ProteoCloud

• News
• What is ProteoCloud?
• Downloads
• Using ProteoCloud
• Libraries
• Screenshots

News

October 09. 2012: ProteoCloud v1.1 is now available with major updates and improvements: * IMPROVEMENT: The results view was added to retrieval of the cloud database results and shows in-depth inspection on peptide and protein identifications. * IMPROVEMENT: Project management made easier on startup, creating new projects and opening come along with the startup dialog. * IMPROVEMENT: AWS and datbase management dialog. * IMPROVEMENT: S3 Bucket selection possible now in the startup dialog. * Various bugfixes regarding the program start and graphical user interface. * The ProteoCloud user manual has been updated to version 1.1.

June 25. 2011: ProteoCloud v1.01 is now available with some minor updates: * BUGFIX: The job status table shows now the current filename of the processed spectrum and the error in separate columns. * BUGFIX: The upload button now works correctly. * BUGFIX: The S3 bucket name can be specified by the user and is submitted correctly to the application. * IMPROVEMENT: The different buttons under master control are enabled/disabled depending on which tab hab been selected.

June 23. 2011: ProteoCloud v1.0 is now available: * The ProteoCloud application represents a local client controller to handle a proteomics protein and peptide identification pipeline in the cloud using the Amazon Cloud System. * ProteoCloud supports MGF files as MS/MS files input.

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What is ProteoCloud?

ProteoCloud is a Java-based proteomics cloud computing pipeline system for peptide and protein identfications. It supports database searching and de novo. Requiring only MGF files as input the pipeline is able to identify peptides and proteins from tandem mass spectra. The search can be done on multiple servers and the results are stored on a centralized SQL server in the cloud.

What is needed to work with our pipeline is an Amazon Web Services account for the cloud usage. More information you can find here: Amazon Web Services

The application is being developed by Thilo Muth (MPI Magdeburg/Germany) under the guidance of Prof. Dr. Lennart Martens (UGent/Belgium).

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Downloads

The zip file in the downloads section contains the ProteoCloud jar file and all the libraries needed to run the controller.

In the downloads section you will also find the ProteoCloud manual.

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Using ProteoCloud

The Controller Unit

The Controller Unit represents the user interface and the master controller for ProteoCloud pipeline. Via the Controller Unit you can easily handle uploading of MS/MS files, launching the virtual server instances and the job managment for the different used search engines.

To start the Controller Unit download the latest version of ProteoCloud in the downloads section, unzip the downloaded file, fill the AWS credentials in the properties file (see below) and double-click on the ProteoCloud-X.Y.Z.jar file. For additional help see the ProteoCloud manual which is also found in the downloads section.

Properties file

The properties file (proteocloud.properties) can be found in the conf folder. In the properties file you need at least specify your AWS credentials (awsAccessKey, awsSecretKey, keypair and group) and the Amazon S3 bucket folder to have access to the cloud system.

For running searches in the cloud you also need to specify and EC2 ProteoCloud instance identifer (ami) and the availability zone. This can also be done in the application itself.

Further parameters can be set for the SQL database and project specific setting, such as taxon, precursor and fragment ion tolerances.

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Libraries

The following libraries were used for the general user interface: * JSparklines * SwingX * JGoodies * Substance

These libraries handle the communication and storage in the cloud: * typica * JetS3t

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Screenshots

(Click on the screenshot to see the full size version)

| Storage View: | Results View: | |:------------------|:------------------| | ](http://proteocloud.googlecode.com/svn/trunk/images/storage.png) | ](http://proteocloud.googlecode.com/svn/trunk/images/results.png)|

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