First released in 2010, the Rivet library forms an important repository for
analysis code, facilitating comparisons between measurements of the final
state in particle collisions and theoretical ...calculations of those final
states. We give an overview of Rivet's current design and implementation, its
uptake for analysis preservation and physics results, and summarise recent
developments including propagation of MC systematic-uncertainty weights,
heavy-ion and ep physics, and systems for detector emulation. In addition,
we provide a short user guide that supplements and updates the Rivet user
manual.
A new release of the Monte Carlo event generator Herwig (version 7.2) is now available. This version introduces a number of improvements over the major version 7.0, notably: multi-jet merging with ...the dipole shower at LO and NLO QCD; spin correlations in both the dipole and angular-ordered parton showers; an improved choice of evolution variable in the angular-ordered parton shower; improvements to mass effects and top decays in the dipole shower, improvements to the simulation of multiple-parton interactions, including diffractive processes; a new model for baryonic colour reconnection; improvements to strangeness production; as well as a new tune of the hadronisation parameters and support for generic Lorentz structures in BSM models. This article illustrates new features of versions 7.1 and 7.2.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Meiosis requires conserved transcriptional changes, but it is not known whether there is a corresponding set of RNA splicing switches. Here, we used RNAseq of mouse testis to identify changes ...associated with the progression from mitotic spermatogonia to meiotic spermatocytes. We identified ∼150 splicing switches, most of which affect conserved protein-coding exons. The expression of many key splicing regulators changed in the course of meiosis, including downregulation of polypyrimidine tract binding protein (PTBP1) and heterogeneous nuclear RNP A1, and upregulation of nPTB, Tra2β, muscleblind, CELF proteins, Sam68 and T-STAR. The sequences near the regulated exons were significantly enriched in target sites for PTB, Tra2β and STAR proteins. Reporter minigene experiments investigating representative exons in transfected cells showed that PTB binding sites were critical for splicing of a cassette exon in the Ralgps2 mRNA and a shift in alternative 5' splice site usage in the Bptf mRNA. We speculate that nPTB might functionally replace PTBP1 during meiosis for some target exons, with changes in the expression of other splicing factors helping to establish meiotic splicing patterns. Our data suggest that there are substantial changes in the determinants and patterns of alternative splicing in the mitotic-to-meiotic transition of the germ cell cycle.
Alternative splicing amplifies the information content of the genome, creating multiple mRNA isoforms from single genes. The evolutionarily conserved splicing activator Tra2β (Sfrs10) is essential ...for mouse embryogenesis and implicated in spermatogenesis. Here we find that Tra2β is up-regulated as the mitotic stem cell containing population of male germ cells differentiate into meiotic and post-meiotic cells. Using CLIP coupled to deep sequencing, we found that Tra2β binds a high frequency of exons and identified specific G/A rich motifs as frequent targets. Significantly, for the first time we have analysed the splicing effect of Sfrs10 depletion in vivo by generating a conditional neuronal-specific Sfrs10 knock-out mouse (Sfrs10(fl/fl); Nestin-Cre(tg/+)). This mouse has defects in brain development and allowed correlation of genuine physiologically Tra2β regulated exons. These belonged to a novel class which were longer than average size and importantly needed multiple cooperative Tra2β binding sites for efficient splicing activation, thus explaining the observed splicing defects in the knockout mice. Regulated exons included a cassette exon which produces a meiotic isoform of the Nasp histone chaperone that helps monitor DNA double-strand breaks. We also found a previously uncharacterised poison exon identifying a new pathway of feedback control between vertebrate Tra2 proteins. Both Nasp-T and the Tra2a poison exon are evolutionarily conserved, suggesting they might control fundamental developmental processes. Tra2β protein isoforms lacking the RRM were able to activate specific target exons indicating an additional functional role as a splicing co-activator. Significantly the N-terminal RS1 domain conserved between flies and humans was essential for the splicing activator function of Tra2β. Versions of Tra2β lacking this N-terminal RS1 domain potently repressed the same target exons activated by full-length Tra2β protein.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
UFO – The Universal FeynRules Output Degrande, Céline; Duhr, Claude; Fuks, Benjamin ...
Computer physics communications,
June 2012, 2012-6-00, Letnik:
183, Številka:
6
Journal Article
Recenzirano
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We present a new model format for automatized matrix-element generators, the so-called Universal FeynRules Output (UFO). The format is universal in the sense that it features compatibility with more ...than one single generator and is designed to be flexible, modular and agnostic of any assumption such as the number of particles or the color and Lorentz structures appearing in the interaction vertices. Unlike other model formats where text files need to be parsed, the information on the model is encoded into a Python module that can easily be linked to other computer codes. We then describe an interface for the Mathematica package FeynRules that allows for an automatic output of models in the UFO format.
Rivet user manual Buckley, Andy; Butterworth, Jonathan; Grellscheid, David ...
Computer physics communications,
12/2013, Letnik:
184, Številka:
12
Journal Article
Recenzirano
Odprti dostop
This is the manual and user guide for the Rivet system for the validation and tuning of Monte Carlo event generators. As well as the core Rivet library, this manual describes the usage of the rivet ...program and the AGILe generator interface library. The depth and level of description is chosen for users of the system, starting with the basics of using validation code written by others, and then covering sufficient details to write new Rivet analyses and calculational components.
Program title: Rivet
Catalogue identifier: AEPS_v1_0
Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPS_v1_0.html
Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 571126
No. of bytes in distributed program, including test data, etc.: 4717522
Distribution format: tar.gz
Programming language: C++, Python.
Computer: PC running Linux, Mac.
Operating system: Linux, Mac OS.
RAM: 20 MB
Classification: 11.9, 11.2.
External routines:
HepMC (https://savannah.cern.ch/projects/hepmc/),
GSL (http://www.gnu.org/software/gsl/manual/gsl-ref.html),
FastJet (http://fastjet.fr/),
Python (http://www.python.org/),
Swig (http://www.swig.org/),
Boost (http://www.boostsoftware.com/),
YAML (http://www.yaml.org/spec/1.2/spec.html)
Nature of problem:
Experimental measurements from high-energy particle colliders should be defined and stored in a general framework such that it is simple to compare theory predictions to them. Rivet is such a framework, and contains at the same time a large collection of existing measurements.
Solution method:
Rivet is based on HepMC events, a standardised output format provided by many theory simulation tools. Events are processed by Rivet to generate histograms for the requested list of analyses, incorporating all experimental phase space cuts and histogram definitions.
Restrictions:
Cannot calculate statistical errors for correlated events as they appear in NLO calculations.
Unusual features:
It is possible for the user to implement and use their own custom analysis as a module without having to modify the main Rivet code/installation.
Running time:
Depends on the number and complexity of analyses being applied, but typically a few hundred events per second.
Herwig 7.0/Herwig++ 3.0 release note Bellm, Johannes; Gieseke, Stefan; Grellscheid, David ...
European physical journal. C, Particles and fields,
04/2016, Letnik:
76, Številka:
4
Journal Article
Recenzirano
Odprti dostop
A major new release of the Monte Carlo event generator Herwig++ (version 3.0) is now available. This release marks the end of distinguishing Herwig++ and HERWIG development and therefore constitutes ...the first major release of version 7 of the Herwig event generator family. The new version features a number of significant improvements to the event simulation, including: built-in NLO hard process calculation for virtually all Standard Model processes, with matching to both angular-ordered and dipole shower modules via both subtractive (MC@NLO-type) and multiplicative (Powheg-type) algorithms; QED radiation and spin correlations in the angular-ordered shower; a consistent treatment of perturbative uncertainties within the hard process and parton showering. Several of the new features will be covered in detail in accompanying publications, and an update of the manual will follow in due course.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A
bstract
A new method providing general consistency constraints for Beyond-the-Standard-Model (BSM) theories, using measurements at particle colliders, is presented. The method, ‘Constraints On New ...Theories Using Rivet’, Contur, exploits the fact that particle-level differential measurements made in fiducial regions of phase-space have a high degree of model-independence. These measurements can therefore be compared to BSM physics implemented in Monte Carlo generators in a very generic way, allowing a wider array of final states to be considered than is typically the case. The Contur approach should be seen as complementary to the discovery potential of direct searches, being designed to eliminate inconsistent BSM proposals in a context where many (but perhaps not all) measurements are consistent with the Standard Model. We demonstrate, using a competitive simplified dark matter model, the power of this approach. The Contur method is highly scaleable to other models and future measurements.
Herwig++ physics and manual Bähr, Manuel; Gieseke, Stefan; Gigg, Martyn A. ...
European physical journal. C, Particles and fields,
12/2008, Letnik:
58, Številka:
4
Journal Article
Recenzirano
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In this paper we describe
version 2.2, a general-purpose Monte Carlo event generator for the simulation of hard lepton-lepton and hadron-hadron collisions. A number of important hard scattering ...processes are available, together with an interface via the Les Houches Accord to specialized matrix element generators for additional processes. The simulation of Beyond the Standard Model (BSM) physics includes a range of models and allows new models to be added by encoding the Feynman rules of the model. The parton-shower approach is used to simulate initial- and final-state QCD radiation, including colour coherence effects, with special emphasis on the correct description of radiation from heavy particles. The underlying event is simulated using an eikonal multiple parton-parton scattering model. The formation of hadrons from the quarks and gluons produced in the parton shower is described using the cluster hadronization model. Hadron decays are simulated using matrix elements, where possible including spin correlations and off-shell effects.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Tra2β regulates a number of splicing switches including activation of the human testis-specific exon HIPK3-T in the Homeodomain Interacting Protein Kinase 3 gene. By testing HIPK3-T exons of ...different intrinsic strengths, we found Tra2β most efficiently activated splicing inclusion of intrinsically weak exons, although these were spliced at a lower overall level. Both the RRM and N-terminal RS-rich region of Tra2β were required for splicing activation. Bioinformatic searches for splicing enhancers and repressors mapped four physically distinct exonic splicing enhancers (ESEs) within HIPK3-T, each containing the known Tra2β AGAA-rich binding site. Surprisingly disruption of each single ESE prevented Tra2β-mediated activation, although single mutated exons could still bind Tra2β protein by gel shifts and functional splicing analyses. Titration experiments indicate an additive model of HIPK3-T splicing activation, requiring availability of an array of four distinct ESEs to enable splicing activation. To enable this efficient Tra2β-mediated splicing switch to operate, a closely adjacent downstream and potentially competitive stronger 5′-splice site is actively repressed. Our data indicate that a novel arrangement of multiple mono-specific AGAA-rich ESEs coupled to a weak 5′-splice site functions as a responsive gauge. This gauge monitors changes in the specific nuclear concentration of the RNA binding protein Tra2β, and co-ordinately regulates HIPK3-T exon splicing inclusion.
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