SynBioWorld

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Synbioworld is a collaborative web platform created to give the synthetic biology community a place to talk, share data and resources, and stay abreast of new developments in the field. The site is based on a CMS system that allows for all the normal features of a blog, but also allows for seamless user management in the various apps we have on the site. SynBioWorld inludes the following features:

Contents 1 News 2 Librarian 3 Forum 4 Events 5 openProtocol 6 Usage Ideas 7 FAQ 8 Collaboration

News

SynBioWorld will aggregate several Twitter and RSS feeds related to synthetic biology. Original content will also be created by the team and members of the community.

Librarian

Librarian is an algorithm and UI frame that automatically aggregates, displays and allows to search through papers, scientists, and institutions relevant to synthetic biology.

Forum

This feature will finally answer the repeated request of members of the community, in particular iGEM participants. It will be moderated by volunteers from the community (over 50 people have already expressed interest in helping out.)

Events

All events relevant to the synthetic biology community will be announced on the site. Furthermore, we are working on a partnership with the new talk aggregation site SittingO, which has been described as the “imdb of the conference circuit” to provide a huge annotated database of synthetic biology talks.

openProtocol

Experimental Protocols are an important tool of synthetic biologists both when doing and publishing experiments. The ideal protocol must be flexible: both detailed enough for a beginner to complete the experiment successfully, but concise enough for an expert to be able to comfortably make use of it to guide their experiment.

In addition, an ideal protocol is easily sharable with those who wish to replicate your experiment or carry out similar experiments of their own. At present, there is no tool that allows for the creation of such a protocol, so this summer at the CRI we decided to build one of our own called openProtocol and share it with the synthetic biology community.

openProtocol is a website that allows people to create protocols using a simple web form, and have them come out automatically formatted and laid out in a beautiful and easy to use way. Every openProtocol has its own URL, and can therefore be shared with a link. Each protocol on the site can be commented on by users and other researchers, allowing you to receive feedback on the way you carry out a certain experiment, as well as solve problems with tricky protocols. Further, each protocol can be "forked," that is, you can make a copy of any protocol you like to customize for your own lab's situation. Adding pictures and audio to your protocols is easy, and even videos can be embedded as part of your procedure. You also have the choice of associating a "cheat sheet" type list with each protocol, so that you can have something to take with you to the bench in lieu of the full protocol.

Usage Ideas

We envision several groups of people using openProtocol in quite a few different ways. Here are some examples to get you started thinking about ways you can use openProtocol in your own research!

• Teachers teaching an experimental class can use openProtocols and allow their students to individually annotate and edit the protocols for future classes. In this way, extremely clear and usable protocols can be developed for classroom use.

• Researchers publishing a paper that involves several new methods can include a link to an openProtocol as a supplement to their Materials and Methods section. Having easy access to a complete protocol online greatly increases the speed at which new and interesting methods can catch on and become popular.

• Lab managers can place all of a labs protocols on openProtocol to make standardization within a lab easier. Individual lab personnel can customize protocols to their liking, and can directly embed them in online lab-notebooks or use the beautifully formatted printed versions in a traditional lab notebook.

• iGEMers can use openProtocol to clearly lay out new and interesting ways to manipulate biobricks, as well as to standardize protocols for the most commonly done procedures like enzyme digestions and minipreps. Many common mistakes can in this way be eliminated ("with enough eyes, all bugs are shallow.")

FAQ

• OK, so where can I get started?
• You can sign up http://synbioworld.org/openprotocol here . Additionally, there will be a demo of openProtocol at the iGEM jamboree during our workshop on Saturday!

• Is openProtocol open source?
• Yes, openProtocol is open source, and all protocols included on the site are by default licensed under a Creative Commons license. However, if some labs desire to have a protocol be kept private or copyrighted, that does not preclude its inclusion for viewing by others on openProtocol.

• Can I contribute to the openProtocol project?
• Absolutely! We are particularly interested in recruiting new members to our team that have expertise in versioning control systems, the jQuery javascript framework, and scaling database solutions. Others are also welcome: get in touch with our project lead Eric at eric.meltzer at google's popular webmail client dot com.

• If you have any other questions, let us know at openprotocol @ that google mail product dot com.

Collaboration

Our vision for openProtocol actually started when we saw a comic-book protocol produced by Gingko Bioworks last year at Foo Camp. We realized that comic-book style protocols could be very information dense and at the same time be easy to use for beginners. Inspired, we began to draw sketches for a series of comic-style protocols, and hacked together some javascript to make creating and editing them easier.

Once we had a sort of storyboard going for how these books would look, we sent it to our partners at UCSF and asked for their help in taking pictures and producing a test run: a mini-prep comic book. As it turned out, the original form of a comic book isn't actually that great for biological protocols. There are many steps for which a picture is totally useless, which left us and our UCSF buddies scratching our heads (its very hard to take a picture of a pipette adding 1uL of liquid to a tube...)

Still, we felt that there are some steps for which pictures (and even video) are incredibly helpful. Back to the drawing board! The next iteration of our design was essentially a comic-book type layout but with some text overlays... it was a mess. UCSF patiently continued to provide us with the raw pictures and video of their molecular experiments that we needed during this most trying of times.

Finally, we realized that what was most compelling about the idea of a multimedia protocol was not necessarily the comic book layout, but merely the ability to put pictures, video, and audio in whenever you needed them. We also realized that being able to share these protocols was going to be incredibly important. Since we had benefited so much from UCSF's real life feedback on the earlier versions, we had a meeting with a group of students in Paris who are dedicated to providing low-cost protocols for science in developing countries, and got some of their feedback on what they would want in a protocol.

One of the most obvious requests that came out of this meeting was that the protocols be available in multiple languages. Since one of the students working on this protocol idea is going to school at Peking University, we called them up and had another little meeting on internationalization of our protocols. PKU kindly provided us with Chinese versions of many of their own experimental protocols, which have been useful to us in testing our multi-language support!