Inhalt

•  
  1 General Introduction
•  
  1.1 Fostering data reuse and reproducibility by providing software that simplifies annotating phylogenetic data with necessary metadata
•  
   1.1.1 Metadata annotation is important to make data accessible and reusable
•  
   1.1.2 Metadata annotation is important to increase reproducibility
•  
   1.1.3 Phylogenetic data formats
•  
   1.1.4 Linking metadata using ontologies
•  
   1.1.5 Public databases
•  
   1.1.6 Software components developed in this thesis provide missing functionality to fostering data reuse and increasing reproducibility
•  
   1.2 Providing tools to compare, combine and present results from alternative analyses
•  
  1.3 How the developed software components combine
•  
   1.3.1 Basic general-purpose components
•  
   1.3.2 Bioinformatical libraries
•  
   1.3.3 Applications for researchers
•  
   Part I – Fundamental software libraries to process, display and edit phylogenetic data and metadata
•  
  2 JPhyloIO: A Java library for event-based reading and writing of different phylogenetic file formats through a common interface
•  
   2.1 Introduction
•  
   2.2 Design and implementation
•  
   2.2.1 Event streams for reading documents
•  
   2.2.2 Data adapters for writing documents
•  
   2.2.3 Supported formats
•  
   2.2.4 Generalization over different metadata concepts
•  
   2.2.5 Ways to extend JPhyloIO
•  
  2.3 Discussion
•  
   2.3.1 Comparison with other libraries
•  
   2.3.2 Event-based processing versus predefined library data structures
•  
   2.3.3 Current usage
•  
   2.3.4 Future development
•  
   2.4 Conclusion
•  
   2.5 Data Accessibility
•  
  2.6 Declarations
•  
   2.6.1 Author contributions
•  
   2.6.2 Acknowledgements
•  
  3 LibrAlign: A flexible Java GUI library for displaying and editing multiple sequence alignments and attached raw- and metadata data
•  
   3.1 Background
•  
  3.2 Implementation
•  
   3.2.1 GUI component architecture
•  
   3.2.2 TIC and the abstraction over Swing and SWT
•  
   3.2.3 Data model
•  
   3.2.4 I/O and interaction with JPhyloIO
•  
  3.3 Results and discussion
•  
   3.3.1 Alignment GUI components and editing capabilities
•  
   3.3.2 Data model
•  
   3.3.3 I/O and metadata access
•  
   3.3.4 Comparison to other software
•  
   3.3.5 Current usage
•  
   3.3.6 Future perspectives
•  
   3.4 Conclusion
•  
   3.5 Availability and requirements
•  
  3.6 Declarations
•  
   3.6.1 Authors' contributions
•  
   3.6.2 Acknowledgements
•  
   Part II – Applications to model, visualize, edit and compare phylogenetic data and metadata
•  
   4 Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens
•  
   4.1 Introduction
•  
  4.2 Conceptual foundations of integrated sample data processing
•  
   4.2.1 Organismic samples, their associations and data
•  
   4.2.2 Processing sample metadata
•  
   4.2.3 Linking specimen-based character data to sample metadatasets
•  
   4.2.4 Taxon assignment of samples and their data
•  
   4.2.5 Aggregating specimen-based character data at the taxon level
•  
  4.3 Workflow implementation using the EDIT Platform
•  
   4.3.1 Extending the EDIT Platform to handle the variety of sample data
•  
   4.3.2 Basic functionalities of the EDIT Platform, scalability and use cases
•  
  4.4 Steps of the integrated sample data workflow
•  
   4.4.1 Scope of the workflow
•  
  4.4.2 Establishing a reproducible connection between sampled individuals and all types of samples derived from them
•  
   4.4.2.1 Searching, retrieving and importing of sample metadata
•  
   4.4.2.2 Editing metadatasets
•  
   4.4.2.3 Building and editing specimen derivative hierarchies
•  
   4.4.2.4 Versioning, synchronizing and exchanging metadatasets
•  
   4.4.3 Stably linking character datasets to the sample derivative hierarchy
•  
  4.4.4 Recording and storing specimen-based morphological and molecular character data
•  
   4.4.4.1 Storage
•  
   4.4.4.2 Structured morphological character data
•  
   4.4.4.3 Molecular character data
•  
  4.4.5 Taxon assignment of sample metadata and character datasets
•  
   4.4.5.1 Adding sample data to a classification
•  
   4.4.5.2 Aggregating specimen-based character data at the taxon level
•  
   4.4.5.3 Publishing sample metadata and character data with the CDM Data Portal
•  
   4.4.6 Data exchange via standard exchange formats and enabling persistent, specimen-linked storage in research collections
•  
   4.5 Perspectives
•  
   4.6 Acknowledgements
•  
   4.7 Funding
•  
  5 The molecular components of the Taxonomic Editor
•  
   5.1 Introduction
•  
   5.2 Implementation
•  
   5.3 Results and discussion
•  
   5.4 Conclusion
•  
   5.5 Availability and requirements
•  
   5.6 Acknowledgements
•  
  6 A new version of the alignment editor PhyDE based on the recently developed functionality of JPhyloIO and LibrAlign
•  
   6.1 Introduction
•  
   6.2 Implementation
•  
  6.3 Results and discussion
•  
   6.3.1 User interface
•  
   6.3.2 Supported formats
•  
   6.3.3 Comparison to other software
•  
   6.3.4 Future development
•  
   6.4 Conclusion
•  
   6.5 Availability and requirements
•  
  6.6 Declarations
•  
   6.6.1 Authors contributions
•  
   6.6.2 Acknowledgements
•  
  7 AlignmentComparator: Comparing alternative multiple sequence alignments of the same dataset
•  
   7.1 Introduction
•  
   7.2 Algorithms
•  
   7.2.1 Profile alignment approach
•  
   7.2.2 Average position approach
•  
   7.2.2.1 Calculating the unaligned positions
•  
   7.2.2.2 Performing the initial superalignment
•  
   7.2.2.3 Improving the superalignment
•  
  7.2.2.4 Space and time complexity
•  
   7.2.2.4.1 Time complexity
•  
   7.2.2.4.2 Space complexity
•  
   7.2.2.5 Example
•  
  7.2.3 Maximum sequence pair match approach
•  
   7.2.3.1 Performing a superalignment between two other superalignments or MSAs
•  
   7.2.3.2 Superaligning more than two MSAs
•  
  7.2.3.3 Space and time complexity
•  
   7.2.3.3.1 Time complexity
•  
   7.2.3.3.2 Space complexity
•  
   7.2.3.4 Example
•  
  7.3 Implementation
•  
   7.3.1 Data model and user interface
•  
   7.3.2 I/O and NeXML metadata
•  
  7.4 Results and discussion
•  
   7.4.1 Features and user interface
•  
   7.4.2 Supported formats and storage of comparison results
•  
   7.4.3 Differences between the comparison algorithms
•  
   7.4.4 Comparison to other software
•  
  7.4.5 Future development
•  
   7.4.5.1 Extension and improvement of the comparison approaches
•  
   7.4.5.2 Additional user interface features
•  
   7.4.5.3 Further metadata visualization
•  
   7.4.5.4 Further improved interoperability using NeXML
•  
   7.5 Conclusion
•  
   7.6 Availability and requirements
•  
  7.7 Declarations
•  
   7.7.1 Authors contributions
•  
   7.7.2 Acknowledgements
•  
  8 TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
•  
   8.1 Background
•  
   8.2 Implementation
•  
  8.3 Results and discussion
•  
   8.3.1 Importing data
•  
   8.3.1.1 Mapping statistical support onto congruent nodes
•  
   8.3.1.2 Finding conflicting nodes and mapping contradictory support
•  
  8.3.2 Editing and formatting capabilities
•  
   8.3.2.1 Editing of node/branch data
•  
   8.3.2.2 Editing operations
•  
   8.3.2.3 Searching, replacing and translating tree leaf names
•  
   8.3.2.4 Formatting document elements
•  
   8.3.2.5 Automatically setting line width, text height, and color
•  
   8.3.3 Different view modes
•  
   8.3.4 Exporting to graphic formats and printing
•  
   8.3.5 Help
•  
   8.3.6 Comparison to previous software
•  
   8.4 Conclusions
•  
   8.5 Availability and requirements
•  
  8.6 Declarations
•  
   8.6.1 Authors' contributions
•  
   8.6.2 Acknowledgements
•  
  9 New features of the tree editor TreeGraph 2 to handle rich metadata and compare phylogenies
•  
   9.1 Introduction
•  
   9.2 Implementation
•  
  9.3 Results and discussion
•  
   9.3.1 Interactively comparing trees
•  
   9.3.2 Handling data for ancestral state reconstruction
•  
   9.3.3 Extended I/O functionality
•  
   9.3.4 New ways to calculate metadata
•  
   9.3.5 Additional new features and improvements
•  
  9.3.6 Ongoing extension of the metadata model
•  
   9.3.6.1 Status
•  
   9.3.6.2 Advantages of the new model
•  
  9.3.7 Comparison to other tree editors
•  
   9.3.7.1 Interactive tree comparison
•  
   9.3.7.2 Handling ancestral state reconstruction data
•  
   9.3.7.3 Extended metadata model
•  
  9.3.8 Future development
•  
   9.3.8.1 Implementing remaining components to release the new metadata model
•  
   9.3.8.2 Increasing scriptability
•  
   9.3.8.3 Integrating TreeGraph 2’s features into a larger phylogenetic workbench or the Taxonomic Editor
•  
   9.4 Conclusion
•  
   9.5 Availability and Requirements
•  
  9.6 Declarations
•  
   9.6.1 Author Contributions
•  
   9.6.2 Acknowledgements
•  
   Part III – General purpose software libraries and the bioinfweb portal
•  
  10 The bioinfweb portal
•  
   10.1 Introduction
•  
   10.2 Release manager
•  
   10.3 Social media
•  
   10.4 Aims of the portal
•  
   10.5 Conclusion
•  
  11 bioinfweb.commons: Shared bioinfweb components made available in a library
•  
   11.1 Introduction
•  
   11.2 Modules and provided functionality
•  
   11.3 Conclusion
•  
   11.4 Availability and Requirements
•  
  11.5 Declarations
•  
   11.5.1 Author Contributions
•  
   11.5.2 Acknowledgements
•  
  12 Toolkit Independent Components: Creating GUI components for both Swing and SWT
•  
   12.1 Introduction
•  
   12.2 Concept
•  
   12.3 Implementation
•  
   12.4 Results and discussion
•  
   12.5 Conclusion
•  
   12.6 Availability and requirements
•  
  12.7 Declarations
•  
   12.7.1 Author Contributions
•  
   12.7.2 Acknowledgements
•  
  Appending chapters
•  
  13 General discussion and outlook
•  
  13.1 Increasing data reuse and reproducibility
•  
   13.1.1 Developed functionality
•  
   13.1.2 Conserving relevant metadata throughout the whole taxonomic and phylogenetic workflow
•  
   13.1.3 Externally implemented GUI components for metadata attached by externally defined ontologies
•  
  13.2 Comparing phylogenetic data
•  
   13.2.1 Developed functionality
•  
   13.2.2 Current and future applications in MSA evaluation and improvement for phylogenetic purposes
•  
   14 List of abbreviations
•  
   15 References
•  
   16 Acknowledgements
•  
  17 Appendix
•  
  17.1 Curriculum vitae
•  
   17.1.1 Education
•  
   17.1.2 Higher education
•  
   17.1.3 Ph. D. studies
•  
   17.1.4 Compulsory community service
•  
   17.1.5 Professional occupation
•  
   17.2 List of peer reviewed articles
•  
   17.3 List of conference contributions