ENTRY743

Identification Info

Kind:

Sample

Type:

ENTRY

Registrator:

fabian.plass

Registration Date:

2022-08-09 12:23:57.788513

Modifier:

fabian.plass

Modification Date:

2023-07-26 12:09:05.070674

Parents

ENTRY3602

Children

ENTRY3603

Properties

Name:

Current situation, methodology, and strategy

Document:

Current situation, methodology, and strategy


 

3.1. Current situation from an interdisciplinary point of view

 

The scope of Open Science and research data management, as well as a clear and well-defined data stewardship and governance, has been clearly recognized from the perspective of the DFG-funded Collaborative Research Centre (CRC) 1411 Design of Particulate Products. However, an ELN-LIMS is currently lacking for the use within an interdisciplinary field between engineering, material sciences, natural sciences, mathematics, theoretical modeling and simulation. Furthermore, commercial systems are generally not recommended by the possible financial conditions, in addition to a thereby complementary Open Science policy. Open-source products like chemotion are, again, too subject-specific (here in the particular case chemistry), which would lead to a less beneficial impact on interdisciplinary work and research, such as lower usability, and, thus, in the end, also acceptance in other subject groups. The openBIS system of the Department of Biosystems Science and Engineering and Biology of the ETH Zurich (Barillari et al, 2016; Bauch et al, 2011), on the other hand, shows some promising features that are worth a closer look, even though this system was designed primarily for biological and medical disciplines and is used not only by academic institutions but also by companies in the industry sector(Bauch et al, 2011). 

Accordingly, we describe our system in several subsections, starting with the basic principles and working features of openBIS, continuing with the goals and requirements of researchers within the CRC and the scientific community for a well-functioning ELN tool, and ending with its implementation and usage. OpenBIS is, besides other ELN-LIMS examples, a good starting point and framework to foster cooperativity via a digital environment using an electronic lab notebook version and by fulfilling the requirements by the DFG and NFDI consortia like FAIRmat (for materials science, physics, chemistry, and mathematics) with respect to data management, handling, storage, and publishing. In addition, we also want to share our experiences in further developing the system and its implementation and daily use.

 

3.2. General overview and structure of openBIS

 

Before we shed light on how openBIS can help us with a successful implementation of a beneficial RDM, we first clarify i) what openBIS is, ii) how it works, and iii) what technical requirements need to be met. OpenBIS is an open-source platform that functions both as an Electronic Laboratory Notebook (ELN) and as a Laboratory Information Management System (LIMS). Developed by ETH Zurich, openBIS provides an open-source database for research laboratories, especially designed and implemented in and for life sciences (Barillari et al, 2016). The goal was to build a simple and efficient, yet comprehensive ELN-LIMS system that meets the daily needs of a research institution. Everyday things like storage of materials, instrumental setups and devices, the acquisition, description, and processing of large amounts of data, and the forwarding to possible users and scientists within the openBIS system should be possible (Bauch et al, 2011).

However, the questions arise what kind of technical conditions are needed to build openBIS within a research group and if openBIS is scalable and if such system in the area of a scientific network (EU or DFG fund) or even a comprehensive database within an entire university is conceivable at all. All of these questions are important to know before starting with an ELN-LIMS and will be discussed in the following subsections accordingly. 

The history of openBIS and its platform, on which it is based, started in 2007 and is still actively maintained, nowadays by the Scientific IT Service Team of the ETH Zurich. As operating system (OS), openBIS requires a modern Unix-like OS, for instance Linux systems. However, openBIS can be run on virtual machines and docker containers and is, therefore, mainly platform-independent. A very interesting and detailed look on the general technical background of openBIS is provided by the developers, accordingly (Bauch et al, 2011). Therefore, shortly summarized, in openBIS, an Application Server (AS) and one or several Data Store Server(s) (DSS) are introduced. On the AS, data provenance actions like metadata handling are conducted while on the DSS, the raw data is managed. While, exemplarily, the user access is facilitated via a web browser, the AS uses a Relational Database Management System (RDBMS) to generate persistent information like index information about all data sets, the data itself is covered and stored within the (several) DSS system(s). The latter is responsible for creating, querying, and visualizing data while they are mediated by the AS(Bauch et al, 2011). At the application side, the ELN-LIMS system is accessible browser-based (recommended Chrome, Firefox and Safari) and is reachable from any electronic device as well as operating system. 

Moreover, as part of our INF project of the CRC 1411 (see also Funding information), we want to further extent the concept of ELN-LIMS to a more virtual research environment in the following years (see also section 4.2 for further information). We, in the CRC 1411, as well as probably the most part of the research community, sees VREs, among others, as working environment tool with collaborative and requirements-tailored elements in a web-based environment (Allan, 2009; Candela et al, 2013; Lave and Wenger, 1991). The DFG defines 'Virtuelle Forschungsumgebung' (a literal translation of 'Virtual Research Environment') as a platform for internet-based collaborative working that enables new ways of collaboration and a new way of dealing with research data and information (Reimer and Carusi, 2010).