B-Fabric Project Manual

B-Fabric Project is the place to apply and manage User Lab projects. The management of a User Lab project includes the management of users (project members) as well as the management of the data produced in the project. B-Fabric allows storing, annotating, and search for scientific data. To become acquainted with the system, please have a look at the QuickGuides below.


QuickGuide Proteomics

User Management

  • Click here for B-Fabric user account related issues such creating a user account, resetting user password, or requesting FGCZ access.

Create and Search for Objects

Using the lower navigation menu of the header, the current user can create and search for B-Fabric objects of some major types. Among others, these following types of objects are searchable: Projects, Samples, Workunits, Resources, Datasets etc. By clicking on these links, the corresponding objects of that type which were created by the current user are listed. In case of projects, all projects the current user is member of are listed. By clicking on the plus symbol beside these links an object of that type can be created. In case of projects, a project application will be submitted to FGCZ. Note that all objects are linked together. For instance, using the corresponding menu links of the show project screen, you can get easily to all samples, workunits, datasets etc. belonging to that project. This is also true for other types of objects.

Note: The column filters in data tables are based on "start-with" semantics. If you search for a term anywhere in a value, then use the asterisk symbol * infront of the your filter term, e.g., *rat to match all values containing the term rat. The underscore symbol _ is a reserved placeholder for any single character. If you want to match a value that contains the underscore symbol, you have to escape the it as follows: \_, i.e., use the backslash symbol infront of the underscore symbol.

Project Management

Project Orders

Project Orders allow users to order fee-based services at FGCZ. It helps to manage the entire process of a project order including the submission of the order, the provision and download of the results, and the accounting of the service.

Sample Management

Create Sample: How to create a sample.
Edit Samples: This feature allows you to edit samples in tabular form. You can edit one or more samples of your context project, clone existing samples, or create new samples. This operation consists of two steps:
Move Sample: A sample can be moved to another project if it is not (transitively) assigned to any resource. In this case, the sample will be moved together with all child samples.

Data Import and Annotation

To import data into B-Fabric, the corresponding resources (≈files) have to be described and annotated. This is done by assigning them to a Sample. The Sample contains the information about the source material of the measurement that produced the data to import.

Instrument Reservation

Create Instrument Setting: How to create an instrument setting.
Create Instrument Reservation: How to create an instrument reservation.

Data Analysis and Processing

To analyze data, the needed resources (≈files) have to be selected and in case of certain analysis application assembled into an Experiment Definition. Creating such an experimetn definition allows to gather the needed resources and enrich them with parameters.

Data Download

The B-Fabric Download Manager allows to download single resources as well as entire workunits.
A requirement for using the B-Fabric Download Manager is a working installation of Java.
  1. How to download single resources
  2. How to download entire workunits
The B-Fabric Download Manager supports resume of downloads when stopped by the user or network interruptions. Moreover, it checks the checksums of the downloaded files to ensure that downloaded files are not corrupt. Note that the B-Fabric Download Manager is a Java Rich Internet Application based on Java Web Start, which only requires that Java is installed on the local machine.

If you are using Mac OS X, please be aware of this additional Apple security setting for third party applications.

Resource Basket

The resource basket allows collecting resources for later use as input resources to invoke an application. The resource basket is associated with a user and is persisted in the database. The following operations are supported:

Add a resource to the resource basket:
Show/Edit the content of the resource basket:
Select resources from the resource basket to run an application with:

Annotation Management

Users annotate their experimental data by using attribute vocabularies. These vocabularies can be extended by the users. Newly added annotations are then reviewed and released by FGCZ experts.

Email Management

The B-Fabric email module supports the following functionality:


For Feedback Managers:
For Users:


Created by akal. Last Modification: Friday May 15, 2020 14:37:38 CEST by tuerker.

B-Fabric User Manuals