BOL: Related items

Postdoc position at Centre Méditerranéen de Médecine Moléculaire

Sun, 06 Jul 2014 11:23:06 -0500

The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).
The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ).

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.
Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Comprehensive list of visualization tools for biological pathways

Neel — Tue, 30 Jan 2018 06:01:31 -0600

The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads to a change of state in the cell. Pathways come in different flavors, depending on their functions in the cell – the three main types are metabolic pathways, gene regulatory pathways, and signaling pathways. These biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization.

Following are the comprehensive list of visualization tools for biological pathways:

BiNA

Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures

http://bina.unipax.info/

BioTapestry

Interactive tool for building, visualizing and sharing gene regulatory network models over the web

http://www.biotapestry.org/

Caleydo

Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets

http://www.caleydo.org/

CellDesigner

A modeling tool for biochemical networks

http://www.celldesigner.org/

Edinburgh Pathway Editor

Edit and draw pathway diagrams

http://epe.sourceforge.net/SourceForge/EPE.html

GenMAPP

Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes

http://www.genmapp.org/

Ingenuity IPA

Data integration platform and manually annotated pathways

http://tinyurl.com/IngenuityPath

JDesigner

Graphical modeling environment for biochemical reaction networks

http://jdesigner.sourceforge.net/Site/JDesigner.html

KaPPA View

Plant pathways

http://kpv.kazusa.or.jp/

KEGG Atlas

Interactive Kyoto Encyclopedia of Genes and Genomes pathways

http://www.genome.jp/kegg/

Omix

Visualizing multi-omics data in metabolic networks

https://www.omix-visualization.com

PathVisio

Biological pathway analysis software that allows drawing, editing and analysis of biological pathways

http://www.pathvisio.org/

VitaPad

Application to visualize biological pathways and map experimental data to them

http://tinyurl.com/vitapad/

Web tools for pathways

ArrayXPath

Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG

http://tinyurl.com/ArrayXPath/

GEPAT

Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts

http://gepat.sourceforge.net/

iPath

Web-based tool for the visualization, analysis and customization of pathway maps

http://pathways.embl.de/

Kegg-Based Viewer

KEGG-based pathway visualization tool for complex high-throughput data

http://www.g-language.org/data/marray/

MapMan

User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes

http://mapman.gabipd.org/web/guest/mapman

MetPA

Analysis and visualization of metabolomic data within the biological context of metabolic pathways

http://metpa.metabolomics.ca

Omics Viewer

Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)

http://www.biocyc.org/

Pathway Explorer

Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them

http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml

Pathway projector

Zoomable pathway browser using KEGG atlas and Google Maps API

http://www.g-language.org/PathwayProjector/

PATIKA

Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework

http://www.cs.bilkent.edu.tr/~patikaweb/

Reactome SkyPainter

Visualization of over-represented pathways and reactions from gene lists

http://www.reactome.org/skypainter-2

WikiPathways

Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community

http://www.wikipathways.org/

Nuclear Dynamics Lab

Thu, 17 Jul 2014 15:03:27 -0500

Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all.

More at http://www.babraham.ac.uk/our-research/nuclear-dynamics/

Bandage: interactive visualization of de novo genome assemblies

Shruti Paniwala — Mon, 04 Dec 2017 10:09:37 -0600

Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Address of the bookmark: http://rrwick.github.io/Bandage/

Pimp your brain: Bioinformatics

Wed, 20 Aug 2014 22:09:21 -0500

Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research. In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO More videos are available on www.mpimp-golm.mpg.de

xmatchview: smith-waterman alignment visualization

Rahul Nayak — Thu, 28 Dec 2017 09:00:58 -0600

xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994) http://www.phrap.org) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.

http://www.bcgsc.ca/platform/bioinfo/software/xmatchview

Address of the bookmark: https://github.com/warrenlr/xmatchview

Center for Molecular Dynamics Nepal (CMDN), Nepal

Wed, 23 Jul 2014 13:54:51 -0500

Center for Molecular Dynamics Nepal (CMDN), established 2007 prides itself as a research driven nongovernmental organization. Unlike other civil society organizations, CMDN is dedicated entirely to promoting research in the country. With its team of energetic and highly motivated experts, CMDN is now recognized as the leading public health and wildlife research organization of the country.

More at http://www.cmdn.org.np/main/index.php

G-compass: a comparative genome browser

Jit — Thu, 12 Apr 2018 10:00:27 -0500

G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvDB and its subdatabase Evola, respectively. G-compass is available for free of charge. [ Sample ]

Address of the bookmark: http://www.h-invitational.jp/g-compass/

The Genome 10K Project

Tue, 29 Jul 2014 09:11:04 -0500

https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts. The growing Genome 10K Community of Scientists (G10KCOS), made up of leading scientists representing major zoos, museums, research centers, and universities around the world, is dedicated to coordinating efforts in tissue specimen collection that will lay the groundwork for a large-scale sequencing and analysis project.

Genome U-Plot: a whole genome visualization

Rahul Nayak — Fri, 13 Jul 2018 19:50:41 -0500

Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities.

https://github.com/gaitat/GenomeUPlot

Address of the bookmark: https://github.com/gaitat/GenomeUPlot