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Note: This is the version of FAQ Answers: Experimental Data Entry and Presentation with full-size screen shots. To get the version with reduced-size images, go here.
Although the raw perturbation data tables in BioTapestry are tagged as being "QPCR" data because of the original application to sea urchin studies, the framework is actually relatively generic, and should be able to store and present a variety of types of perturbation data. Please contact us if you think that some modifications to the framework would make it match your needs.
No. While you can enter and edit raw perturbation ("QPCR"), temporal/spatial expression, and temporal input data using dialogs (available off the Data option on the main menu), the picture below highlights that there are several data file import options you can use instead. If you have raw perturbation ("QPCR") data, you can import it using either an XML data format or using two different comma-separated value (CSV) formats. The temporal/spatial expression and temporal input data can be imported using XML data files. To learn about this, work through the Dynamic Submodels Tutorial. The two sample data files that come with the tutorial, the Time Course Data File and the Temporal Input Data File, provide good examples of these input files that you can use to build your own.
The experimental data display that appears when you right-click on a gene and select Experimental Data is configured using a "plug-in" architecture that can be customized by the user. Without modification, BioTapestry will use its built-in plugins to display:
Raw perturbation ("QPCR") data
Temporal/spatial expression data
Temporal input data
Plain text (actually very simple HTML: it supports italic, bold,
paragraph, and line break tags). To enter this text, right-click on a gene, choose Properties..., and select
the Text Annotations tab.
These different types of built-in displays are shown below:
If you want to add additional custom data displays to the experimental data window, there are example plug-ins in the source code tree, which is available here. It would be relatively easy to add data available on a web server to this data window; one of the example plug-ins shows how this is done. Below is an example of this example plug-in. The left window is a web browser, the right window shows how this web content is incorporated into the BioTapestry experimental data window.
Starting with version 2, users are no longer restricted to using hours for the time units. Units from seconds to years are available. Also, the user can specify numbered or customed named stages as the time units. Before you enter any time-dependent data, you are required to set these units. You can do this by selecting Data->Set Time Units... from the main menu:
There are a few different methods for tagging genes and individual links with graphical symbols that can be used to indicate confidence levels and/or experimental evidence, as the following picture shows:
As shown above by the links that are inbound to the gene Target 1, individual links can be assigned three different "evidence level" tags. The three available "levels" have no predefined semantics; the user can use these designations to mean anything they wish. To assign a level to a link, right-click on the link tree, select Properties... from the pop-up menu, and go to the Cis-Reg. Evidence column of the table on the Model Properties tab. Then you can set the evidence from None up to Level 3 for each different link in the tree. When you are done, click OK:
Note that the display of the different link evidence levels can actually take two forms: target diamonds and thick links. Which of these methods is used to show link evidence can be configured as a display option. From the main menu, select Edit->Set Display Options.... In the dialog, as shown below, set the Link Evidence Display to the desired setting. In this case, the setting Show diamonds and thick links uses both methods, as shown in the network pictured above. You can also choose either method, or hide the evidence display completely.
Genes, such as Target 2 in the above network, can also be tagged with an evidence glyph, which again can be used to mean anything the user wishes (though BioTapestry uses the term Isolated when the glyph is selected). To set the evidence level for a gene, right-click on the gene, and set the Evidence level on the Model Properties tab: .
Finally, if you have defined cis-regulatory regions for a gene, you can tag each region with an evidence tag. Region b of the Target 3 gene in the above network has been tagged in this fashion. To set the evidence level for a region, right-click on the gene, and set the Evidence level for each row in the Subregions table on the Model Properties tab:
