Visualization and analysis of 3D multi-edged and multi-layered biological networks

Postgraduate Thesis uoadl:3255792 146 Read counter

Unit:
Κατεύθυνση Βιοπληροφορική-Υπολογιστική Βιολογία
Library of the School of Science
Deposit date:
2022-12-12
Year:
2022
Author:
Kokoli Maria
Supervisors info:
Παντελής Μπάγκος, Καθηγητής, Τμήμα Πληροφορικής με Εφαρμογές στη Βιοϊατρική, Πανεπιστήμιο Θεσσαλίας
Γεώργιος Παυλόπουλος, Κύριος Ερευνητής Β', Ε.Κ.Ε.Β.Ε. "Αλέξανδρος Φλέμινγκ"
Βασιλική Οικονομίδου, Αναπληρώτρια Καθηγήτρια Διευθύντρια του ΠΜΣ "Βιοπληροφορική - Υπολογιστική Βιολογία", Τμήμα Βιολογίας, Πανεπιστήμιο Αθηνών
Original Title:
Οπτικοποίηση και ανάλυση τρισδιάστατων πολυεπίπεδων βιολογικών δικτύων με πολλαπλές ακμές
Languages:
English
Greek
Translated title:
Visualization and analysis of 3D multi-edged and multi-layered biological networks
Summary:
Εfficient integration and visualization of heterogeneous biomedical information in a single view is
a key challenge. In this study, we present Arena3Dweb, the first, fully interactive and dependencyfree, web application which allows the visualization of multilayered graphs in 3D space, as well as
its new features. With Arena3Dweb, users can integrate multiple networks in a single view along
with their intra- and inter-layer connections. For clearer and more informative views, users can
choose between a plethora of layout and clustering algorithms and apply them to a set of
selected layers either individually or in combination. Users can align networks and highlight node
topological features, whereas each layer, as well as the whole scene, can be translated, rotated,
and scaled in 3D space. User-selected edge colors can be used to highlight important paths,
while node positioning, coloring, and resizing can be adjusted on-the-fly. In its current version,
Arena3Dweb supports weighted and unweighted, directed and undirected multi-edge networks.
The application is written in R, Shiny, and JavaScript. We demonstrate the old and new
functionality of Arena3Dweb using different use-case scenarios.
Main subject category:
Science
Keywords:
bioinformatics, networks, graphs, visualization, clustering, layouts, Arena3D, layouts, multi-edged, multi-layered
Index:
Yes
Number of index pages:
2
Contains images:
Yes
Number of references:
110
Number of pages:
83
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