[HTML][HTML] Metabolomics and multi-omics integration: a survey of computational methods and resources

T Eicher, G Kinnebrew, A Patt, K Spencer, K Ying, Q Ma… - Metabolites, 2020 - mdpi.com
As researchers are increasingly able to collect data on a large scale from multiple clinical
and omics modalities, multi-omics integration is becoming a critical component of …

Introducing the FAIR Principles for research software

M Barker, NP Chue Hong, DS Katz, AL Lamprecht… - Scientific Data, 2022 - nature.com
Research software is a fundamental and vital part of research, yet significant challenges to
discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the …

A comparison of single-cell trajectory inference methods

W Saelens, R Cannoodt, H Todorov, Y Saeys - Nature biotechnology, 2019 - nature.com
Trajectory inference approaches analyze genome-wide omics data from thousands of single
cells and computationally infer the order of these cells along developmental trajectories …

Towards FAIR principles for research software

AL Lamprecht, L Garcia, M Kuzak, C Martinez… - Data …, 2020 - journals.sagepub.com
The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility,
interoperability and reusability of digital research objects for both humans and machines …

Big data in drug discovery

N Brown, J Cambruzzi, PJ Cox, M Davies… - Progress in medicinal …, 2018 - Elsevier
Abstract Interpretation of Big Data in the drug discovery community should enhance project
timelines and reduce clinical attrition through improved early decision making. The issues …

A large-scale study on research code quality and execution

A Trisovic, MK Lau, T Pasquier, M Crosas - Scientific Data, 2022 - nature.com
This article presents a study on the quality and execution of research code from publicly-
available replication datasets at the Harvard Dataverse repository. Research code is …

Flexible automation accelerates materials discovery

BP MacLeod, FGL Parlane, AK Brown, JE Hein… - Nature Materials, 2022 - nature.com
Automated experiments can accelerate research and development.'Flexible
automation'enables the cost-and time-effective design, construction and reconfiguration of …

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

J Wolff, V Bhardwaj, S Nothjunge… - Nucleic acids …, 2018 - academic.oup.com
Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of
chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy …

Development of the Community Water Model (CWatM v1. 04) A high-resolution hydrological model for global and regional assessment of integrated water resources …

P Burek, Y Satoh, T Kahil, T Tang… - Geoscientific Model …, 2019 - gmd.copernicus.org
We develop a new large-scale hydrological and water resources model, the Community
Water Model (CWatM), which can simulate hydrology both globally and regionally at …

[HTML][HTML] BornAgain: software for simulating and fitting grazing-incidence small-angle scattering

G Pospelov, W Van Herck, J Burle… - Applied …, 2020 - journals.iucr.org
BornAgain is a free and open-source multi-platform software framework for simulating and
fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small …