Experiments increasingly rely on high-performance computing software that plays a crucial role in producing and interpreting data. Differences in software environments can cause problems when those experiments need to be reproduced – so scientists at the MDC in Berlin are helping find a solution.
Reproducing experiments and results is a cornerstone of science, but researchers acknowledge that actually achieving this feat can be tricky. Specific experimental setups are usually the result of a lab's painstaking work and, in today's environment of high-throughput methods, are increasingly expensive.
The fact that complex, customized sets of software are frequently involved in the analysis and interpretation of data makes it even more difficult to achieve true reproducibility.
Guix – a free software that is used to fully reproduce computational environments – might be part of the solution, says Ludovic Courtès of Inria, the French National Institute for computer science and applied mathematics in Bordeaux. To implement it he has joined forces with Ricardo Wurmus of the platform for bioinformatics and modeling at the the Max Delbrück Center's Berlin Institute of Medical Systems Biology (BIMSB), scientists from the Utrecht University Medical Center and a growing group of international colleagues.
Capturing complete computational environments
The National Science Foundation in the US and journals such as Nature are insisting that researchers share source code and support reproducibility. "The ability to reproduce an experiment depends – among other things – on the ability to reproduce the software environment," Courtès says. "That poses particular difficulties in the many cases which require high-performance computing (HPC) environments.”
Guix is an outgrowth of a project called GNU launched almost 40 years ago at MIT in the USA. It makes up for some deficits of earlier efforts and is addressing several challenges: Users are no longer dependent on software package management by system administrators, empowering them to fully customize the environment to their needs.
It also solves problems that arise when scientists draw on "container solutions," which Courtès compares to receiving a brand-new computer where everything has already been installed. "That works until you make a small modification in the experiment to test a new hypothesis – which often happens in the world of research!"
The advantage of Guix is how it characterizes software environments in unambiguous terms, similar to a mathematical function. It completely describes all its relations and thus can reproduce them bit-for-bit. This way, Guix facilitates both reproducibility and customizability.
Adapting Guix to scientists' needs
Guix was not originally designed for the high-performance computing environments required by today's experiments. So scientists at the MDC, Inria and the partner institutes are building functions that permit Guix to be used on a computing cluster, to implement reproducible workflows. They are also adding packages that were developed at each site.
"Before Guix, the installation of scientific software was necessarily ad-hoc," Wurmus says. "Groups would build their own software, statically link it into existing systems, and hope that it would never have to change – because managing software environments was virtually impossible. Now not only can we manage a single environment per group in a reliable fashion, but we use Guix at all levels: of the group, user, workflow and so on."
The project is scheduled to last two years, at which time its initiators hope to have met the software reproducibility needs of their institutions. "The wider objective," Courtès says, "is to convince others who rely on high-performance computing that Guix represents a major advance toward a fundamental goal in science."
The Max Delbrück Center for Molecular Medicine (MDC)
The Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) was founded in Berlin in 1992. It is named for the German-American physicist Max Delbrück, who was awarded the 1969 Nobel Prize in Physiology and Medicine. The MDC's mission is to study molecular mechanisms in order to understand the origins of disease and thus be able to diagnose, prevent and fight it better and more effectively. In these efforts, the MDC cooperates with the Charité – Universitätsmedizin Berlin and the Berlin Institute of Health (BIH) as well as with national partners such as the German Center for Cardiovascular Research and numerous international research institutions. More than 1,600 staff and guests from nearly 60 countries work at the MDC, just under 1,300 of them in scientific research. The MDC is funded by the German Federal Ministry of Education and Research (90 percent) and the State of Berlin (10 percent), and is a member of the Helmholtz Association of German Research Centers.
https://guix-hpc.bordeaux.inria.fr/ Website of the Guix project
https://www.inria.fr/en/centre/bordeaux/news/towards-reproducible-software-envir... Detailed information at the Inria website
https://insights.mdc-berlin.de/en/2017/09/reproducing-computational-environments... This release at the MDC website
http://bioinformatics.mdc-berlin.de/team.html Website of the BIMSB Bioinformatics platform
Annette Tuffs | Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtz-Gemeinschaft
Powerful IT security for the car of the future – research alliance develops new approaches
25.05.2018 | Universität Ulm
Supercomputing the emergence of material behavior
18.05.2018 | University of Texas at Austin, Texas Advanced Computing Center
The more electronics steer, accelerate and brake cars, the more important it is to protect them against cyber-attacks. That is why 15 partners from industry and academia will work together over the next three years on new approaches to IT security in self-driving cars. The joint project goes by the name Security For Connected, Autonomous Cars (SecForCARs) and has funding of €7.2 million from the German Federal Ministry of Education and Research. Infineon is leading the project.
Vehicles already offer diverse communication interfaces and more and more automated functions, such as distance and lane-keeping assist systems. At the same...
A research team led by physicists at the Technical University of Munich (TUM) has developed molecular nanoswitches that can be toggled between two structurally different states using an applied voltage. They can serve as the basis for a pioneering class of devices that could replace silicon-based components with organic molecules.
The development of new electronic technologies drives the incessant reduction of functional component sizes. In the context of an international collaborative...
At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.
At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...
There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?
At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...
So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics
Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...
25.05.2018 | Event News
02.05.2018 | Event News
13.04.2018 | Event News
25.05.2018 | Event News
25.05.2018 | Machine Engineering
25.05.2018 | Life Sciences