
Jeff Johnson, Herbert Sauro, Deepak Chandran, John Gennari, Michal Galdzicki
|
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.
|
Installation
On Windows: -
Download and run the
stable TinkerCell installer
.
-
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: -
sudo apt-get install
libqt4-core libqt4-gui libqt4-opengl libqt4-xml libxml2 python python-tk subversion
- 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.
|
|
|