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Tuesday, May 05, 2015
Hi, everybody! Have you seen our new OneOmics Discussion on how to get started? Check it out here to see the "ABCs" of multi-omics integration.
Friday, May 01, 2015
A: Latest versions of Chrome, Firefox, and Safari. Internet Explorer is not supported, however, Internet Explorer 9 or higher is required for the installation of the PeakView CloudConnect Micro-App which is used to upload the data to BaseSpace.
Friday, April 24, 2015
A: BaseSpace has an Import tool! See here for instructions: https://help.basespace.illumina.com/articles/tutorials/upload-data-using-web-uploader/
Monday, March 23, 2015
A: Within Protein Expression Browser, you can visualize a heat map of the protein expression data. The hierarchical clustering is a Euclidian distance matrix cluster using pheatmap in R. Currently all proteins which have a significant confidence of abundance change (>75%) are used in the heat map. For this heatmap to be generated, you must have at least 3 experimental groups defined in your study (defined during Protein Expression Assembler data processing). This is critical for the statistical analysis and generation of the plot.
Wednesday, February 18, 2015
Illumina collects various information from you during your use of BaseSpace. Some of this information includes the Internet Protocol (IP) address of your Internet Service Provider, the content you access, the platform operating system and web browser you use, and the date and time of your visit. Additionally, Illumina may collect the following:
a. Personal Information - Illumina also collects personal information about you through your voluntary submission. For instance, in order to access BaseSpace you first must register with Illumina. To register, you will be asked to provide your contact information (e.g. name, institution/company, address, phone number, email, etc.).
b. Information About the Data - For example, Illumina may collect metadata about the data, file types and sizes, instrument diagnostics, biases, errors, and trends within and across data, general trends in the utilization of BaseSpace, Apps, Software, or Illumina’s other products and services, including, by way of examples, features used, reagents used, software used, instrument type and identifiers.
Working with your IT department: If you suspect that use of cloud-based storage and data processing applications are restricted within your institution, there is help to present the relevant information to your IT department. BaseSpace is a highly secure environment with lots of documentation that describes exactly the privacy settings, user agreements, and information protocols. Here is the best source of information to get the conversation started with IT personnel.
Wednesday, February 18, 2015
A: SWATH™ Acquisition data files (*.wiff files) are uploaded into the BaseSpace Environment using the CloudConnect Micro-app which installs on top of PeakView® Software 2.1. There are a number of ways to upload both the data files and the ion libraries to the cloud.
Data files (1 or more per window) can be opened within PeakView Software and then directly uploaded to BaseSpace (menu option 1). An ion library (*.txt file) can also be directly loaded (menu option 2). If your are using either a *.group file (ProteinPilot Software) or an mzIdentML file as the source information for your ion library, these must be loaded into CloudConnect per below and converted to a text file before getting loaded into BaseSpace.
If retention time recalibration is needed between the ion library and the SWATH acquisition data, this can be done within CloudConnect using menu option 3 or 4. Here, the data files and ion library are loaded into CloudConnect and the retention time recalibration is performed. CloudConnect is used to create a Retention Time Calibration Protein within the ion library, which can then be uploaded to the BaseSpace project (menu option 3). If both the data files and the ion library need to be uploaded, menu option 4 can be used. Once any of the menu items are selected, the upload dialogue allows you to select a Project and also provide a name for the specific upload.
Tuesday, February 17, 2015
Only the UniProt protein FASTA format is supported. The IPI database is no longer supported and will not work when processing with the Protein Expression Assembler. Therefore when you are performing your database searches to create your ion libraries, make sure you use a UniProt FASTA. The UniProt accession information will be used within Protein Expression Browser to obtain the ontology information for the various visualizations.
Saturday, February 07, 2015
Your data and results within BaseSpace will be organized in a project structure. Any project that you create will be used and viewed by only yourself. If you wish to share data or results with a collaborator, they can sign up for a BaseSpace account and you can then share a specific project with them (through specifying their email address used for the BaseSpace account creation). They will only be able to work within the specific shared project. You can also transfer ownership of the project to them.
Saturday, February 07, 2015
Getting started with BaseSpace is very easy, the first step is to sign up for a BaseSpace account (go to BaseSpace and sign up). Once you login to your account you will see a ribbon of options across the top of the screen. Select the item that is called Projects or the folder icon and a number of options will appear that allow you to control the projects within your account.
From here you can see that you can create a New Project, as well as other project options.
In addition, a new BaseSpace folder can be created at the time of upload of your data from CloudConnect. If you enter a new project name in the Project dialogue that is not in the list of projects below, a new project will be created for the files to be uploaded.
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