Configuration management and product lines to enhance the replication process in software engineering

This research is concerned with the experimental software engineering area, specifically experiment replication. Replication has traditionally been viewed as a complex task in software engineering. This is possibly due to the present immaturity of the experimental paradigm applied to software development. Researchers usually use replication packages to replicate an experiment. However, replication packages are not the solution to all the information management problems that crop up when successive replications of an experiment accumulate. This research borrows ideas from the software configuration management and software product line paradigms to support the replication process. We believe that configuration management can help to manage and administer information from one replication to another: hypotheses, designs, data analysis, etc. The software product line paradigm can help to organize and manage any changes introduced into the experiment by each replication. We expect the union of the two paradigms in replication to improve the planning, design and execution of further replications and their alignment with existing replications. Additionally, this research work will contribute a web support environment for archiving information related to different experiment replications. Additionally, it will provide flexible enough information management support for running replications with different numbers and types of changes. Finally, it will afford massive storage of data from different replications. Experimenters working collaboratively on the same experiment must all have access to the different experiments.

The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional over-expression

Transcription factors (TFs) are key regulators of gene expression in all organisms. In eukaryotes, TFs are often represented by functionally redundant members of large gene families. Overexpression might prove a means to unveil the biological functions of redundant TFs; however, constitutive overexpression of TFs frequently causes severe developmental defects, preventing their functional characterization. Conditional overexpression strategies help to overcome this problem. Here, we report on the TRANSPLANTA collection of Arabidopsis lines, each expressing one of 949 TFs under the control of a β–estradiol-inducible promoter. Thus far, 1636 independent homozygous lines, representing an average of 2.6 lines for every TF, have been produced for the inducible expression of 634 TFs. Along with a GUS-GFP reporter, randomly selected TRANSPLANTA lines were tested and confirmed for conditional transgene expression upon β–estradiol treatment. As a proof of concept for the exploitation of this resource, β–estradiol-induced proliferation of root hairs, dark-induced senescence, anthocyanin accumulation and dwarfism were observed in lines conditionally expressing full-length cDNAs encoding RHD6, WRKY22, MYB123/TT2 and MYB26, respectively, in agreement with previously reported phenotypes conferred by these TFs. Further screening performed with other TRANSPLANTA lines allowed the identification of TFs involved in different plant biological processes, illustrating that the collection is a powerful resource for the functional characterization of TFs. For instance, ANAC058 and a TINY/AP2 TF were identified as modulators of ABA-mediated germination potential, and RAP2.10/DEAR4 was identified as a regulator of cell death in the hypocotyl–root transition zone. Seeds of TRANSPLANTA lines have been deposited at the Nottingham Arabidopsis Stock Centre for further distribution.