Beilstein Symposium - Open Science and the Chemistry Lab of the Future
DOI (series): 10.5446/s_988
9
2017
39
1 hour 24 minutes
9 results
07:57
5McEwen, Leah et al.Interview with Leah McEwen: Cornell University, Ithaca, USA, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Leah McEwen discusses libraries in transformation with Carsten Kettner. The Physical Sciences Library at Cornell dispersed stacks in 2009, so they are operating totally electronically since nearly 10 years. The library is becoming more digital and getting closer to research process, supporting scientists with publication preparation, data management, working with publishers and repositories. The Cornell University Library system has a technical team of database developers, ontologists, and other technical specialists working with librarians who have specific domain knowledge in various disciplines. A challenge for the Physical Sciences Library today is visibility, which means going out and getting to know the scientists and students, and also describing the value-add can be more difficult now that information access is no longer via printed works. Leah, who is the chemistry librarian at Cornell, enjoys getting beyond the formal aspects and getting to grips with the data. At the symposium Leah has described projects involving environmental health and safety – which necessitates working closely with researchers. In terms of health and safety, chemists look at chemistry on the molecular level; most issues which occur have to do with the transportation of chemicals on the macro level. Students do not generally have any lab background, so they need special consideration. Students are required to do risk assessment exercises during the course. Researchers are not yet required to do safety assessments in the US. Leah is hopeful that this will change.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
11:39
Cronin, Lee et al.Interview with Lee Cronin, University of Glasgow, UK, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Lee Cronin discusses digitizing chemistry with Carsten Kettner. Lee describes his ideas for digitizing the practical process of making molecules, by converting the synthesis information into a code which then can be used by other chemists or automated systems to playback the process and produce the molecule. By automating the parts of chemistry research that are repetitive and error prone we can free up time for researchers to allow them to be more creative and productive. Digitization will also enable chemists to make molecules that they currently are unable to make, give better reproducibility, speed up many processes and lead to more discoveries. Lee’s dream is to make complex molecules from a set of reactions using a small number of lines of synthetic code. This requires a programming approach to digitizing chemistry and will enable reactions that were previously regarded as too messy, to become optimized by robots to work using “fly-by-wire” chemistry. In biology robots are routinely used, in chemistry this is more unusual. In Lee’s opinion this is due to various factors including: cultural, safety, affordability, and flexibility (chemists are more flexible than robots). To make the most of automation, chemists need to apply a more uniform approach to their work, but this apparent limitation will allow them to do more and enable them to exchange the practical process of making molecules more efficiently. Digitization will enable personalized medicine, allow the global access to medicines, drive customization and innovation, and help discover new molecules that may have profound importance.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
06:32
7Tochtermann, Klaus et al.Interview with Klaus Tochtermann, Leibniz Information Centre for Economics, Kiel, Germany, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Klaus Tochtermann discusses the European Science Cloud (EOSC) with Carsten Kettner. He describes the concept for the ESOC which is planned to connect current and future research data centers with one another in an eco-system of infrastructures. Also discussed are the standards necessary to make such an eco-system function: standards for metadata, standards for APIs and standards for authentication. He stressed the need for scientists to make their data FAIR (findable, accessible, interoperable and reusable), to support cross-disciplinary research and re-use. In the EOSC all data should be FAIR. Klaus mentions that in the opinion of the high level expert group on EOSC, about 80% of the reasons that scientists do not share data are cultural, mainly due to the lack of sufficient incentives.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
08:07
6Frey, Jeremy G. et al.Interview with Jeremy G. Frey: University of Southampton, UK, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Jeremy Frey discusses uncertainty in chemistry with Carsten Kettner. Uncertainty in what scientists have done, what you may have done yourself, uncertainty in the results that come out – essentially anything. His own approach to research is to find ways to minimize all types of uncertainty. The first step is of course to document oneself exactly what one did; the problem being that when one carries out an experiment for the first time, one does know what information is essential. On the one hand scientists need better training, but on the other it is sometimes very difficult to describe experiments and give a foolproof description of the method to allow reproducibility. A scientist, who is doing something completely new, pushing at the boundaries, will probably not be able to reproduce the results satisfactorily until the process is fully understood. And it is important for people in science and in the media to realize that at the cutting-edge of discovery, initial lack of reproducibility can be expected and is acceptable. Jeremy concludes that it is vital to correctly manage uncertainty in science.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
11:31
1Bruno, Ian et al.Interview with Ian Bruno: Cambridge Crystallographic Data Centre, Cambridge, UK, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Ian Bruno is discussing making open science sustainable with Martin Hicks. Ian makes the point that simply making data sets available is not sufficient, they need to be discoverable and re-usable. He outlines how the Cambridge Crystallographic Data Centre (CCDC) started producing the Cambridge Structure Database over 50 years ago, and over time have had different models to ensure its sustainability. In the internet era, the challenge has been to provide a level of free access, whilst generating income through the value added services and software that work on top of the database. Sustainability is not just an issue of financial support, but is also driven by the user base. Here the CCDC set up a network of national affiliated centers, responsible originally for the distribution of the database – then on tapes. Nowadays this network helps in attracting funding for local academics to receive the value added services. The driver of sustainability of a resource is its scientific value. Ian discussed the idea of the scholarly commons and different ways of communicating science, in particular looking at the underlying research objects that contribute to a story. To improve discoverability we need to address the issues of publish and perish paradigm, and develop workflows that are much more closely related to the research that people are doing. Here we need the appropriate levels of documentation or meta-data associated with those research objects so that people are able to find them. In terms of standards for chemical structures, Ian notes that people are currently using de-facto standards and have built workflows around them, and thus they will be reluctant to change. There are currently discussions underway, to ensure that the specification of these formats and extensions are made openly accessible.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
09:51
3Rzepa, Henry et al.Interview with Henry Rzepa: Imperial College London, UK, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Henry Rzepa discusses metadata in chemistry with Carsten Kettner. Before the interview moves on to things chemical, Henry recounts his over 300000 miles of motorbike riding in London visiting the many rivers. The discussion started with the meaning of the term “meta”; in this context metadata refers to the data that are needed to describe data, thus metadata are actually more important and more interesting than the data. The question of format for metadata was raised; whilst the format is not so important, one still needs to query it, so it is necessary to know how to ask the right question. It is important to remember that when building a repository, any mistakes would be permanent. But here, good metadata can help; in the curation of data – correcting errors, bringing it up to date, putting it in a more modern form, and hence giving the data a longer life. Metadata helps make data FAIR; Findable, Accessible, Interoperable and tells you how you can Reuse it. When discussing standards for metadata, Henry raised the issue of understanding what a bond is. Most chemists think they know what a bond is, but in reality probably don’t really know, which means that they are going to need to reach an agreement on how to describe them. In Henry’s view, chemists are like cats, it is very difficult to get more than 4 chemists to agree on anything. But to make things work we need open community efforts. Henry is interested in chemical reactions and their transition states and has modeled them in InChI. For him it is import not to discuss hypothetical or abstract descriptions of how to do something but to actually to try things out, get an example out for the community to use. You have to build real things, and take them a part again – that is how science works.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
04:57
4Lisacek, Frédérique et al.Interview with Frédérique Lisacek: Swiss Institute of Bioinformatics, Geneva, Switzerland, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Frédérique Lisacek is talking with Carsten Kettner about challenges for scientific databases. In Switzerland, at the Swiss Institute of Bioinformatics there are two groups responsible for setting up databases in bioinformatics; one in Geneva looking traditionally at protein data, for example SwissProt, and one in Lausanne looking into DNA data. The main challenge in hosting and maintaining data collections is infrastructure, both in terms of hardware and information curation, i.e. carried out by experts in the corresponding field. Financing curation is a big challenge as it does not traditionally fit in either research or infrastructure. Frédérique tells how important standards are. They need to be developed between people who have the scientific knowledge and people who have the technical knowledge. The coexistence of several standards for the same thing is probably an advantage as no one standard will be able to capture all aspects; however, we should narrow the number down
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
13:41
11Bruno, Ian et al.Interview with Ian Bruno, Stuart Chalk, Martin Hicks, Carsten Kettner, Leah McEwen, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). At the end of the Beilstein-Institut’s symposium on Open Science in Chemistry, Carsten Kettner interviews the panel of Ian Bruno, Stuart Chalk, Martin Hicks and Leah McEwen on themes and perspectives for open science in chemistry that came out of the meeting. Listen to the answers on the following themes: 1) Open science and chemistry. Is it a contradiction? 2) Are chemists behind other disciplines, because for example in physics or biology, the projects are often bigger and require collaboration? In chemistry, the projects are often sufficient for one group to carry out. 3) What is the perspective for the chemistry lab of the future? The panel, each an expert from a different area of communicating chemical science information, gave some fascinating insights on how chemistry research might move to become more open, with more collaboration, and a higher degree of digitization in the laboratory. It will be interesting to see how many of these predictions come true.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften
09:47
2Todd, Matthew et al.Interview with Matthew Todd, The University of Sydney, Australia, recorded at the BEILSTEIN OPEN SCIENCE SYMPOSIUM (22 – 24 May 2017). Matt’s view of open science in chemistry is to share everything that you are doing as you are doing it allowing others to reuse your data in their own work. At the moment there are not that many scientists being completely open. Currently, when publishing articles in journals we mainly publish positive results, plus we keep things secret due to protecting potential IP. This inhibits free-flow of data and knowledge. The best order of events would be to publish data and then publish an article as a summary of the project. This allows other people to get better insights and the scientific record will be more complete. It is also important to share what we don’t know. The Open Source Malaria project is a good example of this. Other scientists spot issues that need to dealt with, or suggest other compounds that can be made, provide new insights and generally speed up and improve the project. There is resistance to being open in case you miss some important insight that would then be made by others. In academia it is still important to been seen as owning something, but this inhibits science. Matt believes that we have gone too far with protection of IP and the expectations of what IP research projects would be able to generate.
2017Beilstein-Institut zur Förderung der Chemischen Wissenschaften