CyBy2 : a strongly typed, purely functional framework for chemical data management

Höck, Stefan; Riedl, Rainer

doi:10.1186/s13321-019-0403-2

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-21749

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	CyBy2 : a strongly typed, purely functional framework for chemical data management
Authors:	Höck, Stefan Riedl, Rainer
et. al:	No
DOI:	10.1186/s13321-019-0403-2 10.21256/zhaw-21749
Published in:	Journal of Cheminformatics
Volume(Issue):	11
Issue:	80
Issue Date:	30-Dec-2019
Publisher / Ed. Institution:	BioMed Central
ISSN:	1758-2946
Language:	English
Subjects:	Chemical data management; Functional programming; Lab inventory; Medicinal chemistry; Scala; Type driven development
Subject (DDC):	005: Computer programming, programs and data 540: Chemistry
Abstract:	We present the development of CyBy2, a versatile framework for chemical data management written in purely functional style in Scala, a modern multi-paradigm programming language. Together with the core libraries we provide a fully functional example implementation of a HTTP server together with a single page web client with powerful querying and visualization capabilities, providing essential functionality for people working in the field of organic and medicinal chemistry. The main focus of CyBy2 are the diverse needs of different research groups in the field and therefore the flexibility required from the underlying data model. Techniques for writing type level specifications giving strong guarantees about the correctness of the implementation are described, together with the resulting gain in confidence during refactoring. Finally we talk about the advantages of using a single code base from which the server, the client and the software's documentation pages are being generated. We conclude with a comparison with existing open source solutions. All code described in this article is published under version 3 of the GNU General Public License and available from GitHub including an example implementation of both backend and frontend together with documentation how to download and compile the software (available at https://github.com/stefan-hoeck/cyby2).
URI:	https://digitalcollection.zhaw.ch/handle/11475/21749
Fulltext version:	Published version
License (according to publishing contract):	CC BY 4.0: Attribution 4.0 International
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Chemistry and Biotechnology (ICBT)
Appears in collections:	Publikationen Life Sciences und Facility Management

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Höck, S., & Riedl, R. (2019). CyBy2 : a strongly typed, purely functional framework for chemical data management. Journal of Cheminformatics, 11(80). https://doi.org/10.1186/s13321-019-0403-2

Höck, S. and Riedl, R. (2019) ‘CyBy2 : a strongly typed, purely functional framework for chemical data management’, Journal of Cheminformatics, 11(80). Available at: https://doi.org/10.1186/s13321-019-0403-2.

S. Höck and R. Riedl, “CyBy2 : a strongly typed, purely functional framework for chemical data management,” Journal of Cheminformatics, vol. 11, no. 80, Dec. 2019, doi: 10.1186/s13321-019-0403-2.

HÖCK, Stefan und Rainer RIEDL, 2019. CyBy2 : a strongly typed, purely functional framework for chemical data management. Journal of Cheminformatics. 30 Dezember 2019. Bd. 11, Nr. 80. DOI 10.1186/s13321-019-0403-2

Höck, Stefan, and Rainer Riedl. 2019. “CyBy2 : A Strongly Typed, Purely Functional Framework for Chemical Data Management.” Journal of Cheminformatics 11 (80). https://doi.org/10.1186/s13321-019-0403-2.

Höck, Stefan, and Rainer Riedl. “CyBy2 : A Strongly Typed, Purely Functional Framework for Chemical Data Management.” Journal of Cheminformatics, vol. 11, no. 80, Dec. 2019, https://doi.org/10.1186/s13321-019-0403-2.