Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Two simple uses of Git for writing a thesis: reviewing & focussing

Git is a version control software, which helps software developers develop more software. Sounds complicated? It is! However, it has two features that you may find useful for writing (provided that happens in plain text files such as .txt, .md, .tex, etc.): commits and branches. A project folder for a manuscript, written in LaTeX, and upgraded to a Git repo. But first, a short introduction into Git's basic concepts and terminology. The simplest way to install it is via the gratis GitHub Desk..

Vorträge: Lasst sie nicht verpuffen, sondern nehmt sie auf!

Den Semesterbeginn meiner Uni verfolge ich immer mit einem Lächeln und einer Träne im Gesicht. Denn jetzt gibt die Uni die Vortragspläne für die Fachbereichsseminare und das Studium Generale heraus. Hinzu kommen Gastvorträge in einzelnen Arbeits- und Hochschulgruppen, Ringvorlesungen in benachbarten Hochschulen u.v.m. So viele interessante Lernmöglichkeiten! Zwar kann niemand all das studieren, aber sollte nicht wenigstens die Möglichkeit geschaffen werden, zeitsouverän in möglichst viele The..

Vorträge: Lasst sie nicht verpuffen, sondern nehmt sie auf!

Den Semesterbeginn meiner Uni verfolge ich immer mit einem Lächeln und einer Träne im Gesicht. Denn jetzt gibt die Uni die Vortragspläne für die Fachbereichsseminare und das Studium Generale heraus. Hinzu kommen Gastvorträge in einzelnen Arbeits- und Hochschulgruppen, Ringvorlesungen in benachbarten Hochschulen u.v.m. So viele interessante Lernmöglichkeiten! Zwar kann niemand all das studieren, aber sollte nicht wenigstens die Möglichkeit geschaffen werden, zeitsouverän in möglichst viele The..

Korrekturlesen von PDFs mit pdftotxt & grep automatisieren

In gedruckte & gebundene Abschlussarbeiten guckt man lieber nicht nochmal rein, oder? Der eine oder andere Tippfehler schleicht sich immer durch! Aber mit zwei Kommandozeilenzeilenprogrammen, kann man verhindern, dass sich die gleichen Fehler wiederholen. Fehler per Auge finden:  Das ist auf Dauer weder erquicklich, noch ergiebig. Diese Anleitung eignet sich vor allem für eigene Texte, die man nach dem Schreiben schon gefühlt auswendig kann, sowie für LaTeX-Quelltexte, die aufgrund vieler Be..

Characterisation of biotic interactions between a Dyadobacter strain and the diatom Achnanthidium minutissimum

Diatoms are phototrophic, unicellular algae. Due to their large share in CO2 fixation and O2 production, they are very important for Earth's biogeochemistry. Many diatoms are also of economic relevance, due to their capacity to colonise submerged surfaces such as ship hulls. This so called biofouling includes the undesired growth of biofilms, which form by the aggregation of cells and the secretion of a matrix of extracellular polymeric substances (EPS). Depending on the composition of the biofilm matrix, this microenvironment of the embedded cells can be quite different compared to the surrounding environment. Naturally occurring biofilms are often complex communities of microorganisms from different kingdoms of life, such as photoautotrophic diatoms and heterotrophic bacteria. Complex intercellular interactions occur in such communities, but only few signalling or messenger molecules, which constitute these chemical communication pathways, are known. Therefore, the identification of such molecules is of great interest. In this thesis, a biological assay system ("bioassay") was tested to study biotic interactions between the freshwater diatom Achnanthidium minutissimum and a biofilm-dwelling bacterium from Lake Constance. It was intended to elucidate chemical modes of communication between these species and to identify relevant molecules. An additional goal was the investigation of EPS capsule formation by the diatom in reaction to contact with the bacterium. For these purposes, an assay that quantifies the biofilm formation of the diatom was improved and automated. The assay was also used as a reporter system for the fractionation of bioactive compounds from the bacterial supernatant. The supernatant production was upscaled by optimising the bacterium's growth conditions. A combination of pH-dependent liquid-liquid and solid phase extraction was used for the fractionation of the supernatant. Moreover, light and electron microscopy were correlated in an easily adaptable manner to enable the microstructural analysis of EPS capsules. The bioassay with A. minutissimum and the Dyadobacter-related Bacteroidetes strain clarified that its biofilm induction is mediated by soluble, yet hydrophobic, bacterial compounds. These could be extracted, albeit in low purities and amounts. However, reproducibility and user-friendliness of the staining-dependent bioassay could be enhanced by its partial automation. This was achieved by implementing both human- and machine-readable data structures, which improved the planning of experiments, simplified their repetition, as well as increased the efficiency of data evaluation in the context of medium-throughput screenings. Moreover, tests of biofilm quantification via staining-independent parameters allowed to further simplify the measurement of this bioassay. The scanning electron microscopy uncovered novel fibrillar microstructures both on the diatom frustules as well as in the material of the EPS capsule. It can be postulated that this capsule forms by condensation of a mesh of frustule-attached fibrils. Due to a quantifiable, preferential attachment of bacteria cells to the capsules, their relevance for the interaction of diatom and bacteria is confirmed. The fractionation methods tested here highlight problems and necessary improvement options for the purification of bioactive substances in the A. minutissimum bioassay in sufficient quantities for molecular analyses. Moreover, the partial automation of measurement and data processing workflows highlight additional fields of application for this biofilm assay. The workflows developed here may also be beneficial for other biofilm assays.publishe

Distribution of the number of bacteria cells adherent to diatom valve faces of different surface types (frustule or capsule) in xenic A. minutissimum biofilms.

<p>Bacteria were counted in SEM images, if they were in direct, visible contact with the valve face of either a frustule (N = 54) or a completely encapsulated diatom cell (N = 71; see figures 2B and 3A for illustration). Samples were taken from 11 to 31 days old cultures. Boxes represent 1st and 3rd quartile. Black center lines represent medians. Whiskers extend to 1.5-fold of the inter-quartile range. Diamond symbols represent means. Black dots are outliers.</p

Capsules of the diatom Achnanthidium minutissimum arise from fibrillar precursors and foster attachment of bacteria

Achnanthidium minutissimum is a benthic freshwater diatom that forms biofilms on submerged surfaces in aquatic environments. Within these biofilms, A. minutissimum cells produce extracellular structures which facilitate substrate adhesion, such as stalks and capsules. Both consist of extracellular polymeric substance (EPS), but the microstructure and development stages of the capsules are so far unknown, despite a number of hypotheses about their function, including attachment and protection. We coupled scanning electron microscopy (SEM) to bright-field microscopy (BFM) and found that A. minutissimum capsules mostly possess an unstructured surface. However, capsule material that was mechanically stressed by being stretched between or around cells displayed fibrillar substructures. Fibrils were also found on the frustules of non-encapsulated cells, implicating that A. minutissimum capsules may develop from fibrillar precursors. Energy-dispersive X-ray (EDX) spectroscopy revealed that the capsule material do not contain silicon, distinguishing it from the frustule material. We furthermore show that bacteria preferentially attach to capsules, instead of non-encapsulated A. minutissimum cells, which supports the idea that capsules mediate diatom-bacteria interactions