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Xia X.,Heidelberg Institute for Theoretical Studies HITS
Proceedings of the 2012 ASE International Conference on BioMedical Computing, BioMedCom 2012 | Year: 2013

The policy compliance problem is one of the categories of inconsistency problems existing between access control policies. One of the ways to cope with it is called policy comparison. In this paper we develop and use our approach to perform policy comparison, i.e. when newly specified access control policies for the resources are provided to be compared with certain original policy, we are able to ensure that the noncompliance problem between these newly specified policies and the original policies on the resources will be found. In this paper we propose the READ (Resolution and Abduction based) algorithm to be an approach of finding policy noncompliance. Our approach is based on the resolution and abduction work for Data log rules, and the evaluation of compliance is performed through set implication by Satisfiability Modulo Theories (SMT) Z3 prover. We will illustrate the implementation of READ algorithm with two examples from existing work and one example based on role based access control model. © 2012 IEEE.

Xia X.,Heidelberg Institute for Theoretical Studies HITS
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2013

Organizations collaborate with each other for resource sharing and task performing. To protect their resources from unauthorized access the organization domains adopt own access control models. The collaboration thus faces a problem that how a secure collaboration is built between the domains with distinct access control models. Currently there are approaches focusing on role based access control model (RBAC), where role mapping is considered to be the main technique. It assumes that all organizations adopt RBAC model, then builds a global access control policy on role mappings. However if the organization domains, also including collaboration domain, use distinct access control models, role mapping and global policy can not be built on these models. In this paper we propose an equivalent access based approach and introduce a mediator involved collaboration pattern, where access control model entities have corresponding mapping and linking sets on which the equivalent accesses are built. Collaboration also introduces the "Inter Domain Role Mapping" (IDRM) problem and we thus propose new algorithms for IDRM problem based on flat and hierarchical role structures, in addition we also introduce the necessary constraints transforming between organization and collaboration domains. Finally we analyzes our algorithms and present the testing and comparison results with existed approaches. © IFIP International Federation for Information Processing 2013.

Shi L.,Heidelberg Institute for Theoretical Studies HITS
Journal of integrative bioinformatics | Year: 2013

In systems biology, quantitative experimental data is the basis of building mathematical models. In most of the cases, they are stored in Excel files and hosted locally. To have a public database for collecting, retrieving and citing experimental raw data as well as experimental conditions is important for both experimentalists and modelers. However, the great effort needed in the data handling procedure and in the data submission procedure becomes the crucial limitation for experimentalists to contribute to a database, thereby impeding the database to deliver its benefit. Moreover, manual copy and paste operations which are commonly used in those procedures increase the chance of making mistakes. Excemplify, a web-based application, proposes a flexible and adaptable template-based solution to solve these problems. Comparing to the normal template based uploading approach, which is supported by some public databases, rather than predefining a format that is potentiall impractical, Excemplify allows users to create their own experiment-specific content templates in different experiment stages and to build corresponding knowledge bases for parsing. Utilizing the embedded knowledge of used templates, Excemplify is able to parse experimental data from the initial setup stage and generate following stages spreadsheets automatically. The proposed solution standardizes the flows of data traveling according to the standard procedures of applying the experiment, cuts down the amount of manual effort and reduces the chance of mistakes caused by manual data handling. In addition, it maintains the context of meta-data from the initial preparation manuscript and improves the data consistency. It interoperates and complements RightField and SEEK as well.

Hofberger J.A.,Wageningen University | Hofberger J.A.,Chinese Academy of Sciences | Zhou B.,Chinese Academy of Sciences | Zhou B.,Heidelberg Institute for Theoretical Studies HITS | And 4 more authors.
BMC Genomics | Year: 2014

Background: Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. Results: To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR "gatekeeper" loci sharing syntenic orthologs across all analyzed genomes. Conclusion: By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species. © 2014 Hofberger et al.

Pinzke A.,University of California at Santa Barbara | Oh S.P.,University of California at Santa Barbara | Pfrommer C.,Heidelberg Institute for Theoretical Studies HITS
Monthly Notices of the Royal Astronomical Society | Year: 2013

Many bright radio relics in the outskirts of galaxy clusters have low inferred Mach numbers, defying expectations from shock acceleration theory and heliospheric observations that the injection efficiency of relativistic particles plummets at low Mach numbers. With a suite of cosmological simulations, we follow the diffusive shock acceleration as well as radiative and Coulomb cooling of cosmic ray electrons during the assembly of a cluster. We find a substantial population of fossil electrons.When reaccelerated at a shock (through diffusive shock acceleration), they are competitive with direct injection at strong shocks and overwhelmingly dominate by many orders of magnitude at weak shocks,M< 3, which are the vast majority at the cluster periphery. Their relative importance depends on cooling physics and is robust to the shock acceleration model used. While the abundance of fossils can vary by a factor of ~10, the typical reaccelerated fossil population has radio brightness in excellent agreement with observations. Fossil electrons with 1 < γ < 100 (10 < γ < 104) provide the main seeds for reacceleration at strong (weak) shocks; we show that these are well resolved by our simulation.We construct a simple self-similar analytic model which assumes steady recent injection and cooling. It agrees well with our simulations, allowing rapid estimates and physical insight into the shape of the distribution function. We predict that the Low-Frequency Array (LOFAR) should find many more bright steep-spectrum radio relics, which are inconsistent with direct injection. A failure to take fossil cosmic ray electrons into account will lead to erroneous conclusions about the nature of particle acceleration at weak shocks; they arise from well-understood physical processes and cannot be ignored. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

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