Ludo: A Case Study for Graph Transformation Tools

In this paper we describe the Ludo case, one of the case studies of the AGTIVE 2007 Tool Contest (see [22]). After summarising the case description, we give an overview of the submitted solutions. In particular, we propose a number of dimensions along which choices had to be made when solving the case, essentially setting up a solution space; we then plot the spectrum of solutions actually encountered into this solution space. In addition, there is a brief description of the special features of each of the submissions, to do justice to those aspects that are not distinguished in the general solution space

The Carboxy-Terminal Domain of Dictyostelium C-Module-Binding Factor Is an Independent Gene Regulatory Entity

The C-module-binding factor (CbfA) is a multidomain protein that belongs to the family of jumonji-type (JmjC) transcription regulators. In the social amoeba Dictyostelium discoideum, CbfA regulates gene expression during the unicellular growth phase and multicellular development. CbfA and a related D. discoideum CbfA-like protein, CbfB, share a paralogous domain arrangement that includes the JmjC domain, presumably a chromatin-remodeling activity, and two zinc finger-like (ZF) motifs. On the other hand, the CbfA and CbfB proteins have completely different carboxy-terminal domains, suggesting that the plasticity of such domains may have contributed to the adaptation of the CbfA-like transcription factors to the rapid genome evolution in the dictyostelid clade. To support this hypothesis we performed DNA microarray and real-time RT-PCR measurements and found that CbfA regulates at least 160 genes during the vegetative growth of D. discoideum cells. Functional annotation of these genes revealed that CbfA predominantly controls the expression of gene products involved in housekeeping functions, such as carbohydrate, purine nucleoside/nucleotide, and amino acid metabolism. The CbfA protein displays two different mechanisms of gene regulation. The expression of one set of CbfA-dependent genes requires at least the JmjC/ZF domain of the CbfA protein and thus may depend on chromatin modulation. Regulation of the larger group of genes, however, does not depend on the entire CbfA protein and requires only the carboxy-terminal domain of CbfA (CbfA-CTD). An AT-hook motif located in CbfA-CTD, which is known to mediate DNA binding to A+T-rich sequences in vitro, contributed to CbfA-CTD-dependent gene regulatory functions in vivo

Applying Graph Transformations to Database Re-Engineering

modeling concepts like inheritance, aggregation, and n-ary associations cannot be expressed in the relational data model. Additionally, many physical schemas of LDAs comprise optimizations that makei teven harder to grasp the real semantics of the data structure. Hence, the first activity in the DRE process is analyze available sources of information about the LDA, in order to yield a semantically annotated database schema. The resulting annotated schema is translated into an equivalent object-oriented conceptual schema. Subsequently, the conceptual schema might be extended or used as the basis for further re-engineering activities. Both tasks, legacy schema analysis and conceptual translation, are considered to human-intensive iterative [1,5], i.e., they cannot be perfomed in a fully-automatic, batch-oriented process. The reason for this is that legacy systems vary with respect to many technical and non-technical parameters: they use various hardand software platforms and comprise arcane coding concepts [6]). Computer aided DRE tools have a great potential to reduce the complexity (2 risk) of re-engineering largeLDAs that comprise several hundred thousand 6.1

Visual Programming with Graph Rewriting Systems

This paper gives an informal overview of the language PROGRES and its programming environment. For all details concerning the language's formal semantics definition the reader is referred to [20