Chair: Eetu Mäkelä (Aalto)
Samuli Ollila (NMRLipids/Aalto): Open Collaboration Method Developed in NMRlipids Project
Abstract:
The NMRlipids project is an Open Collaboration project running at nmrlipids.blogspot.fi. The main goal of the project is to find a model which correctly captures the atomistic resolution structure and dynamics of lipid membranes present in cells of living organisms. Such a model would be highly useful, for example, in structural biology, molecular medicine and drug design. The project started in 2013 from the comparison of lipid membrane simulation data with experimental NMR data, which clearly showed that the most used lipid model predicts unrealistic structures and incorrect interactions between membranes and other biomolecules. Consequently, the observations questioned several conclusions in the literature.
In the traditional scientific discourse my options were to immediately publish the findings in a scientific journal or continue the work by testing and improving different models and publish more extensive study later. In practise, the latter option was beyond the resources available for myself or any individual research group. On the other hand, I was suspecting that more extensive evidence would be needed to change the general opinion in the field.
Together with Dr. Markus Miettinen we decided to solve the problem by applying an alternative approach, inspired by the Polymath project (https://en.wikipedia.org/wiki/Polymath_Project) and Linux, to disseminate and progress science. The initial findings were first published in arXiv [1] and then the NMRlipids project was launched at nmrlipids.blogspot.fi. At this point an open invitation was presented for the community to test and improve available lipid models against the experimental NMR data, and report the progress through NMRlipids blog. The contributors were attracted by offering authorship in the peer reviewed publications to be produced by the project.
The NMRlipids project has now published three peer-reviewed publications [2-4], two sub-projects are running at their early stage and there are total ~600 contributions made by 28 contributors. The main goal has not yet been reached, however, the progress has been significantly faster than in traditional scientific discourse. The Open Collaboration workflow optimized during the project can be extended also for wider usage.
In the Open Collaboration all the content from raw data to the final manuscript and their documented history are all the time publicly available for viewing and modifications (for example see NMRlipids project: nmrlipids.blogspot.fi, https://github.com/NMRLipids). This is a significant advancement for the traditional scientific discourse where only the final version of manuscript is publicly available.
[1] O. H. Samuli Ollila, Response of the hydrophilic part of lipid membranes to changing conditions — a critical comparison of simulations to experiments. arXiv:1309.2131v1 (2013)
[2] A. Botan, F. Favela, P. Fuchs, M. Javanainen, M. Kanduc, W. Kulig, A. Lamberg, C. Loison, A. Lyubartsev, M. S. Miettinen, L. Monticelli, J. Määttä, O. H. S. Ollila, M. Retegan, T. Rog, H. Santuz and J. Tynkkynen, Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions, J. Phys. Chem. B, 119 (2015) (49), pp 15075–15088, DOI:10.1021/acs.jpcb.5b04878
[3] O.H. S. Ollila and G. Pabst, Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments, Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858 (2016) 2512–2528, DOI:10.1016/j.bbamem.2016.01.019
[4] A. Catte, M. Girych, M. Javanainen, C. Loison, J. Melcr, M. S. Miettinen, L. Monticelli, J. Määttä, V. S. Oganesyan, O. H. S. Ollila, J. Tynkkynen and S. Vilov, Molecular electrometer and binding of cations to phospholipid bilayers, https://github.com/NMRLipids/lipid_ionINTERACTION/blob/master/Manuscript/LIPIDionINTERACT.pdf
About the speaker:
Dr Ollila earned his PhD in biophysics from Tampere University of Technology and he currently works as a postdoctoral research fellow at the University of Helsinki Institute of Biotechnology. He is the co-founder of the The NMRlipids project, an open scientific collaboration project to understand the atomistic resolution structures of lipid bilayers which was started to experiment new ways of sharing and progressing scientific information by using the modern networking techniques.
Jeffrey Witt (Loyola): Texts as Networks: The Promise and Challenge of Publishing Humanities Texts as Open Data Networks
Abstract:
Using the Scholastic Commentaries and Text Archive (http://scta.info) as a case study, this talk will focus first on the power and potential of open data for the future of humanities research, particularly for our understanding of text corpora and text traditions. Open and collaborative textual data allows us to offer scholars re-usable data. Such data can then be manipulated for a variety of purposes. It can be used to allow scholars fine-tuned access to every aspect of the corpora (on-demand collation, manuscript consultation, and faceted searching). It can be used for various forms of web publication and traditional print publication. Finally, it can also be used for large corpus-wide analysis on a scale never before thought possible.
Second, this talk will argue that these possibilities only emerge when we begin to think about texts differently, namely as open distributed networks of data rather than isolated documents. The focus will turn here to the problems and challenges of creating this kind of paradigm shift. In particular we will highlight two challenges: the challenge of developing common data models and shared ontologies for our texts and the challenge of developing community adoption of these models, ontologies, and open standards.
About the speaker:
Prof. Witt earned his PhD in philosophy from Boston College and he is currently an assistant professor at Loyola University Maryland. He has focused on questions of faith and reason in medieval philosophy. He also has an interest in digital humanities. He is currently the director of the Scholastic Commentaries and Texts Archive (http://scta.info), which is a metadata archive built and aggregated from transcriptions and questions lists of medieval Sentences commentaries and other scholastic texts. He is based in Baltimore, Maryland (USA).