29 research outputs found
APE in the wild: automated exploration of proteomics workflows in the bio.tools registry
The bio.tools registry is a main catalogue of computational tools in the life sciences. More than 17 000 tools have been registered by the international bioinformatics community. The bio.tools metadata schema includes semantic annotations of tool functions, that is, formal descriptions of tools' data types, formats, and operations with terms from the EDAM bioinformatics ontology. Such annotations enable the automated composition of tools into multistep pipelines or workflows. In this Technical Note, we revisit a previous case study on the automated composition of proteomics workflows. We use the same four workflow scenarios but instead of using a small set of tools with carefully handcrafted annotations, we explore workflows directly on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation and extension of the workflow composition method previously used. Moving "into the wild" opens up an unprecedented wealth of tools and a huge number of alternative workflows. Automated composition tools can be used to explore this space of possibilities systematically. Inevitably, the mixed quality of semantic annotations in bio.tools leads to unintended or erroneous tool combinations. However, our results also show that additional control mechanisms (tool filters, configuration options, and workflow constraints) can effectively guide the exploration toward smaller sets of more meaningful workflows.Proteomic
Black hole thermodynamical entropy
As early as 1902, Gibbs pointed out that systems whose partition function
diverges, e.g. gravitation, lie outside the validity of the Boltzmann-Gibbs
(BG) theory. Consistently, since the pioneering Bekenstein-Hawking results,
physically meaningful evidence (e.g., the holographic principle) has
accumulated that the BG entropy of a black hole is
proportional to its area ( being a characteristic linear length), and
not to its volume . Similarly it exists the \emph{area law}, so named
because, for a wide class of strongly quantum-entangled -dimensional
systems, is proportional to if , and to if
, instead of being proportional to (). These results
violate the extensivity of the thermodynamical entropy of a -dimensional
system. This thermodynamical inconsistency disappears if we realize that the
thermodynamical entropy of such nonstandard systems is \emph{not} to be
identified with the BG {\it additive} entropy but with appropriately
generalized {\it nonadditive} entropies. Indeed, the celebrated usefulness of
the BG entropy is founded on hypothesis such as relatively weak probabilistic
correlations (and their connections to ergodicity, which by no means can be
assumed as a general rule of nature). Here we introduce a generalized entropy
which, for the Schwarzschild black hole and the area law, can solve the
thermodynamic puzzle.Comment: 7 pages, 2 figures. Accepted for publication in EPJ