MyLabStocks: a web-application to manage molecular biology materials.

Open AccessLaboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks under an open source licence. © 2014 Laboratoire de Biologie Moleculaire de la Cellule CNRS. Yeast published by John Wiley & Sons, Ltd

The complex pattern of epigenomic variation between natural yeast strains at single-nucleosome resolution

International audienceBackground: Epigenomic studies on humans and model species have revealed substantial inter‑individual variation in histone modification profiles. However, the pattern of this variation has not been precisely characterized, particularly regarding which genomic features are enriched for variability and whether distinct histone marks co‑vary synergistically. Yeast allows us to investigate intra‑species variation at high resolution while avoiding other sources of variation, such as cell type or subtype. Results: We profiled histone marks H3K4me3, H3K9ac, H3K14ac, H4K12ac and H3K4me1 in three unrelated wild strains of Saccharomyces cerevisiae at single‑nucleosome resolution and analyzed inter‑strain differences statistically. All five marks varied significantly at specific loci, but to different extents. The number of nucleosomes varying for a given mark between two strains ranged from 20 to several thousands; +1 nucleosomes were significantly less subject to variation. Genes with highly evolvable or responsive expression showed higher variability; however, the variation pattern could not be explained by known transcriptional differences between the strains. Synergistic variation of distinct marks was not systematic, with surprising differences between functionally related H3K9ac and H3K14ac. Interestingly, H3K14ac differences that persisted through transient hyperacetylation were supported by H3K4me3 differences, suggesting stabilization via cross talk. Conclusions: Quantitative variation of histone marks among S. cerevisiae strains is abundant and complex. Its relation to functional characteristics is modular and seems modest, with partial association with gene expression divergences, differences between functionally related marks and partial co‑variation between marks that may confer stability. Thus, the specific context of studies, such as which precise marks, individuals and genomic loci are investigated, is primor‑ dial in population epigenomics studies. The complexity found in this pilot survey in yeast suggests that high complexity can be anticipated among higher eukaryotes, including humans

epimedtools

A set of useful tools encapsulating some 'GEOquery' functions. This package relies on RC, caching features and memoisation to simplify, homogenize and speed up multi-omic analysis.Useful Tools Allowing Multi-Omics Analysi

protopackage

An empty R package build as a prototype. It illustrates development practices in R: documentation, literate programming, testing, versioning, continuous integration

Conception d'une plate-forme de services ubiquitaires intégrant des interfaces multimodales distribuées

Web-Based Information Technologies & Distributed Systems represent a powerful shift in computation, where people live, work, and play in a seamlessly interweaving computing environment. It postulates a world where people are surrounded by computing devices and a computing infrastructure that supports us in everything we do. Current means of interactions with applications are almost exclusively the keyboard and the mouse or emulations thereof. This kind of interface is well adapted for classic management of information, but the new usages, mobility, ubiquitous access to information need new interfaces and new interaction modes. This thesis aims to modelize and develop a distributed software platform allowing the user access to ubiquitous services through distributed interfaces in these new usage contexts. We propose the original architecture model UbiArch. This system extends the user interface in order to allow several modes of interactions, offering users the choice of using their voice thanks to headset or phone, or an input device such as a keypad, keyboard or other input device. For output, users will be able to listen to audio devices, and to view information on graphical displays such as phones, PDA or TV screen or by using a projector. This concept is called ``distributed modality''. The 3-tiers design of the mVIP services based on UbiArch offers a framework in order to implement multimodal services for many application contexts. Here, we have described the use of our technology in a biometric authentication context, in a multimodal cash point simulator and in a slide show application controlled from a vocal and DTMF remote phone. This thesis has shown the feasibility of such an architecture dealing with many components and protocols.Les technologies web ont permis de définir des services accessibles par tous, n'importe où et depuis de multiples terminaux. Si les utilisateurs intègrent maintenant l'usage des interfaces graphiques traditionnelles, la miniaturisation des équipements et l'émergence de nouvelles modalités offrent de nouvelles perspectives en matière d'informatique ubiquitaire. Dans ce mémoire, nous modélisons l'interaction ubiquitaire selon les principes fondamentaux des modèles de la littérature. Nous proposons une implémentation de notre modèle UbiArch sous forme d'une plate-forme de services et nous mettons à la disposition du concepteur d'applications web un ensemble d'outils interactifs, prêts à être intégrés dans des interfaces web. Nous illustrons les principes de notre modèle et le fonctionnement de notre plate-forme au travers de trois démonstrateurs. Chacune de ces réalisations intègre les capacités d'interaction des téléphones dans une application web et illustre les apports de notre travail en terme d'interaction multimodale distribuée

protopackage

An empty R package build as a prototype. It illustrates development practices in R: documentation, literate programming, testing, versioning, continuous integration

Natural Functional Diversity of the Yeast Galactose Network

International audienceThe aim of our research is to study the natural intra-species variability of the yeast galactose regulatory network. Our approach consists in studying more that 100 natural strains of yeast (S. cerevisiae). we will build a simulator and pepreforfromrm dynamic simulations of the galactose response using SPADES. SPADES is high performance computing platform targeting different supercomputer

dmethr

dmethr: a 3-step pipeline to explore DNA methylation controlled gene expression from omics dat

Conception d'une plate-forme de services ubiquitaires intégrant des interfaces multimodales distribuées

CAEN-BU Sciences et STAPS (141182103) / SudocSudocFranceF