2010 Recent Images

The package updates the programs and databases and adds a new Digital Library called Organism Codes. The new library provides considerably more information about phenotypes.

The package begins with six buttons.

For a discussion of these new software tools within the framework of the project, you might begin by reading the Report for 2010.

The report includes summaries of the project and shows you how to use your data to generate new forms of information.

For example, you can interpreting data graphically by assembling them into a collection of related triplets called a organism code.

The data entry screens of a new digital library translate data pairs (doublets) into triplets and then triplets into organism codes. Such codes can be displayed graphically or expressed as equations.

When a phenotype changes, changes will occur in concentrations, amounts, proportions, and connections. If you currently collect just concentrations, you now have the option of increasing the information content of your data from a factor of one to four. Therefore, the codes increase our chances of finding a change.

Using compound sorting algorithms, which can be run by clicking on buttons, the rows of the data pair table can be rearranged to find triplets. Once found, they can be marked with a green check box. Each search is performed two times, first on the X name and then on the Y name.

This screen assembles the doublets (data pairs) - shown in the central window - into triplets, by collecting all possible permutations. The assembly process operates first on the X names and then on the Y names.

Top Screen: For each paper, a given set of triplets defining an organism code is displayed as a graph consisting of nodes and connections. Use this screen to enter the organism code data.

Bottom Screen: Use this screen to enter node data - one at a time,

Top Screen: Organism Codes.

Bottom Screen: Here, the nodes are entered as variables into the template of the organism code equation.

These screens display the results of data entry.

This table displays the triplets as three columns of names (parts/nodes) with their corresponding proportions. The large collection of stacked buttons either run sorting algorithms or programs. The sorting buttons speed the task of finding patterns in the data.

What happens if you have a lot of concentration data, but only an occasional amount? Since we know that in vivo concentrations have a reliability of only about 50% in an experimental setting, how can we detect biological changes confidently? Rework the data. Convert concentrations into triplets to get an organism code equation and then use an absolute amount as a seed value to transform the remaining proportions into absolute amounts.

The query by example (QBE) interface simplifies the task of retrieving data by writing filtering and sorting algorithms automatically - as you make selections.

On the right hand panel, type in a word or number (or part thereof) between the percents %...%, and click on Retrieve. Click on the View Data button to inspect the results.

Notice at the bottom of the screen, that a link to the methods table of the original Stereology Literature Database allows us to ask questions about the relationship of the codes to the data collection methods.

Click on the Retrieve button to select all the entries. Next, click on the buttons in the following order: view data, examples, and 1184. Continue to click on the down button (or scroll down) until the next image appears. This will show you how the organelles of liver hepatocytes change as they develop, grow, and age.

Continued...

Use this screen to look for patterns in the nodes and connections of the organism codes. First, click on the Retrieve button and then on the one marked view data.

Use the sort and filter buttons to explore the data set.

ENTERPRISE BIOLOGY SOFTWARE PACKAGE FOR 2010

The package updates the programs and databases and adds a new Digital Library called Organism Codes. The new library provides considerably more information about phenotypes.