Besides, the optimal solution is not necessarily the best approximation of the biological system. Analyzing multiple solutions from a repeated stochastic search to determine which parameters are most consistent is an alternative method. An analysis of many solutions can provide more information than the best solution from a single optimization run. Currently, the most precisely described spatio-temporal regulation mechanism for early development is the gap gene network in the fruit fly Drosophila melanogaster. One notable insight is the function of cross-regulatory interactions among gap genes. These interactions are necessary for precise gap gene expression domains to emerge from a larger spread in maternal concentration gradients. In comparison to most other metazoans, gene regulation in early fly embryos such as Drosophila melanogaster is easy to understand, because the regulatory proteins do not require intermediate metabolites to interact with the DNA. These straightforward regulatory interactions are coupled to the early fly morphology: no membranes are present during the first nuclear division cycles, so transcription factors can diffuse between nuclei. In other metazoan embryos, complex signaling pathways operate from the early cleavage stage cells, and many regulatory interactions are mediated by a chain of inter- and intracellular compounds. Even after the formation of membranes around the nuclei, the fly embryo outline does not change much due to its encapsulation in the eggshell. This allows a highly automated procedure for image segmentation and expression profile extraction. However, the shape of most other metazoan embryos changes continuously, especially during blastula formation and gastrulation. An extended pipeline is proposed with the purpose of elucidating gene regulation mechanisms in other animals beyond flies. The particular steps in this pipeline, summarized in Figure 2, already provide means to quantitatively compare external properties like average shapes and expression patterns among different species. The complete procedure may eventually allow the comparison of pattern formation programs. In the current study, the starlet sea BKM120 anemone Nematostella vectensis is used as a case study to investigate GRNs during embryonic development. As a model organism, N. vectensis is very convenient since it is sufficiently small and transparent for use with various microscopy methods, it is easily grown in a petri dish and it can reproduce sexually and asexually in a laboratory environment. Also in terms of development.