpacing European governments, which gave their synthetic biologists $160 million over the same period. The emerging field received nearly no funding before 2005, according to a new Woodrow Wilson Center report.

Read More hhttp://www.wired.com/wiredscience/2010/06/synthetic-biology-money/#ixzz0qLLf8UWs

Government funding for synthetic biology on the rise

New report compares US and European funding

WASHINGTON, DC — A new analysis by the Synthetic Biology Project at the Woodrow Wilson Center found that the U.S. government has spent around $430 million on research related to synthetic biology since 2005, with the Department of Energy funding a majority of the research. By comparison, the analysis indicated that the European Union and three individual European countries – the Netherlands, United Kingdom, and Germany – had spent approximately $160 million during that same period.

... http://www.eurekalert.org/pub_releases/2010-06/poen-gff060710.php

The reoprt can be found here : http://www.synbioproject.org/

Ginkgo selected for $6M ARPA-E grant from DOE

..... A Boston company selected to receive $6 million is Ginkgo BioWorks, which seeks to engineer the E. coli bacterium to harness electric current to convert carbon dioxide and water into isooctane, a component of gasoline, the department said......

http://www.boston.com/business/ticker/2010/04/feds_earmark_22.html

Synthetic life is a noble cause - Synthetisch leven is een nobele zaak

The creation of a new life form is the highest for humans. That he went level with the many gods that human culture is rich. Nothing wrong with that so. Or right? As sensational stories prevail in the discussion on synthetic life is becoming louder the call for control and risk mitigation of a research field with many fantastic potential.

Google translate : Volkskrant article

TU Delta - Wetenschap: Green solution for oil spills

Synthetic Biology is a relatively new field, where biology and engineering combine to achieve new biological functions and systems not found in nature. Previous TU Delft teams have won several medals. The pressure is high to uphold that ...

Delta TU Delft - http://www.delta.tudelft.nl/nl/wetenschap/green-solution-for-oil-spills/21312

Congress, Obama Take Sudden Interest in Synthetic Biology

Congress, Obama Take Sudden Interest in Synthetic Biology

Read More http://www.wired.com/wiredscience/2010/05/congress-obama-synthetic-bio/#ixzz0pDtelg4Y

The economist on synthetic biology

An indepth article from the Economist putting in context the groundbreaking work of Dr Venter and Dr Smith.
http://www.economist.com/displayStory.cfm?story_id=16163006

diybio.org organising a tshirt contest on opensciencefund

http://opensciencefund.org/2010/05/19/diybio-shirt-design-contest/

ON "CREATION OF A BACTERIAL CELL CONTROLLED BY A CHEMICALLY SYNTHESIZED GENOME" BY VENTER ET AL

Edge has a piece on the stunning work of Craig Venter covering some very interesting viewpoints from great scientists such as Daniel Dennett, Freeman Dyson and many more.

http://www.edge.org/discourse/creation/creation_index.html

'Artificial life' breakthrough announced by scientists

see the entire article here : http://news.bbc.co.uk/2/hi/science_and_environment/10132762.stm

Maverick U.S. scientist creates first synthetic genome

for the article see the Vancouver Sun: http://www.vancouversun.com/news/videos/index.html#oDGRSh8_b0jeW8FXmYTDa_KleSkVBsro

BioRuby - Open source bioinformatics library for Ruby

There are great open source packages for bioinformatics when you start searching form them. Here is BioRuby :

BioRuby project provides an integrated environment in bioinformatics for the Ruby language. This project is supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.

http://www.bioruby.org/

Motility detection of microorganisms using a hacked optical mouse

Very interesting to see applications where DIYbio meets Open Hardware like arduino.

Marc Dusseiller is hacking optical mice for microbial motility detection :
http://www.dusseiller.ch/labs/?p=941

Hacked optical mouse for detection of motile single cell organisms from dusjagr on Vimeo.

Igem 2010 europe workshops to be held in France

The Europe workshop is sponsored in part by Genopole®. In 1998, Genopole® was founded in Evry (near Paris) under the impetus of the French government, the local authorities and the French Muscular Dystrophy Association (AFM). Genopole® is based on a novel concept: bringing together academic labs, biotech companies and high-level teaching & training facilities on the same campus. Genopole®’s goal is to promote research excellence and entrepreneurship in life science, in order to position France as a scientific and industrial leader in highly competitive global markets. In twelve years, the Genopole® biopark has made its name as a major French player in biotherapy and biotechnology. It currently hosts 69 biotech companies and 20 academic research labs.

http://2010.igem.org/Workshops/Europe

Adventures in synthetic biology

"Adventures in Synthetic Biology", by Drew Endy, Isadora Deese and the MIT Synthetic Biology Working Group, and illustrated by Chuck Wadey.

http://www.nature.com/nature/comics/syntheticbiologycomic/index.html

One of my favourite TED talks : Craig Venter is on the verge of creating synthetic life

"Can we create new life out of our digital universe?" Craig Venter asks. His answer is "yes" -- and pretty soon. He walks through his latest research and promises that we'll soon be able to build and boot up a synthetic chromosome.

DNA Hackers

Na jarenlange studie van de genetische bouwstenen van de natuur is de mens klaar voor de volgende stap. Van achter onze computer gaan we de natuur anders ontwerpen. Labyrint volgt een nieuwe generatie wetenschappers die in laboratoria synthetisch leven bouwen en zet vraagtekens bij deze ontwikkeling. Want de code van het leven is openbaar en DNA is op internet te koop. Kan iedereen met internet en een DNA lab in zijn garage nieuw leven creëren? Wat kunnen we allemaal maken en wie beschermt ons tegen slechte bedoelingen?

Google translate :

After years of studying the genetic building blocks of nature, man is ready for the next step. From behind our computer, we we will design nature differently. Labyrinth is following a new generation of scientists who in laboratories build synthetic life and challenges this development. Because the code of life DNA is public and is on the Internet for sale. Will anyone with internet access and a DNA lab in his garage be able to create new life? What can we build and who protects us from evil intentions?

http://www.wetenschap24.nl/labyrint/node/132

Lecture Do-It-Yourself Biology Natalie Kuldell Reshma Shetty PhD '08

Inspired by the vast potential of bioengineering, ordinary people are seeking their inner Frankenstein -- doctor, not monster. Two speakers who know their way around Petri dish and beaker discuss the possibilities and pitfalls of do-it-yourself biology with an MIT Museum crowd. http://mitworld.mit.edu/video/646

diyBiology - Domestication of biolotechnology

from 'A many colored glass : reflections on the place of life in the universe' by Freeman Dyson

"Domesticated biotechnology, once it gets in the hands of women and children, will give us an explosion of diversity of new living creatures, rather than the monoculture crops that the big corporations prefer. New lineages will proliferate to replace those that monoculture farming and deforestation have destroyed. Designing genomes will be a personal thing, a new artform as creative as painting or sculpture. Few of the creations will be masterpieces, but all will bring joy to their creators and variety to our fauna and flora."