Software
VARNA
A lightweight Java Applet dedicated to the quick drawing of an RNA secondary structure. VARNA is open-source and distributed under the terms of the GNU GPL license. Automatically scales up and down to take the most out of a limited space. Can draw multiple structures simultaneously. Accepts a wide range of documented and illustrated options, and offers basic user interaction.
GeneValorization
High-throughput technologies provide fundamental information concerning thousands of genes. Many of the current research laboratories daily use one or more of these technologies and end-up with lists of genes. Assessing the originality of the results obtained includes being aware of the number of publications
available concerning individual or multiple genes and accessing information about these publications. Faced
with the exponential growth of publications available and number of genes involved in a study, this task is
becoming particularly difficult to achieve. We introduce GENEVALORIZATION, a web-based tool which gives
a clear and handful overview of the bibliography available corresponding to the user input formed by (i) a
gene list (expressed by gene names or ids from ENTREZGENE) and (ii) a context of study (expressed by
keywords). From this input, GENEVALORIZATION provides a matrix containing the number of publications
with co-occurrences of gene names and keywords. Graphics are automatically generated to assess the relative
importance of genes within various contexts. Links to publications and other databases offering information on
genes and keywords are also available. To illustrate how helpful GENEVALORIZATION is, we have considered
the gene list of the OncotypeDX prognostic marker test.
HSIM
HSIM is a simulation tool for studying the dynamics of biochemical processes in a virtual bacteria. The
model is given using a language based on probabilistic rewriting rules that mimics the reactions between
biochemical species. HSIM is a stochastic automaton which implements an entity-centered model of objects.
This kind of modelling approach is an attractive alternative to differential equations for studying the diffusion
and interaction of the many different enzymes and metabolites in cells which may be present in either small or
large numbers. This software is freely. A compiled version is available
for the Windows, Linux and MacOSX operating systems.
CARTAJ
CARTAJ is a software that automatically predicts the topological family of three-way junctions in RNA
molecules, from their secondary structure only. The Cartaj software http://cartaj.lri.fr that implements our
method can be used online. It is also meant for being part of RNA modelling softwares and platforms. The
methodology and the results of CARTAJ are presented in this article.
