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Software reusability – what is needed?

Faruk Diblen
2021 Zenodo  
NL-RSE Meetup, February 11, 2021
doi:10.5281/zenodo.4533775 fatcat:go4jxnrlirf4dmd5rf6rz4awxq

How FAIR is your research software?

Carlos Martinez-Ortiz, Faruk Diblen
2021 Zenodo  
FAIR software is a topic of growing importance in the research software landscape. There have been efforts to describe the how the FAIR principles apply to research software and work in this direction is still ongoing. 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. In this session we would like to introduce howfairis: a Python package to analyse software's
more » ... e with the FAIR software recommendations. We will describe how howfairis analyses your code to measure its level of compliance with the FAIR software recommendations. We will show how our Github Action can test your software automatically. We will also show how to add a badge to your GitHub repository showing to the world how FAIR your software is! Given that the FAIR principles for software are still evolving, howfairis will also evolve to match new developments in the area. We would like new users to give us feedback and to contribute to the development of this tool!
doi:10.5281/zenodo.4552003 fatcat:l6prnilcszffnbwjixqdb5ffim

Adaptive ADMM in Distributed Radio Interferometric Calibration [article]

Sarod Yatawatta, Faruk Diblen, Hanno Spreeuw
2017 arXiv   pre-print
Faruk Diblen and Hanno Spreeuw Netherlands eScience Center Science Park 140 (Matrix I) 1098 XG Amsterdam, The Netherlands Abstract-Distributed radio interferometric calibration based on consensus optimization  ... 
arXiv:1710.05656v1 fatcat:hguxdq3bljg4vkrqyhpqoabdna

CSS workshop on Open Science and Software best practices

Dafne van Kuppevelt, Faruk Diblen
2019 Zenodo  
Slides of the workshop given at Computational Social Science Amsterdam, on 29/5/2019.
doi:10.5281/zenodo.3233889 fatcat:pv57tswbtfenxhwjzte2jpjtne

GPU acceleration of the SAGECal calibration package for the SKA [article]

Hanno Spreeuw, Ben van Werkhoven, Sarod Yatawatta, Faruk Diblen
2019 arXiv   pre-print
SAGECal has been designed to find the most accurate calibration solutions for low radio frequency imaging observations, with minimum artefacts due to incomplete sky models. SAGECAL is developed to handle extremely large datasets, e.g., when the number of frequency bands greatly exceeds the number of available nodes on a compute cluster. Accurate calibration solutions are derived at the expense of large computational loads, which require distributed computing and modern compute devices, such as
more » ... PUs, to decrease runtimes. In this work, we investigate if the GPU version of SAGECal scales well enough to meet the requirements for the Square Kilometre Array and we compare its performance with the CPU version.
arXiv:1910.13908v1 fatcat:cfpzinwajrbofnovgpfxnmvbcy

Interactive web-based visualization of multi-dimensional physical and astronomical data [article]

Faruk Diblen, Luc Hendriks, Bob Stienen, Sascha Caron, Rena Bakhshi, Jisk Attema
2020 arXiv   pre-print
In this manuscript, we propose to expand the use of scientific repositories such as Zenodo and HEP Data, in particular in order to better examine multi-parametric solutions of physical models. The implementation of interactive web-based visualizations enables fast and comfortable re-analysis and comparisons of phenomenological data. In order to illustrate our point of view, we present some examples and demos for dark matter models, supersymmetry exclusions and LHC simulations.
arXiv:2011.03801v1 fatcat:dfprjomf2zesbpoxc2j4f5nw5a

SPOT: Open Source framework for scientific data repository and interactive visualization [article]

Faruk Diblen, Jisk Attema, Rena Bakhshi, Sascha Caron, Luc Hendriks, Bob Stienen
2018 arXiv   pre-print
SPOT is an open source and free visual data analytics tool for multi-dimensional data-sets. Its web-based interface allows a quick analysis of complex data interactively. The operations on data such as aggregation and filtering are implemented. The generated charts are responsive and OpenGL supported. It follows FAIR principles to allow reuse and comparison of the published data-sets. The software also support PostgreSQL database for scalability.
arXiv:1809.08893v1 fatcat:gz5227znbfasrpikgreja6ibxi

A Stochastic LBFGS Algorithm for Radio Interferometric Calibration [article]

Sarod Yatawatta, Lukas De Clercq, Hanno Spreeuw, Faruk Diblen
2019 arXiv   pre-print
We present a stochastic, limited-memory Broyden Fletcher Goldfarb Shanno (LBFGS) algorithm that is suitable for handling very large amounts of data. A direct application of this algorithm is radio interferometric calibration of raw data at fine time and frequency resolution. Almost all existing radio interferometric calibration algorithms assume that it is possible to fit the dataset being calibrated into memory. Therefore, the raw data is averaged in time and frequency to reduce its size by
more » ... y orders of magnitude before calibration is performed. However, this averaging is detrimental for the detection of some signals of interest that have narrow bandwidth and time duration such as fast radio bursts (FRBs). Using the proposed algorithm, it is possible to calibrate data at such a fine resolution that they cannot be entirely loaded into memory, thus preserving such signals. As an additional demonstration, we use the proposed algorithm for training deep neural networks and compare the performance against the mainstream first order optimization algorithms that are used in deep learning.
arXiv:1904.05619v2 fatcat:fliw2aai5fa33nzx2syzl7if5a

Implementing FAIR for research software: attitudes, advantages and challenges [article]

Leyla Jael Castro, Diego Alonso Álvarez, Stian Soiland-Reyes, Markus Löning, Sam Harrison, Faruk Diblen, Abhishek Dasgupta, Morane Gruenpeter
2021 figshare.com  
Here we report on a discussion session that took place during the Collaborations Workshop 2021, organized by the Software Sustainability Institute from the 30th of March to the 1st of April. Software developers and researchers gathered together to discuss different topics around software including FAIR principles; equality, diversity and inclusion; and software sustainability. In our session, we discussed attitudes, advantages and challenges around the adoption (also referred to as
more » ... n in this document) of the FAIR principles for research software.
doi:10.6084/m9.figshare.14453031.v1 fatcat:x4fazaiosnezrkhhizayzecxyi

spot: Open Source framework for scientific data repository and interactive visualization

Faruk Diblen, Jisk Attema, Rena Bakhshi, Sascha Caron, Luc Hendriks, Bob Stienen
2019 SoftwareX  
spot is an open source and free visual data analytics tool for multi-dimensional data-sets. Its web-based interface enables user to do a quick and interactive analysis of complex data. Various operations on data are implemented such as aggregation and filtering. The interface supports OpenGL acceleration, which makes the generated charts very responsive. In order to have scalability, the software also supports PostgreSQL as its database. It follows FAIR principles to allow reuse and comparison of the published data-sets.
doi:10.1016/j.softx.2019.04.006 fatcat:lcqormywpbcjlez5h7olfo5ohu

Implementing FAIR for research software: attitudes, advantages and challenges [article]

Leyla Jael Castro, Diego Alonso Álvarez, Stian Soiland-Reyes, Markus Löning, Sam Harrison, Faruk Diblen, Abhishek Dasgupta, Morane Gruenpeter, Paula Andrea Martinez
2021 figshare.com  
Here we report on a discussion session that took place during the Collaborations Workshop 2021, organized by the Software Sustainability Institute from the 30th of March to the 1st of April. Software developers and researchers gathered together to discuss different topics around software including FAIR principles; equality, diversity and inclusion; and software sustainability. In our session, we discussed attitudes, advantages and challenges around the adoption (also referred to as
more » ... n in this document) of the FAIR principles for research software.
doi:10.6084/m9.figshare.14453031.v2 fatcat:zr5t27fwifbvviprdeyuoxub7m

Interactive Web-Based Visualization of Multidimensional Physical and Astronomical Data

Faruk Diblen, Luc Hendriks, Bob Stienen, Sascha Caron, Rena Bakhshi, Jisk Attema
2021 Frontiers in Big Data  
Diblen et al. Interactive Visualization of Multi-Dimensional Data A version of the pMSSM model was also used in the previous example (Section 4.1).  ...  The technical details of SPOT are given in detail in Diblen et al. (2018) . In this section, we will give an overview of the software components and explain the workflow.  ... 
doi:10.3389/fdata.2021.626998 pmid:34250466 pmcid:PMC8264300 fatcat:f3il3fknpzc7vpy64lvtwyw6h4

matchms - processing and similarity evaluation of mass spectrometry data [article]

Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efrain Manuel Villanueva Castilla, Cunliang Geng, Justin JJ van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan H Spaaks
2020 biorxiv/medrxiv   pre-print
Mass spectrometry data is at the heart of numerable applications in the biomedical and life sciences. With growing use of high throughput techniques researchers need to analyse larger and more complex datasets. In particular through joint effort in the research community, fragmentation mass spectrometry datasets are growing in size and number. Matchms is an open-access Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run an
more » ... follow, easy-to-reproduce workflow from raw mass spectra to pre- and post-processed spectral data.
doi:10.1101/2020.08.06.239244 fatcat:folnxbg2t5aqhf32pcf3mln5b4

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships

Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H Spaaks, Faruk Diblen, Simon Rogers, Justin J J van der Hooft
2021 PLoS Computational Biology  
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
more » ... Vec. 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.
doi:10.1371/journal.pcbi.1008724 pmid:33591968 pmcid:PMC7909622 fatcat:4iugdivf3vgi3o6vcjpz5tatca

matchms - processing and similarity evaluation of mass spectrometry data

Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efraín Castilla, Cunliang Geng, Justin van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan Spaaks
2020 Journal of Open Source Software  
doi:10.21105/joss.02411 fatcat:bqnyr4u6lrcchgjsxelljbf5iu
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