Gene regulatory networks have an important role to study the behaviour of genes. By analysing
these Gene Regulatory Networks we can get the detailed information i.e. the occurrence of diseases by
changing behaviour of GRNs. Many different approaches are used (i.e. qualitative modelling and hybrid
modelling) and various tools (i.e. GenoTech, GINsim) have been developed to model and simulate gene
regulatory networks. GenoTech allows the user to specify a GRN on Graphical User Interface (GUI) according
to the asynchronous multivalued logical functions of René Thomas, and to simulate and/or analyse its
qualitative dynamical behaviour. René
Thomas discrete modelling of gene regulatory network (GRN) is a
well known approach to study the dynamics of genes. It deals with some parameters which reflect the possible
targets of trajectories. Those parameters are priory unknown. These unknown parameters are fetched using
another model checking tool SMBioNet. SMBioNet produces all the possible parameters satisfying the given
Computational Logic Tree (CTL) formula as input. This approach involving logical parameters and conditions
also known as qualitative modelling of GRN. However, this approach neglects the time delays for a gene to
pass from one level of expression to another one i.e. inhibition to activation and vice versa. To find out these
time delays, another modelling tool HyTech is used to perform hybrid modelling of GRN.
We have developed a Java based tool called GenNet http://asanian.com/gennet to facilitate the
model checking user by providing a unique GUI layout for both qualitative and quantitative modelling of GRNs.
As we discussed, three separate modelling tools are used for complete modelling and analysis of a GRN. This
process is much lengthy and takes too much time. GenNet assists the modelling users by providing some extra
features i.e. CTL editor, parameters filtering and input/output files management.
GenNet takes a GRN network as input and does all the rest of computations i.e. CTL verification,
K-parameters generation, parameter implication to GRN, state graph, hybrid modelling and parameter
filtration automatically. GenNet serves the user by computing the results within seconds that were taking hours
and days of manual computation
The Web has evolved from a system of internet servers supporting formatted documents into a web of linked data. In the last years, the Web of Data is constantly growing. Consequently, it has developed a large collection of interlinked data sets from multiple domains. To exploit the diversity of all available data, federated queries are needed. However, many problems such as processing power, query response time, high workload or outdated information are hindering the query processing. In this paper, I am aiming to explain various optimization techniques which have the potential to lead a significant improvement on the final query runtime. I will start by briefly introducing recent approaches of federation and show why SPARQL federation endpoints are mostly in my focus. Specifically, I will compare state-of-the-art SPARQL query federation engines and analyze respective optimization approaches. The main federation engines I will analyze in terms of query optimization are FedX, DARQ and SPLENDID. As the result I provide concrete examples and conclude which of the engines has the best performance based on the query execution time as key criterion.