Software project initiation and planning – an empirical study

This study describes a study of 14 software companies, on how they initiate and pre-plan software projects. The aim was to obtain an indication of the range of planning activities carried out. The study, using a convenience sample, was carried out using structured interviews, with questions about early software project planning activities. The study offers evidence that an iterative and incremental development process presents extra difficulties in the case of fixed-contract projects. The authors also found evidence that feasibility studies were common, but generally informal in nature. Documentation of the planning process, especially for project scoping, was variable. For incremental and iterative development projects, an upfront decision on software architecture was shown to be preferred over allowing the architecture to just ‘emerge’. There is also evidence that risk management is recognised but often performed incompletely. Finally appropriate future research arising from the study is described.

sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background
Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures.

Results
This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies.

Conclusion
The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap