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The structural complexity and bioactivity of natural products often depend on enzymatic redox tailoring steps. This is exemplified by the generation of the bisbenzannulated [5,6]-spiroketal pharmacophore in the bacterial rubromycin family of aromatic polyketides, which exhibit a wide array of bioactivities such as the inhibition of HIV reverse transcriptase or DNA helicase. Here we elucidate the complex flavoenzyme-driven formation of the rubromycin pharmacophore that is markedly distinct from conventional (bio)synthetic strategies for spiroketal formation. Accordingly, a polycyclic aromatic precursor undergoes extensive enzymatic oxidative rearrangement catalyzed by two flavoprotein monooxygenases and a flavoprotein oxidase that ultimately results in a drastic distortion of the carbon skeleton. The one-pot in vitro reconstitution of the key enzymatic steps as well as the comprehensive characterization of reactive intermediates allow to unravel the intricate underlying reactions, during which four carbon-carbon bonds are broken and two CO2 become eliminated. This work provides detailed insight into perplexing redox tailoring enzymology that sets the stage for the (chemo)enzymatic production and bioengineering of bioactive spiroketal-containing polyketides., Nature Chemical Biology, 17 (4), ISSN:1552-4450, ISSN:1552-4469

Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm—Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.

FAIR software is a topic of growing importance in the research software landscape. Even though the definition of the FAIR software principles is still in flux, recommendations are available to improve software in accordance to the spirit of the FAIR principles (https://fair-software.eu/). However there is a gap between the principles at a definition level, and the application of these principles in practice. If compliance with these principles needs to be verified for every new release of the software, it is desirable to have tools which can perform this task automatically and which will ease the work of RSEs who are developing the software. In this session we would like to introduce howfairis: a Python package to analyse a software's compliance with the FAIR software recommendations. We will describe how howfairis Github Action can automatically test your software to measure its FAIRness. In this code-along workshop we will show you how to add a fair-software badge to your GitHub repository showing to the world how FAIR your software is!

This is a guide to software development and projects at the Netherlands eScience Center. It both serves as a source of information for exactly how we work at the eScience Center, and as a basis for discussions and reaching consensus on this topic.

This talk discusses the Research Software Directory: a kind of content management system tailored to research software. The idea is that institutes for whom research software is an important output, can run their own instance of the Research Software Directory, thereby improving the findability, citability, and reproducibility of their software packages, while qualitatively illustrating impact. The system periodically collects data from GitHub, Zenodo, and Zotero. Those data are combined with a description of the software, which developers provide via a web form. The combined data is then used to create a 'product page': a visually attractive, easy-to-consume website that presents a given software package along with its scientific and social context. Product pages contain metadata in schema.org format, which helps to improve the findability and ranking by search engines. Furthermore, product pages offer reference manager files in BibTeX, RIS, and EndNote for download, thus promoting easy, accurate citation of the software. Both the schema.org metadata and the reference files are themselves derived from citation data written in Citation File Format, which are harvested from GitHub. Finally, a minimal OAI-PMH interface was recently added to the system, such that archiving services can automatically harvest the contents of a Research Software Directory.

In the eWaterCycle II project we took up the challenge to “do Open Hydrology right”. This is a presentation from and EGU session on Open Science (https://meetingorganizer.copernicus.org/EGU2019/EGU2019-9276-2.pdf)

We introduce GRPC4BMI, a software package that exposes earth system models (ESM) as remote services, provided these models implement the basic modeling interface (BMI). BMI is a library interface, predominantly used within the hydrological and hydraulic modeling domains, that allows an external component to initialize the model, control it’s time-stepping and retrieve or manipulate its state data at any given moment. The key feature of BMI for this work is that BMI is defined in many different programing languages. Our software wraps a BMI-enabled model into a server process, possibly executed within a docker container or on different hardware, and transfers client site BMI calls to the running model instance. We use Google's protocol buffer framework GRPC to establish the communication between a python client and server. In this way, GRPC4BMI allows the user to address ESM's via a standard python BMI, irrespective of the model language and installation environment. The package can therefore serve as a valuable tool for open and reproducible analysis and coupling of ESM's.

A large number of online systems for creating, processing, or analyzing scientific data exist. More and more such an online environment is seen as the ideal way to give users quick and easy access to large amounts of data, software, and hardware resources. Often these systems provide a web interface for easy access and exploration of the available data. Recently, notebook environments are becoming popular for providing advanced access to large datasets and HPC resources. When designing and building an online system, developers are often faced with a choice: either provide a ready made user interface, with limited options for users, or provide a notebook environment, requiring advanced knowledge about the system from a user to use effectively, hindering explorative use. In the eWaterCycle II project (www.ewatercycle.org) we provide a novel solution to this problem: We have created a web interface allowing a user to select models, data, and other options, from a pre-made set. Our system is then capable of generating a notebook specifically for the settings chosen by the user. This notebook can be run by the users to do the requested computation or analysis (in our case running a Hydrological model and providing a first hydrograph). It also forms the perfect basis for a user to start tinkering with the experiment, and change it any way she or he sees fit. This method thus allows novice users to get going quickly, while still allowing advanced users all the freedom they require. Our system is build on and would not be possible without Free and Open Source Software (FOSS). Our data and model explorer is based on a modified version of Terriajs. The notebook generator builds on OpenAPI to provide a service to create Jupyter notebooks, and in turn calls a JupyterHub service. Of course all our software is available as FOSS, available at https://github.com/eWaterCycle.

The Netherlands eScience Center [1] is the Dutch national center of excellence for the development and application of research software. We provide a combination of in-cash and in-kind funding to Dutch research projects that require a both academic research and software development to solve their research challenges. We firmly believe that open software is just as important to open science as are open access publications and open data. Without open software, the “instrument” that produces the published results from the data is missing. In our view, the FAIR principles [2] should therefore also apply to software; it needs to be findable, accessible, interoperable, and re-usable. Software is not the same as data however, as it requires a complex environment to operate in: compilers, libraries, configuration files, operating systems, etc. It needs to be maintained to fix bugs and to adapt it to changes in its environment. In this respect, software is more volatile than data. As an organization, we want to show that we have a positive impact on the projects that we do. This is a challenge because our contributions are mostly in the form of software. For many scientific domains it is not commonplace to cite software, even when that software is crucial to the research being presented. Because getting credited is not typically within our control, we decided to investigate alternative ways of demonstrating impact of software. This poster presents the Research Software Directory [3,4], a content management system that is tailored to software. At the time of writing, it collects data from GitHub, Zenodo, Zotero (our organization-wide reference manager), CITATION.cff files (for machine readable citation data), Medium (our institute's blog), and more. What little input it requires from our engineers, can be provided through a web form. Using this information, we create a ‘product page’ for each software package on the Research Software Directory. Each software package is presented within its research context, which may include links to scientific papers, projects, presentations, etc. In addition, it also shows a social context: who are the developers, how active is the development, and are there any tutorials, blogs, videos, etc. Importantly, each product page also clearly states how to cite the software package in papers. Besides providing a qualitative assessment of software impact, the Research Software Directory also improves findability of software packages, for example by providing metadata that helps search engines understand what the software is about, but equally importantly, by providing humans with the necessary context to understand the software's purpose. After all, discovery of a software package is often not so much about finding it, but knowing that you found it. [1] https://www.esciencecenter.nl [2] https://www.force11.org/group/fairgroup/fairprinciples [3] https://www.research-software.nl [4] https://zenodo.org/record/1305971#.Wz4UvBx9hzg &nbsp

Presentation that explains what a Research Software Directory is, why it is useful for promoting findability and re-use of research software.

In the 3D-e-Chem projectmany KNIME workflow nodes where made, this presentation explains the build infrastructure behind them.

This article discusses the use of 3D technologies in digital earth applications (DEAs) to study complex sites. These are large areas containing objects with heterogeneous shapes and semantic information. The study proposes that DEAs should be modular, have multi-tier architectures, and be developed as Free and Open Source Software if possible. In DEAs requiring high reliability in the 3D measurements, point clouds are proposed as basis for the 3D Digital digital earth representation. For the development of DEAs, we propose to follow a workflow with four components: data acquisition and processing, data management, data analysis and data visualization. For every component, technological challenges of using 3D technologies are identified and solutions applied for a case study are presented. The case study is a modular 3D DEA developed for the archaeological project Mapping the Via Appia. The 3D DEA allows archaeologists to virtually analyze a complex study area.

Presentation given at the Citation File Format Hack Day on 5 September 2018, co-locating with the 3rd Conference of Research Software Engineers.The presentation explains how the Citation File Format and its tooling is used to drive software citation within the Resesarch Software Directory (https://research-software.nl/) at the Netherlands eScience Center.

Poster presented at Digital Infrastructures for Research (DI4R) conference, Brussels, Belgium, 2017 Open software is essential for open science and reproducible research. Like data, software needs to be FAIR: findable, accessible, interoperable and reproducible. The Research Software Directory helps software reuse by facilitating discovery of existing software. &nbsp