Team:Paris Liliane Bettencourt/Project/Synbioworld

From 2010.igem.org

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user management in the various apps we have on the site.  SynBioWorld inludes the following features:  
user management in the various apps we have on the site.  SynBioWorld inludes the following features:  
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<br>•''' News''': SynBioWorld will aggregate several Twitter and RSS feeds related to synthetic biology.  
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==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.  
Original content will also be created by the team and members of the community.  
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<br>• '''Librarian''': Libriarian is an algorithm and UI frame that automatically aggregates, displays and  
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==Librarian==Libriarian is an algorithm and UI frame that automatically aggregates, displays and  
allows to search through papers, scientists, and institutions relevant to synthetic biology.  
allows to search through papers, scientists, and institutions relevant to synthetic biology.  
   
   
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<br>• '''Forum''': This feature will finally answer the repeated request of members of the community, in  
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==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  
particular iGEM participants. It will be moderated by volunteers from the community (over 50  
people have already expressed interest in helping out.)  
people have already expressed interest in helping out.)  
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<br>• Events: All events relevant to the synthetic biology community will be announced on the site.  
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==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,  
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  
which has been described as the “imdb of the conference circuit” to provide a huge annotated  
database of synthetic biology talks.  
database of synthetic biology talks.  
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<br>- and - as contribution of this year's from our team...:
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<br>- and - as contribution of this year's from our team...
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<br>• '''openProtocol''': openProtocol is a standardized but highly flexible tool for generating and sharing
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==openProtocol==
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protocols.  Creation of a protocol is as simple as filling out a form, and uploading any relevant
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<p style="display:block;">
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media (video, pictures, or even an animation.)  All protocols share the same layout, but the
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specifics of each protocol can be tweaked such that any protocol can easily be adapted into our
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system.  Further, in keeping with several studies on the usefulness of annotated protocols (show
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that EUREKA study, as well as the other oss study here) openProtocol makes use of a wonderful
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set of open-source commenting tools provided by the Public Library of Science (PLoS) to provide
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in-text notes on any protocol.  There are two rather different useage cases for this tool, which we
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outline below.
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<br><br>First, those new to synthetic biology often require a single, simple, well-agreed upon protocol for a
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procedure.  The protocol has to be easily available, and must bear the marks of a mature protocol,
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that is: it must be commented upon, must be well designed, must take into account all the
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possible pitfalls and difficulties an experimenter may encounter when carrying out the experiment.  
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<br>Second, the experienced researcher often would like to have a protocol that is personalised to their  
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<br><br>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. <html><div style="float:left"><a href="https://static.igem.org/mediawiki/2010/b/bb/Op3.png" rel="zoombox"><img src="https://static.igem.org/mediawiki/2010/5/52/Op3thumb.png
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lab situation, but that can nonetheless be shared with colleagues and used as a record for a lab  
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" style="border: 2px black;"></a></div></html> 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.
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journal.  openProtocols are perfect for this usage, as they are saved centrally, and use a versioning
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system that allows for unlimited modification and reversion on a single protocol.  
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Finally, we hope that by providing a pleasant and useful interface for making protocols public, more
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<br><br>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.
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authors will begin to include links to an openProtocol in their “methods” sections, greatly increasing
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the immediate reproducibility of published experiments.  
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Every openProtocol has its own URL, and can therefore be shared with a link. <html><div style="float:right"><a href="https://static.igem.org/mediawiki/2010/f/f9/Op2.png" rel="zoombox"><img src="https://static.igem.org/mediawiki/2010/d/de/Op2thumb.png"></a></div></html>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.
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<br>''read more about our design and specs of the openProtocol here''
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==Usage Ideas==
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<br><br>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!
 +
 
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*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.")
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==FAQ==
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*OK, so where can I get started?
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*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!
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<br>
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*Is openProtocol open source?
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*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.
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<br>
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*Can I contribute to the openProtocol project?
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*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.
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<br>
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*If you have any other questions, let us know at openprotocol @ that google mail product dot com.
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<br><br>
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==Collaboration ==
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<html>
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<p style="display:block;">
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<br><br>In the course of developing our new tech standard "openProtocol" we have received invaluable assistance from both the <b>UCSF team</b> and the <b>Peking University team</b>.  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!
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 +
<html>
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</div>
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</div>
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</html>

Revision as of 16:28, 27 October 2010

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:

==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==Libriarian 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.


- and - as contribution of this year's from our team...

Contents

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


  • 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!

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