Erweiterte Suche

Software components for increased data reuse and reproducibility in phylogenetics and phylogenomics

Die in dieser Arbeit entwickelten Softwarekomponenten tragen zur Erhöhung der Wiederverwendbarkeit wissenschaftlicher Daten und der Reproduzierbarkeit der zugrundeliegenden Studien bei, indem sie eine eindeutige Annotation mit Metadaten (z.B. Verknüpfungen von Rohdaten oder Informationen über verwendete Methoden) ermöglichen und die übersichtliche Gegenüberstellung von Ergebnissen unterschiedlicher Methoden zum Multisequenzalignment und zur Phylogenierekonstruktion erlauben. Während die bioinformatischen Bibliotheken JPhyloIO und LibrAlign grundlegende Funktionalitäten in leicht wiederverwendbarer Form für Entwickler zur Verfügung stellen, bieten die darauf aufbauenden Anwendungen Lösungen für Endnutzer. Der Taxonomic Editor der EDIT Plattform deckt dabei taxonomische Daten ab, während PhyDE 2 und der AlignmentComporator entsprechende Funktionalität für Multisequenzalignments und ihre Metadaten anbieten. TreeGraph 2 bietet entsprechenden Funktionalität für phylogenetische Bäume und ist bereits weltweit in umfangreicher Verwendung. Alle entwickelten Komponenten sind unter http://bioinfweb.info/Software frei verfügbar.

The software components developed in this thesis contribute to an increased reusability of scientific data and to a greater reproducibility of underlying studies by allowing unambiguous annotation with metadata (e.g., links to raw data or information on applied methods) and clear comparison of results from alternative methods for multiple sequence alignment and phylogenetic inference. The bioinformatical libraries JPhyloIO and LibrAlign provide fundamental and easily reusable functionality for developers, while the applications based on them offer solutions for end users. The Taxonomic Editor of the EDIT platform covers taxonomic data, while PhyDE 2 and AlignmentComparator offer respective functionality for multiple sequence alignments and related metadata. TreeGraph 2 provides required functionality for phylogenetic trees and is currently in wide use worldwide. All developed software is freely available at http://bioinfweb.info/Software.

Titel: Software components for increased data reuse and reproducibility in phylogenetics and phylogenomics
Verfasser: Stöver, Ben GND
Gutachter: Müller, Kai F. GND
Dokumenttyp: Dissertation/Habilitation
Medientyp: Text
Erscheinungsdatum: 2018
Publikation in MIAMI: 07.12.2018
Datum der letzten Änderung: 07.12.2018
Schlagwörter: Metadaten; Merkmalsdaten; Multisequenzalignments, phylogenetische Bäume; bioinformatische Software; eindeutige Annotation
metadata; character data; multiple sequence alignments, phylogenetic trees; bioinformatical software; unambiguous annotation
Fachgebiete: Biowissenschaften; Biologie
Sprache: Englisch
Format: PDF-Dokument
URN: urn:nbn:de:hbz:6-96159516963
Permalink: https://nbn-resolving.org/urn:nbn:de:hbz:6-96159516963
Onlinezugriff:
Inhalt:
A Short Contents
1 General Introduction
....................................................................................................
............. 20
Part I – Fundamental software libraries to process, display and edit phylogenetic data and
metadata
....................................................................................................
.............................................. 31
2 JPhyloIO: A Java library for event-based reading and writing of different
phylogenetic file formats through a common
interface...........................................................................................
.... 33
3 LibrAlign: A flexible Java GUI library for displaying and editing multiple sequence
alignments and attached raw- and metadata
data..............................................................................................
46
Part II – Applications to model, visualize, edit and compare phylogenetic data and metadata....
57
4 Sample data processing in an additive and reproducible taxonomic workflow by using
character data persistently linked to preserved individual specimens
............................................................. 59
5 The molecular components of the Taxonomic Editor
............................................................... 79
6 A new version of the alignment editor PhyDE based on the recently developed functionality
of
JPhyloIO and LibrAlign
....................................................................................................
................... 84
7 AlignmentComparator: Comparing alternative multiple sequence alignments of the same
dataset.............................................................................................
.................................................. 90
8 TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses .....
128
9 New features of the tree editor TreeGraph 2 to handle rich metadata and compare phylogenies
137
Part III – General purpose software components and the bioinfweb portal
...............................163
10 The bioinfweb portal
....................................................................................................
........... 165
11 bioinfweb.commons: Shared bioinfweb components made available in a library .................
168
12 Toolkit Independent Components: Creating GUI components for both Swing and SWT........ 171
13 General discussion and outlook
.............................................................................................. 177
14 List of abbreviations
....................................................................................................
............ 190
15
References..........................................................................................
..................................... 193
16 Acknowledgements
....................................................................................................
............. 210
17
Appendix............................................................................................
...................................... 212