CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes

Sommer, Björn; Dingersen, Tim; Schneider, S.; Rubert, Sebastian; Gamroth, Christian

doi:10.1186/1758-2946-2-s1-o21

Cited by 1 publication

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References 4 publications

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“…Therefore, a very effective small team was driving the development, and a very important factor during this time was that I was regularly attending related conferences – such as the German Conference on Bioinformatics or the Molecular Modelling Workshop in Erlangen – and in this way was able to talk to many researchers during our poster presentations and get feedback regarding requirements on our MembraneEditor (e.g. [22], [23]). These ideas were directly injected in the development process and enabled us to create a quite comfortable membrane modelling tool which is still unique in its functionality until today.…”

Section: Developmental History – the Evolution Of Cellmicrocosmos Toolsmentioning

confidence: 99%

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

Sommer

2019

Journal of Integrative Bioinformatics

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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.

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Section: Developmental History – the Evolution Of Cellmicrocosmos Toolsmentioning

confidence: 99%

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

Sommer

2019

Journal of Integrative Bioinformatics

View full text Add to dashboard Cite

show abstract

CELLmicrocosmos 2.2: advancements and applications in modeling of three-dimensional PDB membranes

Cited by 1 publication

References 4 publications

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

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

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