Organization of the geneXplain platform

The user interface

When you open the geneXplain platform for the first time, a window opens that contains the following areas:

A - The Work Space, which is the main part of the window.

B - The Tree Area (to the left of the Work Space), where you find the collection of Databases, the uploaded Data files and the available Analyses methods under the corresponding tabs, organized in a hierarchical tree structure.

C - The Info Box (in the left lower part), where you can select the data resource to Search in, or where you will get Information about the data file or analysis method that you select with a single click in the Tree Area.

D - The Operations Field (right lower part), providing a number of options under the different tabs in a context-dependent manner.

E - The general Control Panel, on top of the different areas, showing a context-dependent set of icons for the available operations.

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Work Space

When you open the platform, the Work Space will show you all those research areas that are supported by a number of bioinformatic workflows each. Clicking on one of these tiled buttons will open a detailed listing of functions and pre-composed workflows, which you can launch by directly activating the given hyperlinks.

The listings of each Area introduce each Chapter of this User Guide that explains the functionality provided.

The first workflow in nearly any Area is Load data, which is separately described , before the individual Areas are being depicted.

Also in the Work Space, all major input requirements will have to be done, the progress of a workflow and the results output will appear here as well.

Tree Area

In the Tree Area (B in the above figure), you find three tabs: Databases, Data, and Analyses. Under each of these tabs, you find a tree-structured listing of contents: the available databases, the data files to work with, and the analysis methods you can apply. You can open any subdirectory by a single mouse click on the respective item and using the button _images/image093.png , or by a double-click on the name of the folder to be opened.

Databases

Under this tab, you find all databases that are at your disposal: a number of public databases (yellow symbols) as well as commercial ones that you have a valid license for (green symbols). Write access may be additionally indicated by a black “W” within the symbol, which may be red in case that write access, although principally possible for this database, has not been activated in your case.

Select one of the databases in the Tree Area by a single click with the left mouse button; double click will open the subdirectory. For instance, when you wish to go to GeneWays, you have to click once on the little white triangle next to the term GeneWays, or double-click on the term itself to open the directory underneath; either operation, or already a single click onto the name of the database, suffice to indicate this data resource in the Info Box, along with a short description.

Presently, by default, you should see the following listing of available databases:

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Data

On the tab Data, you will find your own datasets as well as predefined ones in the directories Examples, Projects, and Public.

In the directory Examples, we provide you with a number of sample data you may use for getting familiar with the system. Presently, these are some optimization examples as well as one application example on expression data of Psoriasis patient samples.

The optimization example refers to the CD95L pathway (Reactome entry REACT_900), shown as diagram CD95 signaling pathway under Diagrams. Under Plots, you find an example for a successful parameter optimization (C3C8_plot), with the dots giving the experimental values for four different molecules, and the straight lines showing the simulation results.

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Under the heading Projects, you should initially find only one directory with your username, with the two subfolders Data and Journal. Data will be the place where all your own data will be deposited. Here, you can define own subdirectories by opening a context menu with the right mouse button and selecting the option New folder:

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Each option in this menu can also be selected by the corresponding icon on top of the tabs.

The sub-directory Journal stores a history of your activities. Opening it in the Work Space shows you a list of all methods that you have previously launched, including time stamp.

The root directory Public is presently not used yet; it is planned to provide a platform for sharing own results with a wider community at a later stage.

Analyses

On this tab, you find Galaxy tools, JavaScript functions, all Methods you may apply using the geneXplain platform, including the pre-defined Workflows:

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In the directory Galaxy, there are sorted groups of tools for mainly RNA-seq and NGS data. Additionally, collections of statistical applications, gene fusion finder, human genome variant detector and effect predictor. You will also find the MatrixCatch, a tool designed to search for potential composite elements (CEs) in DNA sequences.

In the directory JavaScript, a collection of scripts have been gathered that all can be called by your own scripts. The geneXplain platform provides you with the possibility to create your own scripts on the Script tab in the Operations Field. For instance, enter there the command “help (boxPlot);” (boxPlot is the first JavaScript in the subdirectory Functions) and press Execute (or just Enter): Some help text about boxPlot will be printed to the Work Space:

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Under Functions, a number of standard JavaScript functions are listed, whereas in the subdirectory Host object, a collection of scripts have been put together that were specifically developed for the gXp platform.

The directory Methods contains all individual tools, or Bricks, that perform specific tasks in one of the listed areas. A full listing of all analysis methods that are presently available is given in the Help texts. Each method can be launched either by double-clicking on the respective item, which will open the corresponding input mask in the Work Space, or through the context menu that you can open with a right-button mouse click on the method of interest.

In the directory Workflows, you find basically the same functional groups of pre-defined workflows that are also listed on the Start page of the platform (Work Space). Please note that the first two items on the Start page are important preparatory tasks, but not workflows according to the definition of the geneXplain platform. Indiviual workflow desscription is described as separate sections.

The Info Box

The Info Box shows two tabs, Info and Search.

Info tab

Under the Info tab, you will find short descriptions about the database, data file or analysis method that you have clicked in the Tree Area. In many cases, you will just see the name of the directory or file as ID, or the complete path displayed in the field Complete name, and the number of subdirectories and files right under the activated node as Size.

The information shown on the Info tab can be viewed in a separate window by clicking the button _images/info.png

In case the activated file is a table, the number of rows in the table will be indicated as Size. Optionally, a Description is shown as well, depending on whether it has been entered when the file was generated. By clicking on the edit icon, you may edit some of the information in a newly opened window. Depending on the file type, the edit window may look like this:

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Gray fields cannot be edited, contents of fields with white background can be changed manually, additional information can be entered in the pink fields which will then appear on the Info tab, if the changes made are saved afterwards with the [Save] button of the Edit window.

Depending on the type of directory or file that you have activated in the Tree Area, different types of information can be selected for the display on the Info tab. This can be done by the selection box right to the tabs in the Info Box, initially always showing “Default”: _images/image095.png

Please, feel encouraged to find out the effects of the different views offered here.

When you have a network diagram opened in the Work Space (A in the figure above) and you select a molecule or reaction with one click, you find information about the selected element in the Info box.

The Operations Field

In the Operations Field (D in the figure above) a number of essential functions to operate the geneXplain platform are provided on a number of tabs. How many and which tabs are shown depends very much on the context.

Please note that not all tabs are always visible due to space constraints. In these cases, double arrowheads left and right of the tabs indicate that there are additional ones, reachable by clicking on these double arrowheads.

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The function of the individual tabs will be explained in more detail in those sections where their effect is part of a certain operation.

How to organize the user work space

Changing user password and personal data

Your first password for the geneXplain platform is automatically generated and sent to you by e-mail. Once you enter the platform you can change your password and also have an option to edit your personal information.

To change password and edit the personal data, select the Account info button (_images/3675b0521753e8230736ab24b39897c5.png) on the top menu control panel:

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Your account information will be displayed in the work space as shown below:

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The option to change the password is highlighted by the red oval. Once you press [Change], you get an option to enter the new password:

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To change the account details, press the button [Edit account info] in the form above, highlighted by the green oval. The edit form looks like this:

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Fill-in your details and press [Save]. Before saving, the system verifies your password to enable the changes made in the form. After entering the password the changes are saved.

User Project, Data folder, creating new folders

When you enter your account for the first time, you can see the following three folders in the Tree Area under the Data tab (red oval on the picture below): Examples, Projects and Public. Each of these folders can be expanded by clicking on the small triangle on the left side of the folder name (green oval on the picture below).

The folder Projects is your folder in the tree where you are going to make all the analyses.

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If you expand the Project folder, you can see the project that was created upon registration of your account (_images/ab0f0406eb982519b2b38b759586bf59.png), and if you expand it further, you can see the folder Data. This location, data/Projects/User project/Data/ is exactly the location where you can upload your data, and save all the analysis results.

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Upon one mouse click on the folder Data, as in the picture above, you can apply the button _images/image098.png from the top control menu to create a new folder within the selected one.

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In this way, you can define the hierarchical organization of your folders and sub-folders within your project, for example as shown below.

Every time when you run a workflow, you need to specify a location of the results folder, and you can specify any particular location within your project area.

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There are two other folders available for you initially, Examples and Public. The folder Examples contains pre-analyzed publicly available data sets, which you are welcome to have a look through our examples. You can copy tables or tracks from these two folders into your project area and use them, for example, for test runs.

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The Public folder contains publicly available data sets which might be useful to apply for various analysis purposes.

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All users have read access to the folders Examples and Public, but no write access. You cannot save any files directly in the Examples or Public folder. However, you can copy tables and tracks from these two folders into your project area and then modify and work with them as you like.

How to check information about the available work space

To check your totally available work space, go with mouse over to the project name, so that it is highlighted in blue as shown below. In the Info Box you can see information about this project including disk quota. This is the space available for you. If you plan to upload large files, please make sure you have enough work space available.

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To check how much space out of your quota is already occupied, go with mouse over to the Data folder within your project, so that it is highlighted in blue as shown below. In the Info Box you can see information about this folder including its size on the disk.

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In the same way, you can check the size for every individual folder in your project.

Note*.* If additional work space or storage space is required, especially if you plan to upload and analyze large data files, please feel free to ask for details (info@genexplain.com).

User toolbar

In the Control Panel (see E in the above figure), the set of icons on the left side is fixed by default, whereas the right side is customizable. Here, you can create a user-specific toolbar with your most frequently used analysis methods, workflows and datasets. To create your own toolbar you can drag and drop your favorite workflows and files for which you often need a quick access into the Control Panel. The User tool bar will then be located at the top right top corner, highlighted by a red oval in the screenshot below.

To add any analysis method/workflow/gene set, open the respective method in the Tree Area or in the Work Space and drag & drop it onto the user toolbar as shown below.

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You can quickly open your favorite items from this icon menu. To open any method, place the cursor on the symbol and you get the complete name of the method which can be clicked to open in the workspace as shown below:

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In the above screenshot, the method ‘Site search on gene set’ has been opened through the user toolbar. If you want to remove any method from the user toolbar, right click the symbol and you will get an option ‘REMOVE’.

Project properties, or how to fix the releases of the databases to be applied in user’s projects

The GeneXplain platform provides access to several versions of the databases installed.

You can select your desired version of the database and fix it for your project using the Project properties feature. By default the latest version of all databases are applied.

Project Properties form can be opened via the button _images/9e17a94280337bb2f0bafbaee53097e1.png in the control panel:

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The form opens as shown below:

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For each database shown in the form, the available versions can be selected using the drop down menu. As shown below, Ensembl (Homo sapiens) 84.38 database version is selected. After selection press [Save] and the selected version of the database will be used in this project for all the analyses.

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Important to note, this change is applied for one selected project, the project name is shown on the top of the form, highlighted by the red oval on the picture above. If you have several projects, you can fix database versions for each project individually.

How to handle tables, tracks, diagrams: basics

File handling

File selection

All analysis tools, and likewise all prepared workflows, require input data from a file in the Tree Area. The respective file can be loaded into an analysis tool by

  • simple dragging-and-dropping of the file from the Tree Area into the corresponding field in the Work Space, or
  • by clicking into this field and making the selection from the directory which opens.

Multiple selections can be done only in the second way.

File handling in the Tree Area

On mouse-over, the file name will gain a faint-bluish background. Upon a single click on a file name, its background will turn into a persistent light blue, and information about this file will be displayed in the Info Box. Double-clicking on a file will open it under a new tab in the Work Space, and the file name will be additionally emphasized by bold lettering as long as the corresponding tab is in the Work Space’s foreground. Only files with an icon attached can be opened this way.

Files can also be opened by right-clicking on them and selecting the “Open table” option. You can also delete files (“Remove”; default value is “No”) this way. Both functions are also available through the corresponding icons in the Control Panel on top of the different frames. While opening and deleting files works for nearly any file, the third option is different among distinct file types:

Tables (_images/image100.png)

When activating this function, a selection of different formats is provided for the file to be generated. It is also available through the export icon on top of the Tree Area.

Diagrams (_images/image099.png) can be expanded/collapsed to show/hide their components (nodes and edges); this function can also be accessed by clicking on the white arrowhead next to the diagram icon.

Plots (_images/plot.png) can be edited. Only under this option, their complete deletion is possible as well.

Tables

Any table may be opened by double-clicking the corresponding name in the Tree Area. It will open under a new tab in the Work Space.

The contents of the table are sorted according to the values in one of its columns. Being opened for the first time, a default column is defined for sorting, usually the ID column. This default column is indicated by a blue arrowhead. If this arrowhead points upwards, the table rows are sorted in ascending order of this column’s values. Clicking on this arrowhead will change it into a downwards pointing one, while the values are sorted in descending order. Correspondingly, you may sort the table according to the values of any other column in ascending or descending order by clicking on the up- or downwards pointing gray arrowhead on top of this column, respectively.

On top of the table, you can navigate between the individual pages of the table; it is also shown on which page out of how many pages in total you are, and in the right top corner, the page size in terms of number of entries (rows) is shown and can be adjusted.

You can edit the contents of a table by pressing the [Edit] button in the right upper corner. Now, you can manually edit the contents of each cell in the table. With the [Apply] option, you will save this change, while [Cancel] quits it.

Even without activating the Edit function, you can select

  • individual rows with a left-mouse click,
  • several ones by keeping the Ctrl key pressed,
  • a range of rows with the Shift key pressed when clicking on the last row of the range to be selected, or
  • [Select all] by clicking on the corresponding button.

The selected rows can be saved as a separate file, which by default is given the name <original file name> subset, but you can change this name.

Basic operations with tracks

View track in genome browser

Upon double-clicking on a track name in the tree area the track will be opened in the work space in the genome browser.

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In the pop-up window Add tracks to genome browser you can select which tracks, among those available in Ensembl, should be opened together with your track. Here, three tracks are selected, GC-content, Genes, and Variations. When the selection is ready, push the [Ok] to get the following view with your track on top:

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On the tab name you can see genome, species and build information for this track, highlighted by the red oval.

The small triangles on the right side of the track name can be used to jump to the next or previous site of this track:

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Use the buttons _images/6fb7177e3985ae70dbe54dc65e9ce8e5.png in the top control menu to zoom in and out.

The buttons _images/64581c4d344e6bf39275c9ffa53b6c0e.png help to shift the visible part to the left or to the right.

The same effect can be also achieved by dragging the picture with the mouse.

You can also jump between different chromosomes by selecting the chromosome number in the field Sequence (chromosome).

As the next step to enrich the visualization, and to gather more information about your track of interest, you can add the additional pre-existing tracks from the folder Public. There, you can find a sub-folder traXplain with several tracks. This sub-folder is highlighted in blue in the screenshot below. As an example, two tracks have been added, the track with DNAse hypersensitive sites from the ENCODE project (DNAse HS sites clustered ENCODE UCSC hg19), and the track with the experimentally proven transcription factor binding sites from the TRANSFAC® database (TRANSFAC 2018.1 human sites hg19).

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Open track as a table

To open a track as a table, use a right mouse click on the track name in the tree area or [Ctrl + mouse click] for Mac users.

Using the same menu, you can apply other functions to the selected track, e.g. export it in available formats or delete it.

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A tabular view for the same track is shown below. Each row corresponds to one fragment. For each fragment, you can see the column ID with the fragment number, Chromosome, positions in the respective columns From and To, and several additional columns, three in this case.

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Filter track by condition*.*

When any track is opened as a table, it can be filtered by any condition in the specified columns. Filter options are available under the tab Filters in the operations field.

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Here, the filter is applied to select the fragments located on chromosome 1.

Diagram handling

Diagrams are provided by a number of databases and tools in the platform. The general schema of their use is that an overview of the corresponding graph is shown in the Operation Field, under the tab Overview, while a full-sized picture is shown in the Work Space, where usually only a part of the whole diagram fits on the screen. The diagrams exhibit components as ovals, reactions as squares, and links as lines or arrows.

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The section displayed can be shifted either in the Work Space by moving the mouse pointer (hand symbol) keeping the left mouse button pressed, or by shifting the blue-dotted rectangle in the Operation Field (mouse over: pointer symbol turns into a four-arrow plus sign, shifting can be performed while keeping the left mouse button pressed).

To facilitate orientation in large diagrams, individual edges are highlighted (turning from a thin, usually black arrow into a thick light-blue one).

Double-click on an individual node will show information about this component under the Info tab of the Info Box (this works for BioModels).

Diagrams can be zoomed in and zoomed out, by click on the buttons _images/65b191751b9996cc91860bdf1bdc58f0.png or _images/8ae7724b79ee5f10a8cfc01ef9fd5a04.png, correspondingly.

They can be exported in several formats by clicking the button _images/2fde7d826d1a2a88928490c9133c4556.png, _images/dc11c551d7ef6d67cc48328930b74dcd.png

Diagrams can be zoomed in and zoomed out, by clicking on the buttons _images/b59c404c4487a1135a2eab98e0bde155.png or _images/56e2b324f8d8ed08a3d6c714982a193b.png, respectively.

Diagram nodes can be multi-selected via the [Ctrl] button (picture below). Selected nodes can be used for Alignments or Distribution editing within the diagram or can be saved as a subset.

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Five alignment methods are available in the tool bar (see picture below) after opening a diagram in the workspace.

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After pushing one of the buttons in the toolbar, the selected nodes in the diagram are aligned accordingly. The picture below shows an Up alignment of all nodes.

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Two distribution methods horizontally _images/9e7d2ff171070050fd2e2786ea7e7442.png and vertically _images/613428b662c50d261e39bccea9d5cbd5.png are available in the tool bar after opening a diagram in the workspace. After pushing one of the buttons in the toolbar, the selected nodes in the diagram are positioned accordingly. The picture below shows a Vertically distribution of one node.

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For edge editing you can use either the dialog box or a clickable connecting line to add new edges to a diagram.

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