Introduction to LabKey

Overview

LabKey is a data management platform in which researchers can collaboratively manage and analyze their data.

LabKey Server is ideal for groups looking to transition to a more robust solution when working in Excel becomes unmanageable. Compared to other commercial software that are primarily oriented towards data analysis, LabKey Server allows you to manage and collaborate with your data directly through the software: you can easily import your data and keep it organised, you can manage and share your workflows, you can create comprehensive graphs and reports of your data and share them with your collaborators, all within a secure and supported environment, which you and your collaborators can access at all times and from anywhere via VPN. Its API enables scripted data access from languages such as R and Python.

The LabKey Server is a well recognised data management solution, and sciCORE recommends its usage in the context of data management requirement of SNF.

A LabKey server instance is managed by sciCORE and is available for research groups working at University of Basel and associated institutes. As an open source software (Apache 2.0), it can be deployed at no license cost at lab level or in other institutions.

Audience

This full-day course is aimed at PhD students, postdocs, and group leaders without (or very little) experience with the LabKey Server data-management tool.

Learning outcomes

In this course we will go through the LabKey fundamentals. After a short introduction, we will continue to the practical part, and follow a basic workflow:

Create a new project space,
assign permissions to project collaborators,
populate the project with data (import / export data tables),
create graphs and reports on the data,
personalise the project space with web parts, tabs and subfolders
show methods of collaboration within LabKey (message boards, issue tracking, wiki pages), and more.

At the end of the course, participants will be able to work more efficiently with their data, in terms of having an organised project space where i. the data can be imported, analysed and visualized and ii. the data and workflows can be followed, shared and discussed upon with the collaborators.

Prerequisites

Knowledge / competencies

This course is designed for LabKey beginners and there is no programming knowledge required.

Participants should have practical knowledge about working with data and data-sets i.e. in other analysis applications such as Excel (Ms Office). We will provide the test data, however, participants can bring their own (non-sensitive) data-sets for testing during the course.

Technical

You need to have signed-in the sciCORE LabKey development server once with your university email and password (detailed instructions to participants will follow).

Application

The registration fees for academics are 60 CHF and 300 CHF for for-profit companies. Participants from non-academic institutions should contact us before application.

Applications close on [09/05/2022]. Deadline for free-of-charge cancellation is set to [09/05/2022]. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Venue and Time

This course will be hosted online.

The course will start at 9:00 and end around 16:00 CET. Precise information will be provided to the participants in due time.

Additional information

Coordination: Sofia Georgakopoulou, Eva Pujadas

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.