Introduction to the LabKey data management tool

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 objectives

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)

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 1) the data can be imported, analysed and visualized and 2) 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 are required to bring your own laptop. 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. This includes course content material and coffee breaks. Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set is set to 18/11/2019. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

University of Basel, Klingelbergstrasse 61, SkyLounge Biozentrum Annex, 13th Floor.

The course will start at 9:00 and end around 17:00. Precise information will be provided in due time.

Additional information

Coordination: Sofia Georgakopoulou, Geoffrey Fucile

The preparation of this course benefited from support of the EnhanceR project.

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.