User ManualB-Fabric is the tool to work with at the Functional Genomics Center Zurich. B-Fabric comprises all the major functionality needed to run and work with a core facility.
Among others, it is used 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.
Table of contents
- User Manual
- For Employees Only
- How to register a user.
- How to change a user password.
- How to request a password reset.
- How to request access to the FGCZ.
- How to request a project. Watch Project Request Demo as Quicktime Movie.
- How to edit a project.
- How to add/remove project members.
Order ManagementUsers may order fee-based services at FGCZ. B-Fabric helps to manage the entire process of a order process including the submission of the order, the provision and download of the results, and the accounting of the service. Depending on the services, an order can be executed with or without the requirement of a project. In the latter case, the order application will ask for an existing project the user is member of.
- How to work with Orders. Watch Order Management Demo as Quicktime Movie.
Sample ManagementThere different way to create samples. Users create implicitly sample when placing their orders. In addition, there is the possibility to add and edit sample within a project:
- How to create a sample.
- Samples of a project can also be created, cloned, and edited in tabular form.
- 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. How to move a sample from one project to another.
- Certain sample attributes refer to specific annotations which are dynamically managed vocabularies. These vocabularies can be extended by the users. Newly added annotations are then reviewed and released by FGCZ experts: How to work with annotations.
Data Import and AnnotationTo 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.
Data ViewMost data is structured in "workunits" which contain "resources".
As a simplification and the knowledge how data is usually stored in a filesystem e.g. on your local computer, you can see the "workunits" as a folder and the "resouces" as the files.
But be aware, that this is only a simple view. In theory a workunit is a organization of your work, where all resources belong together and can be used e.g. in "applications".
WorkunitsResources are grouped in workunits to show they belong together.
For example the resources are measured together as a unit to work with them in succeding tasts.
All workunits belong to a "container" (project/order).
ResourcesIn theory a resource can be anything you want to keep and annotate.
In most cases resources represent simple filesystem files or even folders, but can be anything worth to keep and annotate.
Resources always belong to a workunit.
Data Analysis and ProcessingTo 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 DownloadThe B-Fabric Download Manager allows to download single resources as well as entire workunits, orders, or even projects. A requirement for using the B-Fabric Download Manager is a working installation of Java. Java Web Start is needed for opening the provided jnlp file in order to start the Download Manager.
- How to download a resource
- How to download a workunit
- How to download a container
- How to configure the "Download Manager"
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 BasketThe 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:
- How to add resources to the Resource Basket.
- How to show/edit the content of the Resource Basket.
- How to select resources from the Resource Basket and run an application.
Quick SearchFollowing types of objects are searchable via (Lucene) index: Projects, Orders, Samples, Workunits, Resources, Datasets etc. By clicking on on the corresponding header menu items, the corresponding objects of that type are listed. In case of projects, all projects the current user is member of are listed. 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. be aware that the column filters in data tables are usually based on "contains" semantics.
Instrument ReservationsInstrument reservation manages access to instruments and because each instrument has its own constrains and requirements it is assigned a default setting upon creation.
For further information for customizing the instrument reservation refer Instrument Reservation Setting provided below.
- For all users: How to create an instrument reservation.
- For all users: How to create shift instrument reservations.
- For instrument managers only: How to configure instrument reservation settings.
- For all users: How to submit a feedback.
- For feedback managers only: How to manage feedback templates.
For Employees Only
EventsAny entity having a start date/time and end date/time is considered an event and the following shows available types of bfabric events.
- Event: Formerly known as agenda event.
- Instrument Reservation
- Event Types
- Agenda Events
- Customize Instrument Reservation through Instrument Reservation Setting
- Instrument Reservations
- Instrument Reservation Shifting
AgendaManaging and communicating absences.
- An event is half-day slot that can be associated with different event types, e.g. business trip or vacation.
- Events can either be user-specific or public. Public events are "Public Holiday", "Group Meeting" or "Retreat".
- Events can be edited and deleted before their end date is passed. After the end date has passed more than a week, the event can only be edited and deleted by a user with admin rights.
- A repeating event is an event that occurs in a given interval (weekly, bi-weekly, etc.) until the defined end date is reached.
- Delete Repeating Events: When deleting a repeating event, the system asks whether to:
- DELETE THIS EVENT: Just delete the selected event.
- DELETE ALL FOLLOWING: Delete the selected event and all following events in the series.
- DELETE ALL EVENTS: Delete the entire event series.
- Delete Repeating Events: When deleting a repeating event, the system asks whether to:
- When creating an event, you can optionally send an email to email@example.com and to selected colleagues to inform them about the absence. Here you can also select previously defined mail groups as recipients.
- Mail groups can be created/updated via the menu "Admin > Common data > Mail Groups".
- Vacation Credits
- The vacation credits specify the amount of vacation days for a specific user. Every employee has a number of vacation days depending on her/his employment degree. The new vacation credits are granted using the formula "deployment degree x 25 days".
- When the FGCZ coordinator closes the agenda year (see Admin section below), the vacation credits are created for the corresponding year and the unused vacation credits from the last year are transferred implicitly.
- Event Types
- The event type specifies the kind of event (Sickness, Vacation, etc.). The type determines whether the event duration takes vacation days from the user, etc.
- A user with the role coordinator can add and edit event types, e.g., change the color of an event type.
- Admin: The admin area is visible for users with the role agendaManager. This page contains the following functions:
- Close Agenda Year: Usually at the beginning of a new year, the past agenda year can be closed in the sense that the unused vacation credits of the past year are taken over for the current year and all employees receive a vacation credit for the current year. The number of credited days is based on the employment degree of each employee. Therefore, every employee as well as the secretary should check whether all entered employment degrees are still valid (i.e. reflecting the current degree of employment).
- Set Accounted Days: This function is needed once after the migration to compute and set the accounted days for all vacation events. Of this function can be rerun later ant any time, e.g. if a public holiday event was forgotten and added later on. In this case, the re-computation is required to avoid that too much vacation days are counted for an event.
- Employees: Gives an overview of total credited and taken vacation days.
- Hints for FGCZ employees: Please enter all your missing events and credits before the end of the corresponding year. To ensure a correct computation of credits, please go your login details and check whether your employment degree is still valid. If not, please update it.
- Troubleshooting: To avoid that the generated PDF files for the overview and vacation reports are opened within your web browser, please check ensure that browser settings for PDF are not set to "Preview (in Firefox)". The preview of the agenda overview report in the browser takes a lot of time. Instead open the PDF files with an application of your choice.
- How to find the plate menu.
- How to create a barcode.
- How to create a barcode kit.
- How to create a plate layout.
- How to create a plate type.
- How to create a plate.
- How to create a control sample
- Custom View for NGS Orders
- Plate tasks
- Email sent by users: How to send emails manually.
- Email logging and history: How to list the email history.
- Email sending triggered by events: See a list of events that trigger an email sending.
- Hot-Keys: B-Fabric keyboard shortcuts
- Data analysis applications
- Schedule B-Fabric Restart
- Working with B-Fabric using SWITCHaai Accounts (deactivated functionality): How to work with a SWITCHaai account. B-Fabric uses a dual login mechanism which also allows users log into B-Fabric with their Switch AAI/Shibboleth accounts as well as with their B-Fabric accounts. Watch Using SwitchAAI/Shibboleth with B-Fabric Demo as Quicktime Movie.