Systems biology of lactic acid bacteria: a critical review

Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute

Three-valued completion for abductive logic programs

AbstractIn this paper, we propose a three-valued completion semantics for abductive logic programs, which solves some problems associated with the Console et al. two-valued completion semantics. The semantics is a generalization of Kunen's completion semantics for general logic programs, which is known to correspond very well to a class of effective proof procedures for general logic programs. Secondly, we propose a proof procedure for abductive logic programs, which is a generalization of a proof procedure for general logic programs based on constructive negation. This proof procedure is sound and complete with respect to the proposed semantics. By generalizing a number of results on general logic programs to the class of abductive logic programs, we present further evidence for the idea that limited forms of abduction can be added quite naturally to general logic programs

Proving deadlock freedom of logic programs with dynamic scheduling

In increasingly many logic programming systems, the Prolog left to right selection rule has been replaced with dynamic selection rules, that select an atom of a query among those satisfying suitable conditions. These conditions describe the form of the arguments of every program predicate, by means of a so-called delay declaration. Dynamic selection rules introduce the possibility of deadlock, an abnormal form of termination that occurs if the query is non-empty and it contains no `selectable' atoms. In this paper, we introduce a simple compositional assertional method for proving deadlock freedom. The method is based on the notion of suspension cover, a static description of the possible dynamic schedulings of the body atoms of a clause, according to a given delay declaration. In the method, we assume that monotonic assertions are used for specifying the conditions of the delay declaration. Apart sections are devoted to two more practical instances of the method, that use types and modes, respectively

FAME, the Flux Analysis and Modeling Environment

<p>Abstract</p> <p>Background</p> <p>The creation and modification of genome-scale metabolic models is a task that requires specialized software tools. While these are available, subsequently running or visualizing a model often relies on disjoint code, which adds additional actions to the analysis routine and, in our experience, renders these applications suboptimal for routine use by (systems) biologists.</p> <p>Results</p> <p>The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at <url>http://f-a-m-e.org/</url>.</p> <p>Conclusions</p> <p>With FAME, we present the community with an open source, user-friendly, web-based "one stop shop" for stoichiometric modeling. We expect the application will be of substantial use to investigators and educators alike.</p

Proving termination of logic programs with delay declarations

In this paper we propose a method for proving termination of logic programs with delay declarations. The method is based on the notion of recurrent logic program, which is used to prove programs terminating wrt an arbitrary selection rule. Most importantly, we use the notion of bound query (as proposed by M. Bezem) in the definition of cover, a new notion which forms the kernel of our approach. We introduce the class of delay recurrent programs and prove that programs in this class terminate for all local delay selection rules, provided that the delay conditions imply boundedness. The corresponding method can be also used to transform a logic program into a terminating logic program with delay declarations

Symposium on Lactic Acid Bacteria-reading while waiting for a meeting

This special thematic issue of FEMS Microbiology Reviews is truly special, because it contains contributions to a meeting that is yet to happen! As many others, the thirteenth Interna- tional Symposium on Lactic Acid Bacteria (LAB13) was a victim of the COVID-19 pandemic and has been postponed to next year. The conference is held every 3 years in The Netherlands, and is attended by researchers from academia and industry from all over the world, reflecting the importance of these microorgan- isms in food, health and basic science. As a tradition, the invited speakers are asked to contribute not only by a talk, but also by a thorough review on the topic of their presentation. These papers were already under review by the time it became clear that the coronavirus would not be contained and that we had to post- pone the meeting. However, we decided to move on and publish the reviews now, when still timely, and we are eagerly awaiting updated presentations next summer