Abstract:
:The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Hoksza D,Gawron P,Ostaszewski M,Hasenauer J,Schneider Rdoi
10.1093/bib/bbz067subject
Has Abstractpub_date
2020-07-15 00:00:00pages
1249-1260issue
4eissn
1467-5463issn
1477-4054pii
5527141journal_volume
21pub_type
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