Chiral-Yang-Mills theory, non commutative differential geometry, and the need for a Lie super-algebra

In Yang-Mills theory, the charges of the left and right massless Fermions are independent of each other. We propose a new paradigm where we remove this freedom and densify the algebraic structure of Yang-Mills theory by integrating the scalar Higgs field into a new gauge-chiral 1-form which connects Fermions of opposite chiralities. Using the Bianchi identity, we prove that the corresponding covariant differential is associative if and only if we gauge a Lie-Kac super-algebra. In this model, spontaneous symmetry breakdown naturally occurs along an odd generator of the super-algebra and induces a representation of the Connes-Lott non commutative differential geometry of the 2-point finite space.Comment: 17 pages, no figur

AceView: a comprehensive cDNA-supported gene and transcripts annotation

BACKGROUND: Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Annotation Assessment Project (EGASP) competition aimed at reproducing Gencode and finding new genes. The organizers evaluated the protein predictions in depth. We present a complementary analysis of the mRNAs, including alternative transcript variants. RESULTS: We evaluate 25 gene tracks from the University of California Santa Cruz (UCSC) genome browser. We either distinguish or collapse the alternative splice variants, and compare the genomic coordinates of exons, introns and nucleotides. Whole mRNA models, seen as chains of introns, are sorted to find the best matching pairs, and compared so that each mRNA is used only once. At the mRNA level, AceView is by far the closest to Gencode: the vast majority of transcripts of the two methods, including alternative variants, are identical. At the protein level, however, due to a lack of experimental data, our predictions differ: Gencode annotates proteins in only 41% of the mRNAs whereas AceView does so in virtually all. We describe the driving principles of AceView, and how, by performing hand-supervised automatic annotation, we solve the combinatorial splicing problem and summarize all of GenBank, dbEST and RefSeq into a genome-wide non-redundant but comprehensive cDNA-supported transcriptome. AceView accuracy is now validated by Gencode. CONCLUSION: Relative to a consensus mRNA catalog constructed from all evidence-based annotations, Gencode and AceView have 81% and 84% sensitivity, and 74% and 73% specificity, respectively. This close agreement validates a richer view of the human transcriptome, with three to five times more transcripts than in UCSC Known Genes (sensitivity 28%), RefSeq (sensitivity 21%) or Ensembl (sensitivity 19%)

Bridging the Gap Between Formal Methods and Software Engineering Using Model-based Technology

International audienceModel-based technology has evolved rapidly in the last decade, bringing immediate benefits to its users. Defining domain specific languages has never been easier, thanks to the infrastructure provided by frameworks such as eclipse EMF and XText. Industrial adoption is easy, you provide specialists with just the language they need. But this is also an opportunity for formal methods and tools to find a wider user base. A problem hindering adoption of formal methods is the effort one needs to invest in learning a particular formalism and the possible gap that exists between a handcrafted model and the reality. Model translation provides an easy way to obtain formal models from domain models that contain fine grain behavioral information, since a DSL typically also has some runtime or code generation support. This talk will present our experiences in building tools for model-checking of various languages using models and transformations and thus lever-aging the state of the art in model engineering technology

A new pooling strategy for high-throughput screening: the Shifted Transversal Design

BACKGROUND: In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplication of the individual experiments, thereby correcting for experimental noise. The main difficulty consists in designing the pools in a manner that is both efficient and robust: few pools should be necessary to correct the errors and identify the positives, yet the experiment should not be too vulnerable to biological shakiness. For example, some information should still be obtained even if there are slightly more positives or errors than expected. This is known as the group testing problem, or pooling problem. RESULTS: In this paper, we present a new non-adaptive combinatorial pooling design: the "shifted transversal design" (STD). It relies on arithmetics, and rests on two intuitive ideas: minimizing the co-occurrence of objects, and constructing pools of constant-sized intersections. We prove that it allows unambiguous decoding of noisy experimental observations. This design is highly flexible, and can be tailored to function robustly in a wide range of experimental settings (i.e., numbers of objects, fractions of positives, and expected error-rates). Furthermore, we show that our design compares favorably, in terms of efficiency, to the previously described non-adaptive combinatorial pooling designs. CONCLUSION: This method is currently being validated by field-testing in the context of yeast-two-hybrid interactome mapping, in collaboration with Marc Vidal's lab at the Dana Farber Cancer Institute. Many similar projects could benefit from using the Shifted Transversal Design

Symbolic Model-Checking using ITS-tools

International audienceWe present the symbolic model-checking toolset ITS-tools. The model-checking back-end engine is based on hierarchical set decision diagrams (SDD) and supports reachability, CTL and LTL model-checking, using both classical and original algorithms. As front-end input language, we promote a Guarded Action Language (GAL), a simple yet expressive language for concurrency. Transformations from popular formalisms into GAL are provided enabling fully symbolic model-checking of third party (Uppaal, Spin, Divine...) specifications. The tool design allows to easily build your own transformation, leveraging tools from the meta-modeling community. The ITS-tools additionally come with a user friendly GUI embedded in Eclipse

Topologically massive nonabelian BF models in arbitrary space-time dimensions

This work extends to the D-dimensional space-time the topological mass generation mechanism of the nonabelian BF model in four dimensions. In order to construct the gauge invariant nonabelian kinetic terms for a (D-2)-form B and a 1-form A, we introduce an auxiliary (D-3)-form V. Furthermore, we obtain a complete set of BRST and anti-BRST transformation rules of the fields using the so called horizontality condition, and construct a BRST/anti-BRST invariant quantum action for the model in D-dimensional space-time.Comment: 7 page