Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
Conference Contributions (7)
J. P. Thiele, and O. Dössel. Fast optical recording of membrane potential in rat trabecular muscle with a triggered CCD-system: a preliminary study. In Gemeinsame Jahrestagung der Deutschen, der Österreichischen und der Schweizerischen Gesellschaft für Biomedizinische Technik, vol. 51(V 175) , 2006
The paper presents a simulation of the transient temperature distribution in the human body caused by induced eddy currents during magnetic resonance imaging (MRI). In a first simulation the validity of the used heat conduction equation was proven using a simple example of a cool-down-process of a sphere. Thereafter the heating of a phantom model with an implanted electrode placed in a MRI-System (active body coil) was examined. The resulting increase in temperature was compared with existing measurements. Finally the implications of the heating of the tissue are discussed based on the observed experimental and numerical results.
M. Janich, G. Seemann, J. Thiele, and O. Dössel. Elastic registration of optical images showing heart muscle contraction. In 4th European Conference of the International Federation for Medical and Biological Engineering ECIFMBE 2008, vol. 22(7) , pp. 676-679, 2008
Image registration is used to reduce movement artifacts caused by contracting heart muscle in transmembrane voltage measurements using fluorescence microscopy. The applied registration methods include Thin-Plate Splines (TPS) and Gaussian Elastic Body Splines (GEBS). Landmarks are established automatically using regional cross-correlation. Then these landmarks are filtered for meaningful correspondences by requiring a minimum correlation coefficient and clustering adjacent and identical displacements. Registration of an image sequence showing a contracting muscle is realized by spatially aligning the images at maximum contraction and at rest. For the other images the movement of the muscle is interpolated using an analytical description of the contraction of heart muscle.TPS cause amplification of displacements at the image border, while GEBS restrict landmarks influence to a local region. Over a set of 81 images GEBS are shown to register images better and more robust than TPS, which in some cases cannot reduce movements. Validation through visualization of transmembrane voltages on contracting muscle reveals that GEBS registration removes movement artifacts better than TPS. Image regions with prominent structures are successfully tackled by GEBS registration.
M. A. Golombeck, J. Thiele, and O. Dössel. Magnetic resonance imaging with implanted neurostimulators: numerical calculation of the induced heating. In Biomedizinische Technik, vol. 47-1, pp. 660-663, 2002
Magnetic resonance imaging (MRI) is still contraindicated in patients with implanted active medical devices, as the applied radiofrequency (RF) fields can lead to significant heating of the implants and the electrodes. A head model with an implanted deep brain stimulation electrode (DBS) was exposed to a continuous RF-field similar to the excitational field used in MRI at a frequency of 64 MHz. In this study a two-step procedure for the accurate estimation of electrode-heating during MRI is presented. First the energy loss was calculated in the frequency domain during an applied RF-pulse. Then a thermodynamic algorithm taking heat transfer mechanisms into account was used. The applied method showed to be numerically stable and gave more accurate results than first calculated using a simple worst-case approximation.
J. Thiele. Optische und mechanische Messungen von elektrophysiologischen Vorgängen im Myokardgewebe. Universitätsverlag Karlsruhe. Dissertation. 2008
Die vorliegende Arbeit befasst sich mit der optischen Erfassung von elektrischen Signalen im Herzen, welche eine kontaktlose Messung der elektrischen Signale von der Herzoberfläche ermöglicht. Hieraus lassen sich elektrophysiologische und mechanische Parameter bestimmen, welche für die Erstellung von virtuellen Computermodellen des menschlichen Herzens essentiell sind. Mit rechnergestützten Simulationen können z.B. Erkrankungen im Herzen nachgestellt und deren Auswirkungen beobachtet werden.
Student Theses (2)
J. Thiele. Eine Simulation der thermischen Belastung von Patienten durch Einkopplung hochfrequenter elektromagnetischer Felder. Institut für Biomedizinische Technik, Universität Karlsruhe (TH). Diplomarbeit. 2002
J. Thiele. Rekonstruktion bioelektrischer Quellen-Modellierung und Evaluierung mit einem Phantom. Universität Karlsruhe (TH), Institut für Biomedizinische Technik. . 2000