Treffer: The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.

Title:
The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.
Authors:
Sommer B; Royal College of Art, School of Design, Innovation Design Engineering, London SW7 2EU, UK.
Source:
Journal of integrative bioinformatics [J Integr Bioinform] 2019 Sep 27; Vol. 16 (3). Date of Electronic Publication: 2019 Sep 27.
Publication Type:
Historical Article; Journal Article
Language:
English
Journal Info:
Publisher: De Gruyter Open Country of Publication: Germany NLM ID: 101503361 Publication Model: Electronic Cited Medium: Internet ISSN: 1613-4516 (Electronic) Linking ISSN: 16134516 NLM ISO Abbreviation: J Integr Bioinform Subsets: MEDLINE
Imprint Name(s):
Publication: Berlin : De Gruyter Open
Original Publication: Bielefeld : IMBio e.V.
MeSH Terms:
Cell Membrane*/genetics , Cell Membrane*/metabolism , Models, Biological* , Programming Languages*, Computational Biology/*history , Computer Graphics/*history, History, 20th Century ; History, 21st Century ; Humans
References:
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Contributed Indexing:
Keywords: Cell Modelling; Integrative Bioinformatics; Java; Molecular Modelling; Open Source Software
Entry Date(s):
Date Created: 20190928 Date Completed: 20200213 Latest Revision: 20200213
Update Code:
20250114
PubMed Central ID:
PMC6798854
DOI:
10.1515/jib-2019-0057
PMID:
31560649
Database:
MEDLINE

Weitere Informationen

For more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.