Is Mathematics the Theory of Instantiated Structural Universals?

This paper rejects metaphysical realism about structural universals as a basis for mathematical realism about numbers, and argues that one construal of structural universals via non-well-founded sets should be resisted by the mathematical realist

A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk

Motivation: Hormone pathway interactions are crucial in shaping plant development, such as synergism between the auxin and brassinosteroid pathways in cell elongation. Both hormone pathways have been characterized in detail, revealing several feedback loops. The complexity of this network, combined with a shortage of kinetic data, renders its quantitative analysis virtually impossible at present. Results: As a first step towards overcoming these obstacles, we analyzed the network using a Boolean logic approach to build models of auxin and brassinosteroid signaling, and their interaction. To compare these discrete dynamic models across conditions, we transformed them into qualitative continuous systems, which predict network component states more accurately and can accommodate kinetic data as they become available. To this end, we developed an extension for the SQUAD software, allowing semi-quantitative analysis of network states. Contrasting the developmental output depending on cell type-specific modulators enabled us to identify a most parsimonious model, which explains initially paradoxical mutant phenotypes and revealed a novel physiological feature. Availability: The package SQUADD is freely available via the Bioconductor repository at http://www.bioconductor.org/help/bioc-views/release/bioc/html/SQUADD.html. Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

POLYPHEMUS: R package for comparative analysis of RNA polymerase II ChIP-seq profiles by non-linear normalization

Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) is increasingly used to map protein–chromatin interactions at global scale. The comparison of ChIP-seq profiles for RNA polymerase II (PolII) established in different biological contexts, such as specific developmental stages or specific time-points during cell differentiation, provides not only information about the presence/accumulation of PolII at transcription start sites (TSSs) but also about functional features of transcription, including PolII stalling, pausing and transcript elongation. However, annotation and normalization tools for comparative studies of multiple samples are currently missing. Here, we describe the R-package POLYPHEMUS, which integrates TSS annotation with PolII enrichment over TSSs and coding regions, and normalizes signal intensity profiles. Thereby POLYPHEMUS facilitates to extract information about global PolII action to reveal changes in the functional state of genes. We validated POLYPHEMUS using a kinetic study on retinoic acid-induced differentiation and a publicly available data set from a comparative PolII ChIP-seq profiling in Caenorhabditis elegans. We demonstrate that POLYPHEMUS corrects the data sets by normalizing for technical variation between samples and reveal the potential of the algorithm in comparing multiple data sets to infer features of transcription regulation from dynamic PolII binding profiles

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Editing New Testament Arabic Manuscripts in a TEI-base: fostering close reading in Digital Humanities

Accepté pour un numéro spécial JDMDH (ed. M. Büchler et L. Mellerin); version finale (v4)International audienceIf one is convinced that " quantitative research provides data not interpretation " [Moretti, 2005, 9], close reading should thus be considered as not only the necessary bridge between big data and interpretation but also the core duty of the Humanities. To test its potential in a neglected field – the Arabic manuscripts of the Letters of Paul of Tarsus – an enhanced, digital edition has been in development as a progression of a Swiss National Fund project. This short paper presents the development of this edition and perspectives regarding a second project. Based on the Edition Visualization Technology tool, the digital edition provides a transcription of the Arabic text, a standardized and vocalized version, as well as French translation with all texts encoded in TEI XML. Thanks to another Swiss National Foundation subsidy, a new research project on the unique New Testament, trilingual (Greek-Latin-Arabic) manuscript, the Marciana Library Gr. Z. 11 (379), 12th century, is currently underway. This project includes new features such as " Textlink " , " Hotspot " and notes: HumaReC

Editing New Testament Arabic Manuscripts in a TEI-base: fostering close reading in Digital Humanities

Accepté pour un numéro spécial JDMDH (ed. M. Büchler et L. Mellerin); version finale (v4)International audienceIf one is convinced that " quantitative research provides data not interpretation " [Moretti, 2005, 9], close reading should thus be considered as not only the necessary bridge between big data and interpretation but also the core duty of the Humanities. To test its potential in a neglected field – the Arabic manuscripts of the Letters of Paul of Tarsus – an enhanced, digital edition has been in development as a progression of a Swiss National Fund project. This short paper presents the development of this edition and perspectives regarding a second project. Based on the Edition Visualization Technology tool, the digital edition provides a transcription of the Arabic text, a standardized and vocalized version, as well as French translation with all texts encoded in TEI XML. Thanks to another Swiss National Foundation subsidy, a new research project on the unique New Testament, trilingual (Greek-Latin-Arabic) manuscript, the Marciana Library Gr. Z. 11 (379), 12th century, is currently underway. This project includes new features such as " Textlink " , " Hotspot " and notes: HumaReC

HumaReC : humanities research and continuous publishing : a digital New Testament test-case

How is Humanities research reshaped and transformed by the digital rhythm of data production and publication ? HumaReC investigates this question using the test-case of the edition of a unique trilingual Greek, Latin and Arabic New Testament manuscript; it is supported by a SNF grant (169869). Humanities research is reshaped and transformed by the digital rhythm of data production and publication. The challenge of the project is to develop a new model of Humanities research that affords a continuous publication of data and analysis as well as the evaluation of experts . In this perspective, HumaReC offers several levels of publications. The manuscript viewer offers images and transcriptions that will be continuously updated with new folios. The research blog will regularly provide postings of research results and input regarding the manuscript and the digital development of the project. Communicate with HumaReC! Continuous publishing offers the possibility of an involving document that can change in response to discussions and reactions. We encourage you to comment on the blog and to discuss in the forum. The web book offers a completely new format for the Humanities: it will present research results peer-reviewed by an editorial board of experts and by the publisher Brill, change and grow over the course of the project period and be able to respond quickly to advancements in Humanities research. http://www.helveticat.ch/lib/item?id=chamo:1893712 http://permalink.snl.ch/bib/sz00189371