Jeff Johnson, Herbert Sauro, Deepak Chandran, John Gennari, Michal Galdzicki

Source code  Browse on SourceForge
Examples WikiDustWiki

Update 12/5/2011: Added OpenWetWare support.

WikiDust does two main things: First, it uses the Standard Biological Parts knowledgebase (SBPkb) to download information about publicly available DNA components (parts) into TinkerCell. This makes it fast and easy to diagram genetic regulatory networks that include common promoters, coding sequences, etc. Second, WikiDust creates and publishes imagemaps based on TinkerCell diagrams. Parts for which a URL is available in TinkerCell are clickable in the final image. This streamlines research because detailed, up-to-date information about each part in the network is just a click away.
    On Windows:
  1. Download and run the stable TinkerCell installer .
  2. When prompted, choose to install Python and Subversion if you don't have them already. Note: Testing focuses on Python 2.5 as distributed with TinkerCell, but 2.6 and 2.7 also seem to work.
    On Ubuntu:
  1. sudo apt-get install libqt4-core libqt4-gui libqt4-opengl libqt4-xml libxml2 python python-tk subversion
  2. Then, follow TinkerCell installation for Ubuntu starting from step 2.
Annotating DNA Parts
Network diagrams are created in TinkerCell by dragging DNA components (parts), small molecules, and other items onto the canvas. Each item can hold information about its author, date created, etc. WikiDust fills in that information by querying the Standard Biological Parts knowledgebase. Adding information to a part is easy: right-click on a part and choose Annotate using parts database (SBPkb). Alternatively, you can click on the part to highlight it, then click the purple WikiDust icon () that pops up. A search window will appear showing some likely parts. You can use the "Open in Browser" button to get more information about a part. If the right one isn't found at first, you can also refine the search by typing a keyword or Biobrick name. Then, double-click on a result or click Use selected to copy that part's annotation into TinkerCell. To view the added information, click the icon. You can also speed things up by highlighting multiple parts. WikiDust will annotate them one after another, circling the current part in purple.

Generating an Imagemap
To create an imagemap of the current diagram in TinkerCell, choose Run→Export Imagemap. This brings up a set of controls. The map name is used to name the generated image file. If the imagemap is uploaded to a MediaWiki site, it will also be used as the name of the file page created. This name should be unique to avoid conflicts; WikiDust will warn you if uploading it would replace an existing image on the wiki. You can also adjust the size of the imagemap and preview the result; around 500-700 pixels wide looks good on most webpages. WikiDust also needs to know what you want done with your imagemap. You can upload it directly to a MediaWiki site, or copy and paste the code into any website yourself. The iGEM wiki and Parts Registry are peculiar in that the expect HTML imagemaps. Otherwise, the rule of thumb is to use Wiki Markup on MediaWiki sites, and HTML for pasting into anything else. When you have everything set up, click Generate.

Automatically Sharing an Imagemap
If you chose to upload your imagemap directly, you will be asked for a destination page, as well as a username and password for the wiki. You can leave these blank if the wiki doesn't require registration to upload images or edit pages. Click Upload imagemap to create a new file page for your image and insert code referencing it at the top of the destination page. Afterward, you can open the page and move the imagemap by editing the Wiki Markup source if you like.

WikiDustWiki is a good place to try uploading and customizing your imagemaps.

Manually Sharing an Imagemap
If you chose to display the imagemap instead, you can now copy and paste the code into your website. You will also need to upload the image yourself. For Wiki Markup imagemaps, go to Upload file on the wiki and follow the instructions. If you chose a different page name than your map name, edit the imagemap code to reflect the changes. For HTML imagemaps, you need to supply the URL of the image. It can be hosted on the website, on your own server, or by a free hosting service like ImageShack. Adding the imagemap manually is less convenient, but it gives you more control and should work with any website.
Future Plans
This same method for retrieving part information could be extended to gather reaction kinetics and other data from sources like the CellML Model Repository or the Biomodels Database. It could also be integrated more directly into TinkerCell to allow for browsing available parts. For now, it demonstrates the feasability of using the Standard Biological Parts Knowledgebase (SBPkb) to retrieve part information using Semantic Web standards.