This repository contains protocols that are intended for testing Beta versions of LabBench. Beta versions of LabBench are versions of LabBench that are not yet officially released but are being tested by research groups collaborating with Inventors' Way as part of the LabBench Beta Program. The purpose of the LabBench Beta Program is a collaboration between researchers at academic institutions and the developers of LabBench that aims to create novel and open methods and devices for neuroscience research.
Currently, the following laboratories and sites participate in the LabBench Beta Program:
| Site | Principal Investigator | Area |
|---|---|---|
| Concordia Research Station, European Space Agency (ESA), Antarctica | Enrico De Martino | Research investigating the effect of isolated, confined, and extreme environments on pain sensitivity: A Longitudinal Study in High Altitude in Antarctica Beta Program focus: Development of functionality in LabBench for studying pain perception in isolated, confined, and extreme environments (Project selected by the European Space Agency, ICE Pain Study, AO-2021-Concordia_020) |
| The Clinical Research Facility at the University of Exeter | Sam Hughes | Research investigating the spinal mechanisms of endogenous pain modulation using neurophysiological measures. Beta Program focus: Develop optimised stimulation protocols for the reliable assessment of spinal nociception. |
| Klinik für Allgemeine Innere Medizin und Psychosomatik, Medizinische Fakultät Heidelberg | Jonas Tesarz | Research unraveling Pain Perception Processes through the Lens of Predictive Coding. Beta Program focus: Implementation and testing of novel computational modelling tasks targeting different pain modalities. These modalities may include electrical stimulation or cuff pressure, among others. The program aims to explore and evaluate the effectiveness of these new tasks in simulating and understanding different pain experiences. |
| Translational Biomarkers in Pain and Precision Medicine Research Group, Aalborg University | Laura Petrini | Research in how to assess pain in elderly and vulnerable populations. Beta Program focus: Development of functionality in LabBench for studying pain catastrophizing |
| Integrative Neuroscience Research Group, Aalborg University | Carsten D. Mørch | Research into the neuroscience of pain that aims at understanding the basic mechanisms of the pain system. Development of methods to investigate how nociceptors generate and mediate pain signals in healthy humans and pathological situations. Beta Program focus: Development of functionality in LabBench for Perception Threshold Tracking. |
| Center for Neuroplasticity and Pain (CNAP), Aalborg Univeristy | Carolina Ceruti | Research on reward and motivational pathways in pain perception. Beta Program focus: Functionality in LabBench for cuff pressure evoked potentials and its integration into psychophysical research paradigms for studying the mechanisms behind the reward and motivation pathways in pain |
| Neural Engineering and Neurophysiology Research Group, Aalborg University | Sabata Gervasio Daniel Skak Mazhari-Jensen |
Research on sensory thresholds and sensory processing in children with autism. Beta Program focus: Development of functionality in LabBench for studying sensory processing, such as auditory and tactile psychophysical tests, and functionality for recording auditory and tactile evoked potentials |
If LabBench does not adequately support your research and you would like to see that change, then write to (help@labbench.io) to become a member of this Beta program. By participating in this program, you will gain access to versions of LabBench before they become generally available, have its development tailored to fit your exact research needs, and have access to extensive support in running your experiments. In return the LabBench developers gain access to your expert knowledge and help in making LabBench better for your area of research.
The Beta version of LabBench is what we call a release candidate (rc) for the next upcoming release of LabBench; this means that it has yet to go through the official release process and contains experimental functionality yet to mature enough for general use.
Installation and use of LabBench Beta is done in close collaboration with the developers of LabBench. The current version of LabBench Beta can be downloaded from:
Portable version:
Installer:
To use protocols from the LabBench Beta Protocol Repository, you will need to add this repository to LabBench. There are two methods by which LabBench can access a repository:
- The repository is served from a web server and is accessed through its URL. The URL of the LabBench Beta Protocol Repository is https://labbench-society.github.io/Protocols.Beta/.
- The repository is available as a folder on the lab computer or as a folder on a network.
Method 1 can be used if you do not need to modify your protocol. Method 1 may be the case if the LabBench developers handle all of the protocol development for you as part of the LabBench Beta program. Method 2 is needed if you want to change the protocol by yourself.
Follow the URL in Method 1 for instructions on adding the repository to LabBench when accessed directly from Github. The rest of this guide assumes that you will need to change the protocols and will access the repository with Method 2.
To download a copy of the LabBench Beta Repository, click the <> Code button in the top right corner of this page. This opens a dropdown menu, in that menu select Download Zip:
Once you have downloaded the zip file with the repository's contents, the contents of a subdirectory (docs) in this zip file must be copied to a directory on your computer. We suggest placing it in C:\Tools\Repositories\Protocols.Beta.
Multiple directories exist within the downloaded zip file, as this file contains the entire site content you are now reading, including this guide.
The actual repository is located in the docs subfolder of this zip file, and it is the content of that directory that must be placed in the C:\Tools\Repositories\Protocols.Beta folder. If done correctly, the contents of this folder will look something like this once you copied the contents of the docs folder:
When you perform this installation, the repository hopefully contains many more subfolders (protocols); however, most importantly, the repository.xml must be located in the root of the C:\Tools\Repositories\Protocols.Beta folder, as it is this file that turns a folder into a LabBench Repository.
Without question, the best way to access a copy of the repository is to clone it (for members of the LabBench Society) or fork it (outside collaborators), as this will allow you to submit pull requests to have your changes merged back into the official repository. This way also provides a much higher degree of certainty that the version of your protocol will be preserved with no ambiguities about the protocol when you are to write your scientific papers.
If this is your preferred way of working with the repository, it means you are an accomplished Git user, and we will not insult you by providing a guide on how to Clone or Fork repositories.
If you are unfamiliar with Git but this has sparked your curiosity, here is a list of excellent Git tutorials. This guide is from the point of view of a software developer. Still, there are many similarities between the demands for version control and reproducibility in software development and scientific studies.
Adding a repository to LabBench, allow you to install protocols from this repository as experiments on your lab computer. In essence, to do anything with LabBench, you need access to a repository from which you can install protocols.
To add the LabBench Beta Protocol Repository you copied to C:\Tools\Repositories\Protocols.Beta previously, open the LabBench Designer program, go to the Protocols tab, and click the repository configuration button (marked with red in the figure below).
This opens the repository configuration dialog, in this dialog write or copy the path (C:\Tools\Repositories\Protocols.Beta) to the repository on the green line and click the ADD button:
This add the LabBench Beta Protocol repository to LabBench. You can now return to the Protocols tab by click the OK button.
To select the repository, click the dropdown in the upper left corner and select the beta.labbench.io repository.
Once your protocol is perfected and ready for your study, you are encouraged to submit the final protocol back to the LabBench Beta Protocol repository if you want the protocol saved for posterity.
How to do this depends on how you obtained a copy of the repository:
- [Download from Github]: Zip the your copy of the repository and place it in a storage that allows you to send a link to this file (such as Sharepoint or Dropbox (preferred). Then send this link to
help@labbench.io. - [Cloning or Forking the repository] Submit a pull request.