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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

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.

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

To paraphrase Sigmund Freud,

“Sometimes a reference is just a reference…”

But not all the time. By the time we’re reading an OpenWetWare (OWW) page and notice a reference to a published paper, we’ve come to the page through a search engine. At this point, a reference is no longer a starting point for a new search. It’s now contextually enlivened information.

We want to read it now. Our interest has already been qualified. Searching is behind us. Is this the time to go to another site to read about the article and to find more? For me, at this point, I want to decide how relevant an article is by reading it. “Let me decide!”.

PubMed’s website is where OWW references typically end up. The PubMed ID (PMID) is a common identifier for research articles for most biological research output. The US NIH acts as a proxy for redirecting us to the actual article. If we have rights to read it via online subscription, we eventually get to see it.

As we’ve experienced far too often, getting to the article through PubMed isn’t direct. The process looks something like this:

  1. You see a citation.
  2. You want to read it.
  3. You click the link.
  4. You read the reference.
  5. You click the link.
  6. You go to the publisher’s site.
  7. You click the link.
  8. If your institution has a subscription, you read the article.

Enter Pubget.

Pubget is a service that cuts through this process. It allows you to click on a link and read the article.

Using it, the process gets collapsed to this:

  1. You see a citation.
  2. You want to read it.
  3. You click the link.
  4. If your institution has a subscription, you read the article.

Note the steps. Once click is now required. The rest is all about thinking, wanting, and reading. So. What if some of the power of this service were to be brought to bear within OpenWetWare?

Based upon a request last week, we looked into how Pubget works. With no official affiliation with Pubget, I’ve added a number of features to OWW that now make this possible in an almost invisible manner.

What do you have to do to take advantage of Pubget

If you’re a member of OWW, you can start by going to your preferences page to set your institution. Just log in, click on the “My Preferences” link at the top of the page, and go to the ‘Misc’ tab. It’s the last tab on the right. Look for the list of participating universities here:

Select the name of the institution where your lab is located. Like Pubget itself, this feature will only work when you’re physically working on that network. Once you set this, you need never change it until you graduate! If you’re at home and not at work, pubmed will use the default setting: any subscriptions by your university will be unavailable util you get back to the lab. This isn’t part of OWW’s Orwellian plot to keep you at your bench for as much of your life as possible. It’s a technical issue. At MIT, we use browser certificates that extend this so that I still get access to the same content at home. I’m sure this isn’t universal. But try it and see how it works. We’re evaluating how we can extend this capability over time for other universities. If your university uses VPN connections, you are virtually on your lab’s network: all subscriptions will continue to work.

Even if your university isn’t on the list, this feature will allow you access to the full text of all open source journals such as those published via PLoS.

The effect is that a growing number of OWW lookup features will use this label to pre-set the URL’s you use to ‘cut to the chase’ and make content available when you click and not a few seconds later. If you want to review several articles, those few seconds do add up quickly. In addition to this, Pubget provides a search interface that ‘knows’ the format of many of the most important journals.

What parts of OWW can use Pubget?

General OWW text.

Try this. Edit an OWW article you’ve created containing a pubmed reference. Reformat the reference to use this format:

PMID 12345

Save the document. The text is now a clickable reference. If you’ve set your preference, the article will be opened for you to read if it’s available as a PDF file as well as associated reference information. You can use the PubMed search to find related content as well. Any existing pages using the ‘PMID’ tag will beave the same way.

Biblio References

If you use the Bibio extension for publishing citations, a Pubget link is now present if there’s already a pubmed reference for it. Just click on the link to to read the text.

Pubget Gadgets

A Pubget gadget is a code snippet you can create at the pubget site to provide a search using their service. To create one, go to the pubget site and create it using this url:

http://pubget.com/widgetizer/create

To paste it onto your page, do the following:

  1. Create the widget on the Pubget page.
  2. Copy the widget to your clipboard after you create it.
  3. Paste the html code onto an OWW page.
  4. Place an  “<html>” tag right before the code you pasted.
  5. Place an “</html>” tag right after the code you pasted.
  6. Save the page.
  7. Instant widget!

RSS Feeds

A side effect of the way pubget works is that RSS feeds, already supported within OWW, can use the same feature. To create and RSS feed that uses Pubmed, do the following.

  1. Open one of your OWW pages for editing.
  2. Create an RSS feed using the with a search term inside of it like this:<xfeeds>OpenWetWare</xfeeds> (replace OpenWetWare with your text)
  3. Add the ‘bubget’ attribute (pubget=”Y”) inside of the “<xfeeds> tag. The sequence will now look like this:   <xfeeds pubget=”Y”>OpenWetWare</xfeeds>
  4. Save the OWW page

This will now tell the xfeeds extension in OWW to map all of the URL’s in the returned RSS feed to use your specified university tag. The references will now direcly load when you click on them.

There’s a shortcut to do this if you have a page name you want to use as the search term. As an example, consider your user page.

  1. Edit your user page.
  2. Find a place you want to insert the search feed.
  3. Insert the following tag: “{{PubgetRSS}}” (no quotes but with the curly braces)
  4. Save the page. Done!

If anyone sees other places this capability would fit, please let me know.

Also, if anyone has a problem using this feature, let me know. I’m not trying to push one company versus another. But the service to OWW this offers seems worth the effort.

Thanks!

Bill

One recent SciFoo related post that caught my eye was Mario Pineda-Krch’s thoughts on the idea of distributed open notebook science. Yes, distributed.

As Mario mentions, by using a client based wiki setup like Tiddlywiki, the user has more flexibility by not having to rely on network access. Furthermore, a version control system like Git brings redundancy allowing anyone to download the latest version of the notebook. The wiki + the data with full control.

The idea of open notebook science is not necessarily a new one. The term was coined by JC Bradley roughly two years ago. However, it’s been tough to go mainstream due to the fact that notebooks are usually foreseen to be private, thus failing in the “open” department. However, this hasn’t stopped many from setting up lab notebooks online like Jean-Claude Bradley, Garrett Lisi or any of the dozens of OpenWetWare lab notebook users.

It’s almost officially Summer here in the northern hemisphere but there is still time to do some spring cleaning.

As you can see, we’ve changed the name of our main blog from Steering Committee to Community, to reflect what we thing it should be about – Not only the steering committee’s views and operations but what the OWW community at a whole has to show the world.

The name change is just the first step among many new features we’ll be bringing to the OWW Community blog over the next weeks. To keep up-to-date, we suggest that you visit us regularly or subscribe to our feed.

Note: Although we’ve changed the title and subsequently the blog’s address, our RSS subscribers should not see much of a glitch. If you do happen to find anything broken, please let us know.

With the ability to get information anywhere in the world in seconds, and the virtually immediate obsolescence of any printed work, why are journals such an important part of academic research?

This question, under the heading “Are Academic Journals Obsolete?” was posted yesterday on Ask Slashdot. As you might expect, the comments are wide ranging and interesting.

When page layout software was first introduced and do-it-yourself desktop publishing became popular, many people wondered if publishers would become obsolete. Now, twenty years later, we have blogs, newsfeeds, and even better DIY publishing tools like blurb.com. Anyone can publish anything and reach a wider audience than ever before. And publishers still exist.

The arguments about whether academic journals are obsolete is a long and complex one, and you’ll see a wide range of opinions on this and other questions like it. Perhaps the print journal is a vanishing breed, for many of the reasons stated in the Slashdot posting. But much of the value, such as peer review, that academic publishers bring to their work is still very valid. Either way, until the systems for academic tenure and funding change, the academic journal in print or web-based form is unlikely to vanish.

Having a presence on OWW can help a lab gain exposure in some unexpected ways. Last week the French, Keymer, and McKinney labs, all of whom maintain wikis on OWW, were mentioned in Virtual networking for microbiologists, a Nature review about Web 2.0 applications and science. Check out the full review at http://www.nature.com/nrmicro/journal/v6/n6/full/nrmicro1922.html.

OpenWetWare is a strong supporter of iGEM (iGem.org) the International Genetically Engineered Machine Competition, which is now shifting into high gear for 2008. iGEM and OpenWetWare share some important core values including openness, community, and sharing of information. Check out the 2008 iGEM team wikis on OWW and on the iGEM site. If you’re on an iGEM team that hasn’t yet started a team notebook, check out OWW’s new One-Click Lab Notebook. It has lots of great new features.

Registration for iGEM 2008 closes on Friday, May 9, at 6pm U.S. EDT, so if you haven’t already done so, be sure to complete your registration in time!

oww-lab-notebook-perspectiveA part of our mission at OpenWetWare is to lower the technical barriers to sharing and dissemination of knowledge in biological research. In carrying out this mission we implement new tools and technologies that make it easier to introduce, organize and present biological research data. One such tool is the new OWW open lab notebook.

By harnessing the powerful features that mediawiki provides and creating some custom features, we’ve made it possible to setup an electronic lab notebook on OpenWetWare with little more than a few keystrokes and a click of the mouse!

The new OWW lab notebook was built with three key groups in mind: individual users, iGEM teams and labs.

The lab notebook now includes these new features:

  • A dynamic calendar that allows you to create or view project entry dates with a simple click.
  • Local search that allows you to easily find content located only within your project.
  • Improved navigation that allows you easily jump back and forth between entries.
  • Customizable template pages specifically for your project. These pages automatically pull in any logo, project title or graphics every time you make a new entry)

These are just a few of the new features we’re working on. There will be more in the coming months.

If you are an OWW member, what are you waiting for? Go to our new one-click setup tool to create your personal lab notebook. If you are not an OWW member, request an account today and let us know what you think!

To keep up with the latest lab notebook developments, visit our OWW Lab notebook page.

Today, April 17, from 12noon to 1pm, the OWW steering committee will be online at http://openwetware.org/chat/ to chat with the community about the latest goings on at OWW. Anyone is welcome, so please join us.

To join, click the above link and log in using your OWW user name and password. When the chat window opens, click on “conferences” at the bottom of the page. At the next window, double-click on “Lounge” to enter the chat session.

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