SCENIC: https://www.nature.com/articles/nmeth.4463
At the Max Planck Institute of Psychiatry (MPIP) people with different programming skills, from wet-lab scientists to bioinformaticians, work together. Also, quite a lot of PhD students who haven't received a formal education in computer
science perform primarily computational work. After more than a one and half year break, we revived the Code Club at the MPIP with monthly meetings. There we...
DynamicalSystems.jl is an award-winning software library for nonlinear
dynamics and nonlinear timeseries analysis. It was born out of
frustration when facing two problems: (1) the lack of a general-purpose
accessible software for nonlinear dynamics for using in the lecture
hall, and (2) the complete and utter lack of reproducibility of the
entire field. DynamicalSystems.jl was...
Over the last few years, evolutionary biologists have tagged with short sequences the individuals of bacterial populations, yeast populations, and cancer cells to understand better the eco-evolutionary dynamics that shape their biodiversity, as well as the dynamics that govern microbial communities. A crucial technical stepping stone for understanding these questions is quantifying these...
The field of traditional historical linguistics has long since applied
various techniques for the historical comparison of languages which aim
to reconstruct certain aspects of ancestral languages which are not
witnessed in sources through the comparison of extant language varieties
for which sources exist. Although the techniques are in theory highly
formalized, they are up to now almost...
Topics of this contribution:
- Jupyter notebook as user interface
- reproducibility, interactive documentation
- special feature of ubermag: provides domain specific language (for micromagnetic research) how to express problem, which is then translated into configuration files for the simulation engine automatically
- software engineering
- github actions for CI
- unit tests,...
Ever since the awarding of the Nobel Prize in Physics to J.M.
Kosterlitz, D. J. Thouless and D. Haldane in 2016 for their pioneering
work on topological phase transitions, these exotic phases of matter
have become one of the most sought-after features in quantum materials.
They are of particular interest for their unconventional and
dissipationless transport properties, and are a key...
In this talk I will present the problem of calculating the circular
photogalvanic effect in topological semimetals[1], a property for
which we would like to study the effects of symmetry breaking of. One
of the approaches explored in this ongoing project, different than in
previous studies, is to evaluate the resulting implicit surface
integrals directly. Previous studies used an...
Syncopy (www.syncopy.org) is aimed to be a completely open source, user-friendly yet powerful data analysis suite for the Neurosciences. It is developed in Python and makes extensive use of distributed computing via Dask, and achieves low memory footprints by using on-disc hdf5 data structures in the backend per default. For our users, we supply highly abstracted frontend functions, which...
Software is both a cause of unreliable research and part of the solution. The bulk of scientific research relies upon specialized software for data management and analysis. The bad news is that much of this software is poorly tested and documented, and researchers often use software in unreliable ways. Part of the problem is that researchers are being asked to perform a job they have not been...
Computational reproducibility is a building block for transparent and cumulative science. It enables the
originator and other researchers, on other computers and later in time, to reproduce and thus understand
how results came about while avoiding various errors that may lead to erroneous reporting of statistical
and computational results. But what does it take to make something...
Software for research has to keep up with the methodological developments in its
field. All too often, only a handful of maintainers bear the load of maintaining and
extending software. In consequence, they are swamped with demands for adding addi-
tional features, resulting in long delays until new innovations become available.
However, in many disciplines, methodological researchers are...
The usual mode of accessing High Performance Computing (HPC) resources involves
interactively connecting to the command-line interface and submitting job
scripts to a job scheduler.
Some services which provide a user interface by themselves (e.g. when working
with graphical data) or services which require HPC resources as a compute
backend for an already existing workflow engine,...
A lot of good software is abandoned once the PhD
student graduates or the programmer leaves the institute. Also
maintaining software doesn’t generate papers which is the unit used to
measure scientific prowess. I believe there are a few low-hanging fruits
that scientific programmers can use to improve the state of research
software development.
Research software is vital to research.
In this talk I will discuss what could be meant by the term "research software".
I will show some examples of research software in the field of game theory (and
others) but
also give an overview of what the published literature says on the topic.
This will conclude with a proposal for a definition of research software with a
discussion of the...
The Climate Model „ICON“ has been developed at MPI for Meteorology for climate and weather
research.
The model consist of approx. 500 k lines of (much legacy) code developed by 100s of people
across the world and is under constant change due to porting to the most modern HPC
architectures. Code owner are 4 institutions: MPI-M, DWD, KIT and DKRZ
These institutions had been developing the...
After you have clarified the target license of your software, you need to ensure that this information is properly documented.
But what aspects do you need to consider and how can you achieve it in an efficient way?
In this talk we discuss minimum practices for documenting copyright and license information for software and show practical examples.
Particularly, we introduce REUSE Software...
Experimental and theoretical scientists in the turbulence department at the MPI-DS in Göttingen produce a large variety of heterogeneous data and analyze it in a number of different environments. In an MPDL project, the open source research data management software CaosDB was enhanced to meet these needs and hopefully those of other research groups as well.
We will show the results of this...
Pandemics, war, inequality, environmental and climatic degradation, identitarian conflicts, and the rise of extreme political movements are not isolated phaenomena but rather intertwined in ways often difficult to detect. This reminds us that human societies are complex dynamical systems and themselves part of a broader human-environmental system or ...
Our StudyDB inherits a lot of functionality from previous Django development efforts. However, StudyDB faces some additional challenges as it is intended for data collection in the context of translational human studies (empirical and prospective research, clinical trials) and »electronic« questionnaires (interfacing with and processing data from our LimeSurvey server).
We would like to...
MathRepo, located at https://mathrepo.mis.mpg.de, is an online repository for mathematical research data, in particular for code, software, and teaching material. In this talk I will discuss its current content, the role software plays in mathematical research, and future improvements of the repository regarding the FAIR principles.
