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Dear OpenWetWare Community,

Thank you for your participation in the OWW improvement survey. We thank you for all your valuable input toward making OpenWetWare one of the most effective tools to facilitate your research.

We are thrilled to announce the winners of the OWW survey:

• Two $25 Amazon gift cards, at random, to two participants who completed the survey questions:
  1. Marko Dolinar, University of Ljubljana, Slovenia.
  2. Leanna Morinishi, MIT, USA
• One $50 Amazon gift card, to a participant who gave the best original suggestion(s) for OWW based on usefulness and feasibility:
  1. Lee Farrand, Seoul National University, Seoul, Korea

We will contact you individually to arrange the delivery of the prizes. Congratulations to the three of you!

It has been a challenging process to choose the winner for the top prize due to the high number of great comments we received. Among these valuable suggestions, Lee Farrand suggested that “On the discussion pages, authors could have ‘reputation points,’ allowing us to see who is rated by the community as being a reliable source of information.” Such an approach could contribute to a system for scoring/ranking protocols and other sources of information, a feature that many of you have requested. OWW contributors could increase their reputation points in many ways, including by other users voting their comments as being valuable.

Once again, thank you so much for your participation and valuable input. We wish you a productive year filled with new ideas and discoveries.

Sincerely,

Thi Thach
Communications and Development Manager
The BioBricks Foundation
thi@biobricks.org

Dear Friends of the BioBricks Foundation,

Here’s the latest news from the BioBricks Foundation‘s campaign to raise $50K by December 31, 2011. As of today, we have already raised $35K. So that leaves just $15K to go! Already made a gift? Thank you so much! Haven’t given yet? Please do so. Help us make it to the top!

Your tax-deductible gift of $10, $20, $50, $100, or any amount will have a big impact.

With your support, the BBF will have resources to conduct such activities as launching OWW2.0, providing scholarships to young researchers for SB 6.0, hosting workshops on exciting themes, and launching initiatives to unite global BIOFABs and create a road map for the field of SynBio. The time to give is now. Make a secure, online donation to the BBF today.

Thank you so much for your support.

Sincerely,

Dear Friends of the BioBricks Foundation,

Here’s the latest news from the BioBricks Foundation and our fundraising campaign to raise $50K by December 31, 2011. As of today, we have already raised $25K toward our goal. So that leaves just $25K to go! Already made a gift? Thank you so much! Haven’t given yet? There’s still time to do so. Help us make it to the top!

The BioBricks Foundation (BBF) is a public-benefit organization dedicated to advancing synthetic biology (SynBio) to benefit all people and the planet. We work to create a sustainable future by supporting the development and free exchange of standardized biological parts that are safe, ethical, cost effective and publicly accessible. The funds raised in this campaign will support the BBF’s work for SynBio in technology, the law, education, and community building for the coming year.

If you work in the BioTech industry, attended the SB 5.0 Conference, follow the BIOFAB, or are one of 9,000 people who use OpenWetWare, you are part of the BBF community. Please act now by making a personal financial gift to support the BBF.

Your tax-deductible gift of $10, $20, $50, $100, or any amount will have a big impact. With your help, the BBF will have resources to conduct such activities as launching OWW2.0, providing scholarships to young researchers for SB 6.0, hosting workshops on exciting themes, and launching initiatives to unite global BIOFABs and create a road map for the field of SynBio. The time to give is now. Make a secure, online donation to the BBF today.

SynBio has the power to transform our world. Let’s work together to ensure a strong, safe, open SynBio field. Please support the BBF mission.

Thank you so much for your support.

Sincerely,

Holly Million Executive Director, The BioBricks Foundation	Natalie Kuldell Board of Directors, The BioBricks Foundation OpenWetWare “Super User”

P.S. Want to get more involved? The BBF is making plans to better serve the SynBio community. Want to find out when SB6.0 is taking place? Want to give input on our new Education Program? Send us a message.

Dear Friends of the BioBricks Foundation,

Here’s the latest news from the BioBricks Foundation and our fundraising campaign to raise $50K by December 31, 2011. As of today, we have already raised $25K toward our goal. So that leaves just $25K to go! Already made a gift? Thank you so much! Haven’t given yet? There’s still time to do so. Help us make it to the top!

The BioBricks Foundation (BBF) is a public-benefit organization dedicated to advancing synthetic biology (SynBio) to benefit all people and the planet. We work to create a sustainable future by supporting the development and free exchange of standardized biological parts that are safe, ethical, cost effective and publicly accessible. The funds raised in this campaign will support the BBF’s work for SynBio in technology, the law, education, and community building for the coming year.

If you work in the BioTech industry, attended the SB 5.0 Conference, follow the BIOFAB, or are one of 9,000 people who use OpenWetWare, you are part of the BBF community. Please act now by making a personal financial gift to support the BBF.

Your tax-deductible gift of $10, $20, $50, $100, or any amount will have a big impact. With your help, the BBF will have resources to conduct such activities as launching OWW2.0, providing scholarships to young researchers for SB 6.0, hosting workshops on exciting themes, and launching initiatives to unite global BIOFABs and create a road map for the field of SynBio. The time to give is now. Make a secure, online donation to the BBF today.

SynBio has the power to transform our world. Let’s work together to ensure a strong, safe, open SynBio field. Please support the BBF mission.

Thank you so much for your support.

Sincerely,

Holly Million Executive Director, The BioBricks Foundation	Natalie Kuldell Board of Directors, The BioBricks Foundation OpenWetWare “Super User”

P.S. Want to get more involved? The BBF is making plans to better serve the SynBio community. Want to find out when SB6.0 is taking place? Want to give input on our new Education Program? Send us a message.

Dear Friends of the BioBricks Foundation,

Here’s the latest news from the BioBricks Foundation and our fundraising campaign to raise $50K by December 31, 2011. As of today, we have already raised $21K toward our goal. So that leaves just $29K to go! Already made a gift? Thank you so much! Haven’t given yet? There’s still time to do so. Help us make it to the top!

The BioBricks Foundation (BBF) is a public-benefit organization dedicated to advancing synthetic biology (SynBio) to benefit all people and the planet. We work to create a sustainable future by supporting the development and free exchange of standardized biological parts that are safe, ethical, cost effective and publicly accessible. The funds raised in this campaign will support the BBF’s work for SynBio in technology, the law, education, and community building for the coming year.

If you work in the BioTech industry, attended the SB 5.0 Conference, follow the BIOFAB, or are one of 9,000 people who use OpenWetWare, you are part of the BBF community. Please act now by making a personal financial gift to support the BBF.

Your tax-deductible gift of $10, $20, $50, $100, or any amount will have a big impact. With your help, the BBF will have resources to conduct such activities as launching OWW2.0, providing scholarships to young researchers for SB 6.0, hosting workshops on exciting themes, and launching initiatives to unite global BIOFABs and create a road map for the field of SynBio. The time to give is now. Make a secure, online donation to the BBF today.

SynBio has the power to transform our world. Let’s work together to ensure a strong, safe, open SynBio field. Please support the BBF mission.

Thank you so much for your support.

Sincerely,

Holly Million Executive Director, The BioBricks Foundation	Natalie Kuldell Board of Directors, The BioBricks Foundation OpenWetWare “Super User”

P.S. Want to get more involved? The BBF is making plans to better serve the SynBio community. Want to find out when SB6.0 is taking place? Want to give input on our new Education Program? Send us a message.

Dear Friends of the BioBricks Foundation,

Here’s the latest news from the BioBricks Foundation and our fundraising campaign to raise $50K by December 31, 2011. As of today, we have already raised $10K toward our goal. So that leaves just $40K to go! Already made a gift? Thank you so much! Haven’t given yet? There’s still time to do so. Help us make it to the top!

The BioBricks Foundation (BBF) is a public-benefit organization dedicated to advancing synthetic biology (SynBio) to benefit all people and the planet. We work to create a sustainable future by supporting the development and free exchange of standardized biological parts that are safe, ethical, cost effective and publicly accessible. The funds raised in this campaign will support the BBF’s work for SynBio in technology, the law, education, and community building for the coming year.

If you work in the BioTech industry, attended the SB 5.0 Conference, follow the BIOFAB, or are one of 9,000 people who use OpenWetWare, you are part of the BBF community. Please act now by making a personal financial gift to support the BBF.

Your tax-deductible gift of $10, $20, $50, $100, or any amount will have a big impact. With your help, the BBF will have resources to conduct such activities as launching OWW2.0, providing scholarships to young researchers for SB 6.0, hosting workshops on exciting themes, and launching initiatives to unite global BIOFABs and create a road map for the field of SynBio. The time to give is now. Make a secure, online donation to the BBF today.

SynBio has the power to transform our world. Let’s work together to ensure a strong, safe, open SynBio field. Please support the BBF mission.

Thank you so much for your support.

Sincerely,

Holly Million Executive Director, The BioBricks Foundation	Natalie Kuldell Board of Directors, The BioBricks Foundation OpenWetWare “Super User”

P.S. Want to get more involved? The BBF is making plans to better serve the SynBio community. Want to find out when SB6.0 is taking place? Want to give input on our new Education Program? Send us a message.

Dear Friends of the BioBricks Foundation,

The BioBricks Foundation (BBF) is a public-benefit organization dedicated to advancing synthetic biology (SynBio) to benefit all people and the planet. We work to create a sustainable future by standardizing biological parts that are safe, ethical, cost effective and publicly accessible. Your enthusiastic involvement in the SynBio community and the work of the BBF makes a crucial difference.

The BBF is a young organization that has produced results. This year, we successfully created the first-in-the-world BioBrick™ Public Agreement (BPA), a legal tool that enables the free exchange and use of standard biological parts. BIOFAB, our first professional research collaboration, has produced reliable, standardized biological parts that constitute a free operating system for biotechnology. In addition, the BBF also manages OpenWetWare (OWW), an open-source wiki that facilitates teaching, learning, and sharing of data for 9,000 researchers through a culture of collaboration and open science. That’s not all. Just this past June, the BBF successfully organized SB 5.0, an inspiring 3-day global conference in SynBio with the participation of over 70 international speakers and 730 attendees from over 25 countries.

With 2012 approaching, the BBF plans to do even more to support and connect our SynBio community, promoting the effectiveness of OWW, creating new educational programs, and much more. We need your help to make these goals a reality.

To support this exciting work, the BBF has launched a fundraising campaign to raise $50K by December 31, 2011. Thanks to a generous donor, we’ve already raised $8K toward our goal. That leaves just $42K to go!

Your gift of $10, $20, $50, $100, or any amount will have a big impact. With your help, the BBF will have resources to conduct such activities as launching OWW2.0, providing scholarships to young researchers for SB 6.0, hosting workshops on exciting themes, and launching initiatives to unite global BIOFABs and create a road map for the field of SynBio. The time to give is now. Make a secure, online donation to the BBF today.

We live in a world with limited natural resources. Striving to build a sustainable world is no longer a luxury, but a necessity. SynBio may hold the key to our future. The BBF fills a unique need in this field, educating, building community, creating legal tools, and fostering cooperation. Please act now by making a personal financial gift to support the BBF.

We’ll let you know our progress in meeting our campaign goal. Thank you so much for your support.

Sincerely,

Holly Million Executive Director, The BioBricks Foundation

Natalie Kuldell Board of Directors, The BioBricks Foundation OpenWetWare “Super User”

Dear OpenWetWare Community,

In an effort to improve OpenWetWare.org (OWW) to meet your needs better, the BioBricks Foundation is conducting a short survey with five simple questions (< 5min). We hope you will choose to participate! The survey ends on Nov 22.

By participating, you will:

1. Make your life better (by gaining a better OWW experience)
2. Make new friends (by communicating with our staff at the BBF)
3. Be entered to win great PRIZES!

Prizes:

1. Two $25 Amazon gift cards, at random, to two participants who complete these five questions.
2. One $50 Amazon gift card, to a participant who gives the best original suggestion(s) for OWW based on usefulness and feasibility. Please answer question #4 in the survey to be considered for this prize.

For prize winners who live in countries Amazon does not operate, we will provide you an equivalent prize to the Amazon gift card.

Please click on the below button to complete the OWW survey:

We thank you for your time and contribution; we will post (anonymous) information about the survey outcomes on the OWW home page in the coming weeks.

Kind regards,

Thi Thach
Program Manager
BioBricks Foundation
thi@biobricks.org

Dear Synthetic Biology Community,

We are excited to announce The Fifth International Meeting on Synthetic Biology (SB5.0) on June 15 – 17, 2011 at Stanford University. This meeting will be the first time in over two years that an open and self-defined global community will share, consider, debate, and plan efforts to understand life via building, to make biology easier to engineer, and to work together so that the ramifications of such efforts are most likely to benefit all people and the planet.

Palm Drive at Stanford University

For context, SB4.0 was held at the Hong Kong University of Science & Technology in October 2008. Since this time we have seen significant scientific and technical advances, including full genome synthesis, reliable synchronization of multicellular genetic oscillators, and opiate precursor biosynthesis. We have also experienced increased politicization of the field, including the US Presidential Bioethics Commission consideration of synthetic biology, and ongoing popularization of such work through activities such as the iGEM. In addition, given the 7 years since SB1.0 was held at MIT, we find a “second wave” of younger synthetic biology practitioners rising to prominence.

Taken together, June 2011 is the next right time for the world to come together to learn about and help define what is happening in the world of synthetic biology. Please join us.

Please see the links below for schedule, speaker and registration information. Note that there is no registration deadline at this point, however there is a limit on the number of registered attendees we can have at the meeting. To guarantee your spot, we encourage you to register and make travel arrangements as soon as possible.

• Registration: http://sb5.biobricks.org/registration/
• Schedule: http://sb5.biobricks.org/schedule/
• Speakers: http://sb5.biobricks.org/speakers/

We are looking forward to receiving you on the stunning Stanford campus in June.

With Kind Regards,

Thi Van Anh Thach
Conference Manager
SB5.0 | The Fifth International Meeting on Synthetic Biology
Stanford University, June 15-17, 2011
Organized by the BioBricks Foundation
http://sb5.biobricks.org | http://biobricks.org | thi@biobricks.org

MediaWiki is the software that OpenWetWare.org is built on. We customize it by applying out own styling to the page, add out own member management software to it, and either write our own extensions to it or download and install others. In general, we try like hell to not touch the ‘core’ MediaWiki code. It would be like a lab scientist starting with a standard protocol and then making many modifications to it for his or her own purpose. That’s OK until someone makes a set of modifications to the protocol you started with. You now have to figure out how to retrofit your procedures, ingredients, and what-not with the new ones. Sometimes it’s easy. But sometimes it’s just too much and you revert back to the original, throwing out your own potentially useful enhancements.

MediaWiki has a number of built-in features. One of them is the “magic link” feature I mentioned in the last message. For some reason, someone added a feature to MediaWiki that, when a specific keyword was found, it would try to see if the next word was recognizable and do something on that basis. In the case I discussed, it was the “PMID” word followed by a recognizable PubMed number. The rules for such a number are very simple to understand. But they are not always easy to make work reliably. Since any series of numbers will be seen as a PMID, the wiki page will now contain a link to the PubMed database, offering users the chance to see the citation for a paper. If the paper doesn’t exist, the lookup will still take place. As the saying goes, “Garbage in, garbage out”. The change we made was a bit of a “core” change, but we’ve already moved it into an ‘extension’, thus allowing us to move to a new MediaWiki version without losing our ‘core-like’ change.

We removed another built-in document identifier that was built into MediaWiki. This one was ‘RFC’. The term came from the Internet. All aspects of Internet standards are documented in a “Request For Comment”. Biopart RFC standards are based upon similar documents and processes. In this case, we removed the RFC “magic links” to keep OpenWetWare for turning references to Biopart RFC’s into Internet RFC’s.

MediaWiki also supports magic links for ISBN number lookup as well. Again, the very simple syntax of the number itself makes this possible.

One identifier that’s conspicuously absent from this list of global standards is the academic publishing world’s standard, the DOI.The Document Object Indetifier. The standard has a is different from some of the other schemes. For one thing, you need to pay to obtain a license to issue them. Another is that you also, as far as we have ever determined, need to pay for each DOI issued. Unlike the simple, regular nature of the PMID, the DOI label itself is a variable string that isn’t easy to handle. Once you have located a DOI in a document, to resolve the publication it came from, a third-party needs to step in to do the actual lookup.

In the US, the PubMed database is administered by the NIH. Any PMID can be looked up via a single interface. The simplicity of this is what allowed Pubget to step in and cut out the NIH by directing a reader with a valid subscription to the actual text of a PMID-identified reference.

You can do something of the same thing with the a DOI, if the content of a string can be identified clearly as a DOI. At some point OWW may add support for the DOI in this manner. That would mean that Biblio references could contain them as well as any OWW string that either started with “doi:” or followed the word, “DOI” would lead to the article itself. Like Pubget, the resolution of a DOI to a particular publisher and their online repository for articles does require a subscription to the periodical. Another use of the DOI would be OWW issuing a DOI for a page. This bears more explanation. But also more research.

I’ll provide a simple example of a DOI lookup via a resolver if people are curious.

Thanks.

Bill