Introduction

A digital lab in Constellab is a virtual environment where scientists can perform various tasks related to their laboratory activities, such as data storage, data visualization, pipeline development and more. This technology consists of a set of digital tools and resources, such as digital experiments, digital resources, digital reports, curated databases in open access, oriented biological resources, digital views and so more.

On-cloud, on-desktop or on-premises are three different ways of deploying digital labs in Constellab. With an on-Cloud subscription, your digital lab is shared accessed between all scientists within a space and fully managed by Gencovery. Individuals can also use an on-desktop version for free – this self-managed option aims to access to the same set of digital tools to work individually only, but digital resources can be exported on collaborative projects. Academics and enterprises seeking to utilize their own server can access on-premises digital labs.

To know more about digital labs in Constellab, you can watch the video about the virtual laboratory ecosystem or contact our sales department. Hereafter some complementary documentation in Community:

↗️ How to install an on-desktop digital lab (in French) ?

Digital experiments

A digital experiment is a digital procedure to conduct data analysis in order to explore or validate scientific hypotheses or to process your data in a production mode. Each digital experiment provides a no-code playground to run ready-to-use processes in several domains like data science, bioinformatics, modelling and more. A process in Constellab is a specialized scientific task or protocol that takes data as input and generates automatically various type of outputs (data, interactive plots, etc.).

Some processes are specialized scientific functions. To facilitate the organization and access to these tasks and protocols, they are grouped into bricks that serve as a library or collection of processes. Other processes are unspecialized functions like Live Tasks and Smart Tasks. Live tasks are fast and efficient tools to develop, test, use and share R or Python code snippets from the playground. And Smart Tasks democratize and accelerate data science for all scientists, based on a conversational dashboard powered by OpenAI, which generates Python code, interactive charts, and tables automatically.

Digital resources

A digital resource refers to all data-oriented objects manipulated within a digital lab. All digital resources are stored in the Databox (see the image below) and can be associated to projects. Digital resources can be gathered in a resource set. From each digital experiment, processes utilize resources as input and produce resources as output. Users can upload digital resources into the Databox or download them from external sources, such as another digital lab.

Resources can encompass various types of objects, including data files, folders, tables, images, and more. Each resource contains different views, which are utilized to generate visualizations of the data. For example, a table can be viewed in a spreadsheet-like format or visualized as a scatter plot.

Digital views

A digital view in Constellab is a representation of data from a specific digital resource. Resources can have multiple views, such as tables or plots, to navigate through data effectively. Users can create their own views or choose from pre-configured views tailored to specific processes. The majority of digital views in Constellab are interactive, allowing users to zoom and customize graphs. Views can be shared among users and added to reports for enhanced data visualization. All generated views are saved and accessible from experiments, the Resource page, and the Viewbox, which stores the history of all views.

Digital reports

A digital report is a scientific report that you can write to present the results of your experiment. These reports can be synchronized within a project (in your space), allowing your team to access them. In a digital report, you can include various elements such as interactive views of your results (like spreadsheets, plots...), mathematical formulas, images and videos.

Digital protocol templates

A digital protocol template allows you to create a protocol (a predefined series of connected and configured processes) that can then be reused by you, your team or the community. By using a protocol template, you can easily set up a new preconfigured experiment, ensuring consistency. Additionally, the protocol template can be shared with other labs, included in lab reports, or documented within Community.

CodeLab

For bioinformaticians and developers, Constellab has its own development environment. This environment is useful to develop and test libraries of processes (bricks). The development environment includes the Codelab, a pre-configured online IDE using VsCode. Bioinformaticians can easily develop their own brick or any code with Python and quickly test it. CodeLab also supports the Jupyter notebook and a R environment can be simply installed. Developers will also be able to establish a secure connection with remote code repositories (i.e. GitLab, GitHub) and transform their code into tasks for simplified use by all scientists.

The « Core Engine » of Constellab's digital labs is therefore distributed under the GNU General Public License version 3.0 (or later), which is an open source license. This license ensures that you consistently maintain the capability to develop and run your Constellab-based pipelines, guaranteeing your freedom to share and modify free software for your individual projects and businesses.