As already covered several times in our blog, Free Open Source Software (FOSS) is an integral part of our everyday life. However, FOSS is not only a relevant factor in private life or in business, but of course also in science.
In this context, Free Open Source Software and concepts derived from it fulfil several roles. On the one hand, it is about the usability of tools, information, data and methods for scientists themselves; on the other hand, the concept of verifiability, accessibility and reproducibility is often summarised under the collective term “Open Science” and, derived from this, “Open, Reproducible Research”. [1, 2, 3]
Access for Science
In science, it has always been common to provide results that are complete, verifiable and reproducible. In fact, this is exactly a principle of scientific work. But this is also often a major difficulty, because it is not always easy or even possible to provide the research community with all the necessary information and resources. This is often due to licensing or practical reasons, for example in the case of special data sets or the necessary computing power of certain methods. This is especially true in the case of empirical research. [2, 4]
Problems arise, for example, because not all data sets are freely available. Scientists working at universities and other research institutions usually have separate access to data sets and literature, but this often involves high costs and a lot of effort. Actual “Open Data” resources are rare, especially in social and economic scientific research (in Germany). [1, 2, 4, 8]
Further access restrictions arise in connection with the software packages used for research. Especially in the past, analysis or organisational software was often proprietary and expensive. In the past two decades, however, a clear trend reversal can be seen here. [2, 4]
More and more software is not only being made available to research institutions free of charge, but is often being placed completely under an open source licence. This not only allows the software to be used much more cost-effectively or even free of charge, but researchers from a wide range of fields can even contribute to the development and improvement of the software in order to make their research work easier. [2, 4, 5, 6, 7, 8]
Open Science and Open Reproducible Research
However, the use of free open source software in science has another side effect in addition to facilitating access for scientists. The reproducibility of research results is made much easier because others can use the same software without additional costs or effort, and there are often no longer any licensing restrictions. [2, 4, 5]
This circumstance, which sounds quite trivial at first, also leads to the fact that the exchange among researchers is significantly simplified. In addition to basic principles, methods and information of a theoretical nature, programme codes, analysis scripts and entire software frameworks can now be exchanged among each other and new research can be created based on them. [2, 4, 5]
Although the demands and complexity of research in general are continually increasing, it is now easier than ever to draw on the approaches and work of others, not least through the use of free Open Source Software and the application of Open Science approaches, and to deliver new research results based on this. [2, 4, 5]
In this context, the use of Free Open Source Software thus usually enables (or at least considerably facilitates) free access to the research work as well as Open Reproducible Research. This in turn leads to free and collective exchange – the basic premise of modern science – which then usually leads to the improvement and expansion of Open Source Software and Open Science. [2, 4, 5]
Examples
Open Source in Medicine
Open source research collaborations are an important and timely strategy to drive and potentially accelerate medical innovation, including in the field of neglected diseases, where knowledge sharing is even more important than in other areas.
– Els Torreele, Doctors without Borders
In medicine in particular, the advantages of the Open Science or Open Source approach are obvious. Medical research is usually very expensive due to its complexity and high number of test phases. Accordingly, sharing knowledge in the form of research results, software, codes and data can minimise the costs for the individual institution and at the same time maximise the benefits of the researched knowledge. As a result, vital medicines can be offered in greater numbers and at lower prices.
In practice, there are numerous points of contact for Open Source in medical research: [9]
1. Open Source Bioinformatics
In bioinformatics, mainly computer-based methods for the analysis of biological data are used and further developed. In addition to publishing the results, the corresponding data, codes and software can also be made available Open Source in the sense of the open science approach, so that other research teams can use them for further questions.
2. Open Source Pharma
Open Source Pharma is a movement that actively advocates for open access to important medicines and therapeutic interventions. In doing so, they advocate not only the sharing of important results, data and codes, but also more open funding models for research and distribution of medicines, as well as the establishment of more open licences and patents, as strict patent protection in particular can inhibit a more equitable distribution of important medicine. The best-known open source pharmaceutical project is probably Open Source Malaria, which enables the cheap supply of previously $750 expensive malaria drugs. [10]
3. Open Source AI Projects
Artificial intelligence (AI) is also being put to good use in medicine. Modern AI algorithms are used in particular for diagnostic purposes, e.g. for cancer diagnosis, and for gene sequencing. Large amounts of data are needed for a meaningful application of AI. Therefore, in addition to the research results, the data sets and the algorithms should also be published.
The OpenScience Project
The OpenScience Project consists of scientists who actively promote scientific Open Source software. In addition to developing open source software on their own, the OpenScience Project collects links and information about existing software and publishes them to promote awareness. From physics to geography to archaeology, the OpenScience Project supports practical open source projects in all academic fields. [11]
Open Source is used meaningfully every day in science in all areas. We would like to make our contribution to highlighting its benefits and creating awareness of it.
Sources
- Universität Konstanz (2022): Open Science – Offene Wissenschaft. URL: https://www.kim.uni-konstanz.de/openscience/was-bedeutet-open-science/
- OpenScienceASAP (2022): Was ist Open Science?. URL: http://openscienceasap.org/open-science/
- Interfakultatives Institut für Angewandte Kulturwissenschaft der Universität Karlsruhe (1998): Öffentliche Wissenschaft. In: iak newsletter, Jg. 1, Heft 1, S. 3–4.
- Dang, S. (2017): Transparenz statt Ruhm und Ehre? Chancen und Risiken von Open Science. URL: https://hochschulforumdigitalisierung.de/de/blog/chancen-und-risiken-von-open-science
- Bandyopadhyay, A. (2018): How Open Source Approach is Impacting Science. URL: https://itsfoss.com/open-source-impact-on-science/
- Felix Schönbrodt, Anna Baumert, Andreas Glöckner, Mitja Back, Ruben Arslan: Netzwerk der Open-Science-Initiativen (NOSI). 27. September 2022
- European Comission (2019): Open Science. URL: https://research-and-innovation.ec.europa.eu/strategy/strategy-2020-2024/our-digital-future/open-science_en
- Hanwell, M. (2022): What is open science? URL: https://opensource.com/resources/open-science
- Bandyopadhyay, A. (2018): How Linux and Open Tech Empower Medical Healthcare. URL: https://itsfoss.com/medical-linux-ai-blockchain/
- Bandyopadhyay A. (2018): New Leads for Malaria Discovered: Open Source Pharma FTW! URL: https://itsfoss.com/malaria-open-source-pharma/
- Gezelter, D. (2022): The OpenScience Project. URL: http://openscience.org/
Jan is co-founder of ViOffice. He is responsible for the technical implementation and maintenance of the software. His interests lie in particular in the areas of security, data protection and encryption.
In addition to his studies in economics, later in applied statistics and his subsequent doctorate, he has years of experience in software development, open source and server administration.
Pascal founded ViOffice together with Jan in the fall of 2020. He mainly takes care of marketing, finance and sales. After his degrees in political science, economics and applied statistics, he continues to work in scientific research. With ViOffice, he wants to provide access to secure software from Europe for everyone and especially support non-profit associations in their digitalization.