Showing posts from 2017

Tout ça pour ça - Fhtagn - 001

Actes Sud au Pôle Nord Pour hacker de la glace Si elle programme fort Le froid la gèle en place Moralité : L'iceberg ça l'endort Stieg Larsson Millenium

BRANE Clust: cluster-assisted gene regulatory network inference refinement

The joined Gene Regulatory Network (GRN)  inference and clustering tool BRANE Clust has just been published in  BRANE Clust: cluster-assisted gene regulatory network inference refinement  in IEEE/ACM Transactions on Computational Biology and Bioinformatics , 2017 ( doi:10.1109/TCBB.2017.2688355 ). It is also featured on RNA-seq blog  and OMIC tools . Alternative versions are available as a preprint , on  biorxiv , with a  page  and  software  and in  HAL . Another brick in the BRANE  series wall, a series of bioinformatics tools based on graphs and optimization, dedicated to -omics gene expression data for GRN ( Gene Regulatory Network ) inference. While traditional Next-generation sequencing (NGS) pipelines often combine motley assumptions (correlation, normalization, clustering, inference), this work is an first step toward gracefully combining network inference and clustering.  BRANE Clust works as a post-processing tool upon classical network thresholding refinement. F

Co-simulation, state-of-the-art by Claudio Gomes

A few days ago, we had a seminar given by  Claudio Gomes (University of Antwerp, Belgium). He recently produced a  research  report (turned into a paper) on  Co-simulation: State of the Art  with  C. Thule, D. Broman, P. G. Larsen and H. Vangheluwe ( arxiv ). This work is an impressive body of work on tools enabling experts in different disciplines to collaborate more efficiently in the development of ever more complex systems. It overviews "co-simulation approaches, research challenges, and research opportunities" and "summarizes, bridges, and enhances future research in  this multidisciplinary area". The attendant slides   nicely summarize in  a didactic way the main issues pertaining to  coupled systems, via the composition of sub-system simulations. They deal with Terminology, Simulation units, Input extrapolation techniques, Orchestration algorithms, Algebraic loops, Convergence and Stability . Abstract: It is essential to find new ways of enablin

BARCHAN: Blob Alignment for Robust CHromatographic ANalysis (GCxGC)

In 1987, G. P. Barchan et al.   wrote a paper called:  Gas chromatographic method of determining carbon monoxide and dioxide .  But barkhan, or barchan , means more outside gas chromatography. It refers to sand dunes , with crescent shapes, modeled by the wind. BARCHAN: crescent-shaped sand dunes They inspired our image registration tool for comprehensive 2D chromatography peak alignment (GCxGC or GC2D). It was just publish ed as  BARCHAN: Blob Alignment for Robust CHromatographic ANalysis (GCxGC) , Journal of Chromatography A, February 2017. For given 2D chromatogram areas of interest, a baseline removal (BEADS) is applied, a peak detection is performed, blobs are detected and registered with a mixed rigid/non-rigid transformation based on the Coherent Point Drift technique. A pair of GCxGC chromatogram areas of interest. BARCHAN registration, example. The preprint is here . The HAL and the arxiv version. The abstract is next: Abstract: (Comprehensive) Two dim