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User Guide

Christoph Malisi, Sebastian J. Schultheiss

The source code to this application is published under the Apache License 2.0. This product includes software developed by The Apache Software Foundation.

Table of Contents

  1. Program Description and Goals
  2. Projects

1. Program Description and Goals

With the completion of the human genome sequencing effort and many more genomes readily available in databases since then, the focus in life sciences shifts from pure sequencing towards proteomics. In short, understanding the structure and cellular function(s) of proteins, their interaction partners, and putative involvement in disease is now of interest.

Technological advances have contributed to high-throughput generation of a large body of experimental data that exists in heterogeneous databases world-wide. However, determining the structure, function, and interactions of proteins with high reliability has proven to be a difficult task. Bioinformatics tools provide means for efficient analysis of existing data and give biologists a plethora of possibilities to determine function and properties of proteins through database comparisons and de novo prediction methods. Most of these technologies are freely accessible on-line.

Working with these services has become an essential part of every experimental biologist's research. Using the often rough-hewn interfaces and performing the necessary adjustments of parameters and data to fit the input format is tedious and time-consuming. Receiving the different outputs typically requires manual editing before it is possible to compare the results and draw conclusions.

CoMPAS Pro integrates useful web services for biological research, so input is only needed once. The results obtained form the integrated services are homogeneously combined, formatted, and presented in an intuitive fashion, which facilitates easy design of further experiments, publication, and drawing conclusions.

While CoMPAS Pro is designed to run on a local computer, it is at the same time communicating with the individual web services it uses, by distributing requests to several servers to speed up processing time and balance the computational load.

For creators and developers of existing and future web services, we offer an interface with which they can easily integrate their service into our framework. We use the Web Services Description Language (WSDL), a proposal for a World Wide Web Consortium standard, which describes the capabilities of a web service and its input/output formats in a variant of the Extensible Markup Language (XML).

Through WSDL, communication between the services and our stand-alone client is standardized using the protocol SOAP over the Internet.

The source code and binaries are publicly available for extension and modification, under the Apache License, Version 2.0, in order to assist convenient integration of services into CoMPAS Pro.

CoMPAS Pro has an intuitive graphical user interface (GUI), including easily adjustable prediction parameters that are pre-set to scientifically sound defaults for an out of the box start. It is possible to enter several sequences at once, compare their results, and display a synopsis. The output of different services for one or more sequences can be displayed in an comprehensive overview facilitating conclusions to be drawn from their combination.

2. Projects

Main Window

This is the main window of CoMPAS Pro. On the left side you can see the project tree. This is much like a directory tree which lets you navigate through all steps of your project. In the first position you can see all your sequences. By clicking on the sequence folder itself, you can add more sequences to this folder. This screen can be seen on the right and will be described in the next section in detail.

Under the service folder, you can see all the services that are enabled for this project. They can be expanded for access to their parameters and results. The services and their settings are described in the next chapter.

Above the project tree, you can see the toolbar, where you can load and save project files. Only one project can be open at one time. The "Run" button starts all the active services with the parameters that are currently set. Results will be calculated for each sequence and can be viewed on each sequence's settings pane and/or on the service's result pane. That way you can either compare all results for a certain service or all the results for a certain sequence.

Sequences

A screenshot of the sequence input screen, where you can paste your sequence data or load a fasta file. This is the screen you will see when starting a new project from scratch.

To start a project, it is a good idea to add sequence data first. The options are raw sequence data, FASTA-formatted files or text. All sequence-relevant functions can be accessed via the project tree, by clicking on "sequences".

Adding raw sequence data

To add raw sequence data, you can just paste or type your sequence directly. When you are done, click on the button "+ Add sequences" and a new item called "New Sequence" will appear under the "sequences" folder in the project tree.

Adding FASTA formatted sequences

If your sequences are already in FASTA-format, you can paste them in the text area as with raw sequences, or open a FASTA-file by clicking on "Browse for sequence files..." Sequence names and sequence data will be read from the FASTA data and added to the project tree. Changes to the sequences can be made as described above.

After you added some sequences, they will appear in the project tree on the left.

Changing the name and data of a sequence

To change the name or the sequence data, click on the sequence name as it appears in the project tree on the left. A new screen appears on the right that displays your sequence, the name as it was found in the header file, or the words "New Sequence" if you added raw sequence data. Modify them as you like and click on the "Save changes" button.

Here you can modify the sequence header and data. Once results are there, you can see them here.

Deleting sequences

If you want to delete a sequence that is displayed in the current project, select it in the sequence tree and press the "Del" (delete) key on your keyboard. The sequence will be removed from the project.

Results

After a run, results for this sequence from all active services are displayed on the lower part of the sequence screen. Results can be exported and viewed in an XHTML-enabled browser, such as Mozilla Firefox by clicking on the "Export Results" button. These files can be easily used for further analysis or publications.

When the results are here, you can view them sequence-wise by clicking on the sequence name in the project tree and scrolling through the results that are available for this sequence.

Services

All services that are availabe for this project are listed in the "Services" folder in your project tree. If you expand a specific service by clicking on the small "+" box or arrow next to its name, you will see "input parameters" and "results" as selectable pages. Instead of clicking on the expand-symbol, you can also click on the small checkbox icon or the sequence name to activate or deactivate a service. When the box is checked, the service is active and will be queried the next time you press the "Run" button. If it is not checked, the service will not be queried until you activate it. This setting is saved in the project file.

Setting Input Parameters

When you select the "input parameters" page directly under a service, a new screen appears on the right displaying the service name, a description and the parameters that can be adjusted before each run. A short description of each parameter is next to its edit field. Those fields usually are drop-down boxes where you can select one of several options, a spin box where you can set a number for a certain parameter such as a score threshold, or a checkbox for a parameter that can be either on or off.

Service input parameter screen of the Service "SVMHC". Desription and layout depends on the service you are looking at.

Note

The settings you select here are immediately saved and used for the next run. If you want to preserve them between different sessions of using this project file, you still need to save the file.

Results

By clicking on "results", the results received in the last run for this service are displayed. They are either textual results or graphical, depending on the service. If you have many sequences, graphical results may take some time to load since they are computed on the fly for flexibility. Results can be exported and viewed in an XHTML-enabled browser, such as Mozilla Firefox by clicking on the "Export Results" button.

An example of a service that returns a result in text form, "MultiLoc".

Example of a service that returns graphical (SVG) results, "SVMHC".

Running Services

When you have added all the sequences you want and set all the parameters for the services, all you need to do is check that all services you want to use are active. Click on the "Run" button in the toolbar to send the sequences to the services. The results will be computed.

Note that the cursor changes into an hourglass until the run is complete. You can set the timeout on the preferences screen. When all services have responded or timed out, you will be notified with a dialog box that lists the services that have failed, if any.

Dialog box that will appear when the run is complete and no errors have occurred.

Note

Especially when first starting CoMPAS Pro, establishing a connection to the services may take a long time. If a service fails initially, it may be a good idea to re-run it and see if results are now forthcoming.

You can view the results by clicking on either a sequence name or the "results" entry under a service name.

Preferences

By clicking either on "project" in the project tree or the "Preferences" button on the toolbar, you can see the preferences screen. Here, you can set your HTTP proxy server and port if this is necessary for your network environment. You can ignore this setting if your firewall allows outgoing port 80 (HTTP) traffic or if you have a transparent proxy. A good way of finding out is running all services without a proxy. If they all fail, there is a good chance you may need to adjust this setting.

The global preferences screen with a proxy entered.

Define a timeout for the services by adjusting the timeout setting. If you are running with a lot of sequences it may be necessary to set this to a value higher than 60 seconds.