Thesis


Multicellular Systems Biology of Development

Supplementary Online Material

Walter de Back
Center for Information Services and High Performance Computing
Technische Universität Dresden
Germany


PhD thesis

This website contains supplementary material as part of the PhD thesis on “Multicellular Systems Biology of Development” by Walter de Back.

Full text

The thesis can be downloaded in full text (pdf, 10 Mb).

Summary

A two-page summary (pdf, 0.25 Mb) is also available.


Defense

The thesis was successfully defended on November 3rd 2015 at the TU Dresden.

PhD_Defense_WdB_0311151

Committee

Thesis examiners

  • Prof. emer. Hans Meinhardt
    Max-Planck-Institute for Developmental Biology, Tübingen
  • Prof. dr. Christian Dahmann
    Institute of Genetics, TU Dresden

Promotion committee

  • Prof. dr. Christoph Neinhuis (chair)
    Institute of Botany, TU Dresden
  • Prof. dr. Christian Dahmann
    Institute of Genetics, TU Dresden
  • Prof. dr. Andreas Deutsch
    Center for Information Services and High Performance Computing, TU Dresden
  • Prof. dr. Ingo Röder
    Institute for Medical Informatics and Biometry
    Medical Faculty “Carl Gustav Carus”, TU Dresden

Software – Morpheus

The software platform Morpheus, described in Chapter 3, has been developed as part of this thesis. It implements the computational methods that are required for the cell-centered middle-out approach to multi-scale modeling of multicellular systems, as described in Chapters 1 and 2. Morpheus is designed with usability in mind to make computational modeling accessible for biologists.

Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.

Morpheus_screenshot_editor

Morpheus user interface

Installation

Morpheus v1.2 is provided below as a binary application for the most common operating systems. They can be installed using the native installation procedure for these operating systems.

For details, please read the installation_instructions (txt, 1.2 Kb).

Download Morpheus

OS Morpheus package Instructions
windows
  • Uncompress zip file
  • Run installers for Morpheus and Gnuplot
mac_bundle
  • Open disk image (dmg)
  • Drag Morpheus and Gnuplot to Applications
linux
  • Open package with package manager
  • To install using terminal, see instructions.

Documentation

The main sources for information on usage, modeling formalisms and the modeling language MorpheusML are listed below:


Models and Videos

Videos and model files discussed in chapters 3, 5, 6, 8, and 9 are found below.

  • Videos are in mp4 format that can be played in all modern (html5-enabled) web browser.
  • Models are in encoded in MorpheusML and require installation of Morpheus (see above).

How to open a model in Morpheus?

First, download the XML file containing the model description. After downloading, you can open a model in Morpheus in either of the following methods:

  1. Drag and drop the XML file on Morpheus’ user interface.
  2. Use the “Open” button in the toolbar and select the XML file.
  3. Use the menu “File->Open” and select the XML file.

For more details, see these instructions (txt, 1 kb) or the user_manual (pdf, 2Mb).

Chapter 3 – Table 3.1

Model files and videos related to table 3.1.

Differential equation models

A1
Download model
View videoA1

A2
Download model
View videoA1

A3
Download model
View videoA1

A4
Download model
View videoA1

Reaction-diffusion models

B1
Download model
View videoB1

B2
Model and domain.tif
View videoB1

B3
Download model
View videoB1

B4
Download model
View videoB1

Cellular Potts models

C1
Download model
View videoC1

C2
Download model
View videoC2

C3
Download model
View videoC3

C4
Model and crypt.tif
View videoC4

Multiscale models

D1
Download model
View videoD1

D2
Download model
View videoD2

D3
Download model
View videoD3

D4
Download model
View videoD4

Miscellaneous

E1
Download model
View videoE1

E2
Download model
View videoE2

E3
Download model
View videoE3


Chapter 5 – Figure 5.4

Download model (xml, 4.8 Kb)
View video
chapter5_poster

Chapter 6 – Figure 6.3

Development Loss of contact Loss of stabilization
Download model (xml, 4.5 Kb) Download model (xml, 4.5 Kb) Download model (xml, 4.5 Kb)
 View video View video
View video

Chapter 8 – Figure 8.3

Download model (xml, 4.9 Kb)
View video

Chapter 9 – Figure 9.1

Download model (xml, 6.3 Kb)
View video

Chapter 9 – Figure 9.4

Download model (xml, 5.5 Kb)
View video