Virus nomenclature below the species level : a standardized nomenclature for filovirus strains and variants rescued from cDNA

Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratoryadapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming,\virus name[(\strain[/)\isolation host-suffix[/ \country of sampling[/\year of sampling[/\genetic variant designation[-\isolate designation[, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to ‘‘Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1’’ (with the suffix ‘‘rec’’ identifying the recombinant nature of the virus and ‘‘abc1’’ being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as ‘‘EBOV H.sap/COD/95/ Kik-abc1’’) and abbreviations (such as ‘‘EBOV/Kik-abc1’’) could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. ‘‘EBOV’’ would suffice if only one EBOV strain/variant/isolate is addressed.http://link.springer.com/journal/705hb201

Practical methods for proving program termination

Abstract. We present two algorithms to prove termination of programs by synthesizing linear ranking functions. The first uses an invariant generator based on iterative forward propagation with widening and extracts ranking functions from the generated invariants by manipulating polyhedral cones. It is capable of finding subtle ranking functions which are linear combinations of many program variables, but is limited to programs with few variables. The second, more heuristic, algorithm targets the class of structured programs with single-variable ranking functions. Its invariant generator uses a heuristic extrapolation operator to avoid iterative forward propagation over program loops. For the programs we have considered, this approach converges faster and the invariants it discovers are sufficiently strong to imply the existence of ranking functions

Closure Induction in a Z-like Language

Simply-typed set-theoretic languages such as Z and B are widely used for program and system specifications. The main technique for reasoning about such specifications is induction. However, while partiality is an important concept in these languages, many standard approaches to automating induction proofs rely on the totality of all occurring functions. Reinterpreting the second author's recently proposed induction technique for partial functional programs, we introduce in this paper the new principle of "closure induction" for reasoning about the inductive properties of partial functions in simply-typed set-theoretic languages. In particular, closure induction allows us to prove partial correctness, that is, to prove those instances of conjectures for which designated partial functions are explicitly defined

Valigator: A Verification Tool with Bound and Invariant Generation

Abstract. We describe Valigator, a software tool for imperative program verification that efficiently combines symbolic computation and automated reasoning in a uniform framework. The system offers support for automatically generating and proving verification conditions and, most importantly, for automatically inferring loop invariants and bound assertions by means of symbolic summation, Gröbner basis computation, and quantifier elimination. We present general principles of the implementation and illustrate them on examples.