Are We Legislating Away Our Scientific Future? The Database Debate

The ambiguity of the present copyright laws governing the protection of databases creates a situation where database owners, unsure of how IP laws safeguard their information, overprotect their data with oppressive licenses and technological mechanisms (condoned by the DMCA) that impede interoperation. Databases are fundamental to scientific research, yet the lack of interoperability between databases and limited access inhibits this research. The US Congress, spurred by the European Database Directive, and heavily lobbied by the commercial database industry, is presently considering ways to legislate database protections; most of the present suggestions for legislation will be detrimental to scientific progress. The author agrees that new legislation is necessary, but not to provide extra-copyright protections, as database owners would like, but to create an environment wherein data is easily accessible to academic research and interoperability is encouraged; yet simultaneously providing database owners with incentives to produce new databases. One possibility would be to introduce standardized compulsory licensing of databases to academics following an embargo period where databases could be sold at free-market prices (to recoup costs). Databases would be given some sort of intellectual property protection both during and after this embargo in return for a limiting of technical safeguards and conforming to interoperability standards

User-oriented security supporting inter-disciplinary life science research across the grid

Understanding potential genetic factors in disease or development of personalised e-Health solutions require scientists to access a multitude of data and compute resources across the Internet from functional genomics resources through to epidemiological studies. The Grid paradigm provides a compelling model whereby seamless access to these resources can be achieved. However, the acceptance of Grid technologies in this domain by researchers and resource owners must satisfy particular constraints from this community - two of the most critical of these constraints being advanced security and usability. In this paper we show how the Internet2 Shibboleth technology combined with advanced authorisation infrastructures can help address these constraints. We demonstrate the viability of this approach through a selection of case studies across the complete life science spectrum

Locating regions in a sequence under density constraints

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence matching. Mathematically, this corresponds to searching a string of 0s and 1s for a substring whose relative proportion of 1s lies between given lower and upper bounds. We consider the algorithmic problem of locating the longest such substring, as well as other related problems (such as finding the shortest substring or a maximal set of disjoint substrings). For locating the longest such substring, we develop an algorithm that runs in O(n) time, improving upon the previous best-known O(n log n) result. For the related problems we develop O(n log log n) algorithms, again improving upon the best-known O(n log n) results. Practical testing verifies that our new algorithms enjoy significantly smaller time and memory footprints, and can process sequences that are orders of magnitude longer as a result.Comment: 17 pages, 8 figures; v2: minor revisions, additional explanations; to appear in SIAM Journal on Computin

Dys-regulated Gene Expression Networks by Meta-Analysis of Microarray Data on Oral Squamous Cell Carcinoma

Background: Oral squamous cell carcinoma (OSCC) is the sixth most common type of carcinoma worldwide. Development of OSCC is a multi-step process involving genes related to cell cycle, growth control, apoptosis, DNA damage response and other cellular regulators. The pathogenic pathways involved in this tumor are mostly unknown and therefore a better characterization of OSCC gene expression profile would represent a considerable advance. The availability of publicly available gene expression datasets has opened up new challenges especially for the integration of data generated by different research groups and different array platforms with the purpose of obtaining new insights on the biological process investigated.

Results: In this work we performed a meta-analysis on four microarray and four datasets of gene expression data on OSCC in order to evaluate the degree of agreement of the biological results obtained by these different studies and to identify common regulatory pathways that could be responsible of tumor growth. Sixteen dys-regulated pathways implicated in OSCC were mined out from the four published datasets, and most importantly three pathways were first reported. Those regulatory pathways and biological processes which are significantly enriched have been investigated by means of literatures and meanwhile, four genes of the maximally altered pathways, ECM-receptor interaction, were validated and identified by qRT-PCR as a possible candidate of aggressiveness of OSCC.

Conclusion: we have developed a robust method for analyzing pathways altered in OSCC using three expression array data sets. This study sets a stage for the further discovery of the basic mechanisms that may underlie a diseased state and would help in identifying critical nodes in the pathway that can be targeted for diagnosis and therapeutic intervention. In addition, those who are interested in our approach can obtain the software package (MATLAB platform) by email freely

User oriented access to secure biomedical resources through the grid

The life science domain is typified by heterogeneous data sets that are evolving at an exponential rate. Numerous post-genomic databases and areas of post-genomic life science research have been established and are being actively explored. Whilst many of these databases are public and freely accessible, it is often the case that researchers have data that is not so freely available and access to this data needs to be strictly controlled when distributed collaborative research is undertaken. Grid technologies provide one mechanism by which access to and integration of federated data sets is possible. Combining such data access and integration technologies with fine grained security infrastructures facilitates the establishment of virtual organisations (VO). However experience has shown that the general research (non-Grid) community are not comfortable with the Grid and its associated security models based upon public key infrastructures (PKIs). The Internet2 Shibboleth technology helps to overcome this through users only having to log in to their home site to gain access to resources across a VO – or in Shibboleth terminology a federation. In this paper we outline how we have applied the combination of Grid technologies, advanced security infrastructures and the Internet2 Shibboleth technology in several biomedical projects to provide a user-oriented model for secure access to and usage of Grid resources. We believe that this model may well become the de facto mechanism for undertaking e-Research on the Grid across numerous domains including the life sciences