Automation is Documentation: Functional Documentation of Human-Machine Interaction for Future Software Reuse

Preserving software and providing access to obsolete software is necessary and will become even more important for work with any kind of born-digital artifacts. While usability and availability of emulation in digital curation and preservation workflow has improved significantly, productive (re)use of preserved obsolete software is a growing concern, due to a lack of (future) operational knowledge. In this article we describe solutions to automate and document software usage in a way, such that the result is not only instructive but also productive

How Long Can We Build It? Ensuring Usability of a Scientific Code Base

Software and in particular source code became an important component of scientific publications and henceforth is now subject of research data management.  Maintaining source code such that it remains a usable and a valuable scientific contribution is and remains a huge task. Not all code contributions can be actively maintained forever. Eventually, there will be a significant backlog of legacy source-code. In this article we analyse the requirements for applying the concept of long-term reusability to source code. We use simple case study to identify gaps and provide a technical infrastructure based on emulator to support automated builds of historic software in form of source code. &nbsp

Preserving Secondary Knowledge

Emulation and migration are still our main tools for digital curation and preservation practice. Both strategies have been discussed extensively and have been demonstrated to be effective and applicable in various scenarios. Discussions have primarily centered on technical feasibility, workflow integration, and usability. However, there remains one important aspect when discussing these two techniques: managing and preserving operational knowledge. Both approaches require specialized knowledge but especially emulation requires future users to also have a great variety of knowledge about past software and computer systems for successful operation. We investigate how this knowledge can be stored and utilized, and to what extent it can be rendered machine-actionable, using modern large language models. We demonstrate a proof-of-concept implementation that operates an emulated software environment through natural language

CiTAR - Preserving Software-based Research

In contrast to books or published articles, pure digital output of research projects is more fragile and, thus, more difficult to preserve and more difficult to be made available and to be reused by a wider research community. Not only does a fast-growing format diversity in research data sets require additional software preservation but also today’s computer assisted research disciplines increasingly devote significant resources into creating new digital resources and software-based methods. In order to adapt FAIR data principles, especially to ensure re-usability of a wide variety of research outputs, novel ways for preservation of software and additional digital resources are required as well as their integration into existing research data management strategies. This article addresses preservation challenges and preservation options of containers and virtual machines to encapsulate software-based research methods as portable and preservable software-based research resources, provides a preservation plan as well as an implementation. &nbsp

Study of the piezoresistivity of doped nanocrystalline silicon thin films

The piezoresistive response of n- and p-type hydrogenated nanocrystalline silicon thin films, deposited by hot-wire (HW) and plasma-enhanced chemical vapor deposition (PECVD) on thermally oxidized silicon wafers, has been studied using four-point bending tests. The piezoresistive gauge factor (GF) was measured on patterned thin-film micro-resistors rotated by an angle θ with respect to the principal strain axis. Both longitudinal (GFL) and transverse (GFT) GFs, corresponding to θ = 0° and 90°, respectively, are negative for n-type and positive for p-type films. For other values of θ (30°, 45°, 120°, and 135°) GFs have the same signal as GFL and GFT and their value is proportional to the normal strain associated with planes rotated by θ relative to the principal strain axis. It is concluded that the films are isotropic in the growth plane since the GF values follow a Mohr’s circle with the principal axes coinciding with those of the strain tensor. The strongest p-type pirezoresistive response (GFL = 41.0, GFT = 2.84) was found in a film deposited by PECVD at a substrate temperature of 250 °C and working pressure of 0.250 Torr, with dark conductivity 1.6 Ω−1cm−1. The strongest n-type response (GFL =− 28.1, GFT =− 5.60) was found in a film deposited by PECVD at 150 °C and working pressure of 3 Torr, with dark conductivity 9.7 Ω−1cm−1. A model for the piezoresistivity of nc-Si is proposed, based on a mean-field approximation for the conductivity of an ensemble of randomly oriented crystallites and neglecting grain boundary effects. The model is able to reproduce the measured GFL values for both n- and p-type films. It fails, however, to explain the transversal GFT data. Both experimental and theoretical data show that nanocrystalline silicon can have an isotropic piezoresistive effect of the order of 40% of the maximum response of crystalline silicon.Fundação para a Ciência e a Tecnologia (FCT) - PTDC/CTM/66558/2006, bolsa de investigação SFRH/BSAB/883/200

Modeling dose-response relationships of the effects of fesoterodine in patients with overactive bladder

<p>Abstract</p> <p>Background</p> <p>Fesoterodine is an antimuscarinic for the treatment of overactive bladder, a syndrome of urgency, with or without urgency urinary incontinence (UUI), usually with increased daytime frequency and nocturia. Our objective was to develop predictive models to describe the dose response of fesoterodine.</p> <p>Methods</p> <p>Data from subjects enrolled in double-blind, placebo-controlled phase II and III trials were used for developing longitudinal dose-response models.</p> <p>Results</p> <p>The models predicted that clinically significant and near-maximum treatment effects would be seen within 3 to 4 weeks after treatment initiation. For a typical patient with 11 micturitions per 24 hours at baseline, predicted change was -1.2, -1.7, and -2.2 micturitions for placebo and fesoterodine 4 mg and 8 mg, respectively. For a typical patient with 2 UUI episodes per 24 hours at baseline, predicted change was -1.05, -1.26, and -1.43 UUI episodes for placebo and fesoterodine 4 mg and 8 mg, respectively. Increase in mean voided volume was estimated at 9.7 mL for placebo, with an additional 14.2 mL and 28.4 mL for fesoterodine 4 mg and 8 mg, respectively.</p> <p>Conclusions</p> <p>A consistent dose response for fesoterodine was demonstrated for bladder diary endpoints in subjects with overactive bladder, a result that supports the greater efficacy seen with fesoterodine 8 mg in post hoc analyses of clinical trial data. The dose-response models can be used to predict outcomes for doses not studied or for patient subgroups underrepresented in clinical trials.</p> <p>Trial Registration</p> <p>The phase III trials used in this analysis have been registered at ClinicalTrials.gov (NCT00220363 and NCT00138723).</p

CiTAR – Citing and Archiving Research

While the institutional introduction of infrastructure for the collection and conservation of primary scientific data is currently under construction or already exists, a parallel problem awareness arises for the associated models and methods, in particular for data evaluation. However, there is hardly any usable infrastructure and service offerings yet. Although the DFG recommendations on "good scientific practice" currently only recommend the retention of primary scientific data, the remainder of the recommendation refers to mandatory records of "materials and methods" that are not only necessary for comprehensible results but also for the publication process. If scientific results are to be reproducible, for example for an independent verification, a reconstruction of the experimental setup is necessary. However, in the digital age, with its extremely short life span (and availability) of hardware and software components, replicating a data processing process that is identical in all components can not be achieved solely on the basis of records. CiTAR (Citing and Archiving Research), a three-year Baden-Württemberg state project, develops infrastructure to support computer assisted research. One major outcome of this project are means to publish, cite and provide long-term access to virtual research environments. The aim of this project is to develop a cooperative, multidisciplinary technical-organizational service in order to support teaching and research in the further development of "good scientific practice". The service should provide data and scientific methods jointly citable and reproducibly in order to meet the requirements of modern journals. CiTAR realizes re-use of research data and long-term availability in terms of a modern research data management. To achieve the project objectives, three of the four bwFor HPC operators have joined forces to prototype a broader scope in the natural sciences, especially the computational and data-intensive scientific disciplines. The developed service provides automated import of virtual machines and popular container formats like Docker and Singularity. CiTAR assigns persistent identifiers to the imported research environments and provides ressources to re-run the archived objects with external data