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ThermoVis

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ThermoVis is an Omix plug-in for the analysis and three dimensional visualization of network thermodynamics.

Background

Like any other process in nature biochemical reaction steps are governed by ener-getic principles. Roughly spoken, a reaction can only proceed in its nominal direc-tion if the sum of the energetic reaction potentials of the reaction sources is larger than the sum of these of the reaction products. Otherwise, the reaction proceeds in the opposite direction. Here it should be noticed that thermodynamics does only make a statement on possible reaction directions but not on their quantitative magnitude. Even if a reaction step has a large energy gradient there might be some regulatory interaction controlling the amount of flux through this reaction step.

The free Gibbs energy potential of a chemical substance with concentration (or, more precisely, activity) x is given by

ΔG = ΔG0 + RT ln(x)

Here the term ΔG0 is free Gibbs energy potential under standard conditions which are essentially defined by 1 mol concentration of the respective substance. R is the gas constant and T is temperature. If a chemical reaction step has sources A, B,… and targets U, V,… then it must consequently hold

ΔGA + ΔGB + ... > ΔGU + ΔGV + ...

for the reaction to proceed in forward direction. The set of thermodynamic constraints obtained in this way by collecting the respective inequalities for every reaction step imposes a multidimensional relation between possible substance concentrations, free Gibbs energies under standard conditions and flux directions.

Further reading:

1.2. Using ThermoVis

Working with ThermoVis requires a well prepared network model of biochemical reactions in Omix, ΔG0 values for all metabolites of the model as well as measured or assumed concentration data.

Start ThermoVis by selecting the corresponding entry in the Extras menu:

ThermoVis entry in the 'Extras' menu
ThermoVis entry in the 'Extras' menu


Now, ThermoVis opens as an additional window and loads the network diagram given in Omix as 3D scene.

1.2.1. Loading ΔG0 Values

As a first step, you must now enter the ΔG0 values. Therefore, the following dialog window appears that lists all metabolites available in the model:

Setting thermodynamic properties of the network
Setting thermodynamic properties of the network


There are three ways to specify the metabolites' ΔG0 values:
  1. You can enter ΔG0 values for each individual metabolite by editing the table cells on the right side. Be aware of the unit which is used for the values which is by default J/mol. If you want to enter values in another unit select the target unit in the upper combobox.
  2. By selecting the button "Set Default Values" you can enter one fixed value for all metabolites.
    The following image shows the dialog where you can define the default value. Optionally, you can add a random deviation within specific range that is applied on each metabolite individually.

    Setting default values
    Setting default values

  3. By selecting "Load From File" you can import a spreadsheet file containing the ΔG0 values. By default, ThermoVis supports data in the CSV file format. If the Excel or ODF plug-in is installed in Omix, ThermoVis also supports Excel and ODF spreadsheet files, respectively.
    After selecting a data file whether in CSV, Excel or ODF you must tell ThermoVis how the data file is organized and where to find the required information. This can be done as described in sub section About Loading Data.
It is also possible to left a metabolite's ΔG0 value empty. In this case, the metabolite and its involved reactions is not taken into account which is colored grey.
After specifying the ΔG0 values, click OK to visualize the energy potentials in the 3D scene as depicted in the next image.

Screenshot of the ThermoVis main window
Screenshot of the ThermoVis main window

1.2.2. Loading Concentration Data

The next step is to load concentration data. Here, it is possible to load multiple datasets for comparative analyses.

Bottom of the main window you see the "Concentration Data" sidebar. The sidebar provides a number of buttons on the right side to manage the data. Similar to the ΔG0 values, you can edit the concentration values manually, create a (noisy) default value or load data from CSV, Excel or ODF file. The latter is described in the sub section About Loading Data. If a metabolite's concentration value is empty, zerro or NaN (not a number), the metabolite and involved reactions are not considered in the thermodynamic analysis and thus displayed in grey.

Be sure that the imported or edited concentration values have the correct unit. The currentls used concentration unit can be changed in the combobox on the concentration sidebar. If your concentration data has not been measured under standard temperature, you must change the reference temperature.
Therefore, press the "Properties" button in the concentration sidebar and change the temperature value in the following dialog window.

Properties of the thermodynamics visualization
Properties of the thermodynamics visualization


The first column of the data table provides a checkbox in each data row. By checking this box the concentration data in the selected row is used to display the ΔG energy potentials under real condition. If no box is checked, the standard condition is visualized (ΔG0).

1.2.3. The Visualization

1.2.3.1. Concept

ThermoVis visualizes the metabolites' ΔG values by adapting the depth of the metabolites' shapes on a two dimensional network layout. This leads to a skyscraper like fashion. The higher the "building" is, the higher is the metabolite's energy. A negative energy potential value lead to a metabolite whose upper edge is lying on the zerro level and whose lower edge represents the negative value.

As described in the introduction, the sum of the educts ΔGs must be higher than the sum of the products ΔGs. If this is the case for a reaction, the reactions shape and edges are colored green. If the assumed reaction direction is not feasible, the reaction is colored red. By this, an immediate overview about the feasibility of reaction directions is given for the entire network. Whereas the metabolites are displayed with the standard symbol like in the Omix diagram the reactions are shown as spheres in general.
The gradient between the sum of the educts ΔGs and the sum of the products ΔGs is displayed by the reactions sphere radius. Furthermore, the vertical sphere position corresponds to the average of the ΔG values of all educts and products of the reaction.

a) Thermodynamics4.png b) Thermodynamics5.png

network thermodynamic under standard (a) and real conditions (b)

1.2.3.2. Mouse & Key Navigation

It is possible to move, rotate and scale the scene and camera, respectively, by mouse and key navigation.
  • Moving the mouse with pressed left mouse button rotates the camera around the scene center point.
  • Moving the mouse with pressed right mouse button moves the camera relative to the scene center (up, down, left, right).
  • Using the mouse wheel moves the camera towards or away from the scene center point.
  • Arrow keys ↑ and ↓ move the network fore- and backwards.
  • Arrow keys ← and → rotate the network scene around its yaw axis.
  • Page up and down keys rotate the network scene around its pitch axis.
  • + and - keys can be used to zoom in and out.
The ThermoVis toolbar contains a "Home" button. By pressing this button, the scene and camera positions are reset to their respective home position.


1.2.3.3. Item Selection

On the left side of the ThermoVis main window there is the component view providing a list of entries for all network items visible in the scene. By selecting ont of the items, the corresponding element in the scene is highlighted and centered. You can, for instance, select a reaction and place the camera directly over the reaction item and its educts and products. Or you can select a pathway, to only show the reactions that belong to it.
By clicking on the list entry "Reaction Network" the entire scene is visualized again and the home position is brought back to the scene center.

1.2.3.4. Visualization Properties

The three dimensional visualization can be displayed in perspective or parallel projection which is offered on the toolbar.

By pressing on the "Eye" button, the visualization of termodynamic potentials can be enabled or disabled.

Furthermore, the way, data is mapped to the depth of the metabolite shapes can be adapted.
Therefore, press the "Properties" button in the "Concentration Data" sidebar. A dialog window appears that allows you to set an offset for the energy potential values.

By default, no offset is used:

Offset: no offset
Offset: no offset


You can set the minimum of all ΔG as offset:

Offset: minimum
Offset: minimum


Use the ΔG value of a specific metabolite as offset:

Offset: specific metabolite
Offset: specific metabolite


You can also type a fixed value:

Offset: fixed value
Offset: fixed value


And in combination with all other options you can show inverted values:

Showing thermodynamic values inverted
Showing thermodynamic values inverted


Be aware that an offset may hamper the correct interpretation of the energetic relations in some reaction! This especially applies where reactions have unequal number of educts and products.

1.2.3.5. Export to Image

The visualization can be exported to PNG, JPEG and GIF images by pressing the image export button on the toolbar.

1.2.4. About Loading Data

1.2.4.1. Common Properties of Data Tables

One of the most important information required by ThermoVis is where to find the header that describes the data. The header must contain the names of the metabolites so that ThermoVis can assign the data to the corresponding metabolites.
Therefore, you must specify, if the header is horizontal (meaning to be the first row of the table) or vertical (first column). If the header is horizontal, each column represents the data belonging to one metabolite. A column may contain data in multiple rows. You can select which data row shall be loaded.
Vice versa, if the header is vertical, each row represents the data belonging to one metabolite.
If your data is not given in the default unit, you have to select the matching unit in the unit combobox.

The format dialog provides a preview that shows the content of the data file. The preview table displays a header and any number of rows containing data. Make sure that the preview header contains the data header, i.e. the preview header must be filled with the metabolite names!

1.2.4.2. Loading CSV Files

CSV is a popular format to store tables of data without using a proprietary file standard. CSV stands for character separated values. Each line of the file represents a table row whereas the individual columns within each row are separated by a specific delimiter character. Typical delimiters are the TAB or SPACE sign, komma or semicolon. The delimiter character can be specified in the CSV format dialog.

Likewise, you can specify quoting characters like quotation marks. This allows, for instance, to separate cells by komma but however place text with a komma sign in one cell:
A,B,"A,B",C
representing four cells

The escape character also allows to place the quotation sign itself in text:
"He said: \"Hello!\" to her."
is interpreted as one text object

With the start line attribute, you can deside with what line, ThermoVis shall start to read the data table, for instance, if file starts with comment lines.

In case, you use special characters like umlauts, greek letters or accents in the CSV file, you must specify the character set used by your file (cf. character encoding).

If the numbers in your CSV file do not use the scientific or english notation, you have to specify the decimal number format (cf. decimal mark).

CSV format dialog
CSV format dialog

1.2.4.3. Loading Excel and ODF Files

ThermoVis can load Excel and ODF files as long as the corresponding Omix plug-ins are installed. Beside common properties as described above, you can select the sheet to be imported because Excel and ODF files can contain multiple sheets. It is also possible to skip a certain number of rows before reading the table content.

Excel and ODF format dialog
Excel and ODF format dialog