Technical Standard

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. openProtocols can be shared with a link, and furthermore can be annotated, edited, forked, and commented on. They can include pictures and audio, and even video when necessary. Further, openProtocols support the linking of a full protocol and a "cheat sheet" that can be printed out and used at the bench in lieu of the cumbersome 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.")

<p style="display:block;"> OK, so where can I get started? You can sign up at synbioworld.org/openprotocol . 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

In the course of developing our new tech standard "openProtocol" we have received invaluable assistance from both the UCSF team and the Peking University team. UCSF assisted us with the early design for the system, and tirelessly gave us protocols to test the system with. They put up with endless changes and iterations to the design, and without them the current version of openProtocol would be unusable. In return, we have assisted them in turning all of their protocols into openProtocols, facilitating their easy dissemination and standardization. Peking University's team also contributed a large set of protocols, and has provided us with a great deal of useful advice on the internationalization of our openProtocol tool. Thanks guys!