Structure Content

The ARIAweb server provides access to the main ARIA software functionalities (NMR data conversion and structure calculation). In addition, structure calculation results can be easily visualised, with a dedicated molecular viewer and graphical displays […]

Sustainable and comprehensive software distribution for the life sciences

We designed a continuous-flow culture system in which biofilm formation can be reproducibly monitored and controlled in microfermentors handled at flow-rates avoiding accumulation of planktonic bacteria. This model is suited for biofilm macroscopic analysis, […]

This tool allows you to visualize protein-protein interactions at different developmental periods and in different regions of the human brain : http://ppiviz.pasteur.fr/

CapsuleFinder is a program that detects capsule systems with high accuracy in proteic sequences.  It is based on the use of HMM profiles for the detection of the essential proteins of capsule biogenesis and  requires computational models describing […]

checkMyIndex is an application whose goal is to help in finding a set of compatible indexes for a sequencing experiment. It has been developped using the R/Shiny environment and is freely available at https://checkmyindex.pasteur.fr/. […]

This project aims at efficiently storing millions of unique molecular compounds along with some of their already calculated properties. The database named Chem-REST is able to deal with extensive sets of data: millions of […]

A new adapter removal program for next generation sequencing Clean-ngs is available on GitHub: https://github.com/PF2-pasteur-fr/clean_ngs For more information contact Bernd Jagla  

Comparative Gene Set Enrichment Analysis tool

Comat is a R toolbox that provides quality control reports, matrix distances, permutation test, corrected p values and graphics for the 2 by 2 comparison of contingency matrices of same dimension in batches.

Warning: This data is old and the site will be discontinued soon. We are working on an alternative. This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 […]

We have recently developed tools to visualize the results of CRISPR screens and design novel guide RNA for use in bacteria. These tools are available at crispr.pasteur.fr .

Document where are listed different websites dealing with various subjects of cytometry. Cytometry Tutorials

3 Posters gathering  basic cytometry memory aid : what is flow cytometry, controls in flow cytometry, sample preparation tip for cell sorting antibody titration for flow cytometry, doublets tandem dyes. Download : Cytometry Memory […]

Apoptosis-AnnexinV Basic Antibody Titration Protocol Basic Flow Cytometry Staining Protocol with FMOs BrdU Staining Kit for Flow Cytometry CellCycleProtocol Click-iT EdU Flow Cytometry Cell Proliferation Assay Detection of DNA Fragmentation by the TUNEL Technique […]

Dear Flow Core Users, The Flow Core is pleased to announce the EasyPanel New Version! What is Easy Panel ? Fully-automated panel designer and Antibody Stock/Inventory management system that the Pasteur Flow Core has a […]

The EDAM Browser is a client-side web-based visualization javascript widget for the navigation of the EDAM ontology. EDAM is a structured and controlled vocabulary describing bioinformatics and computational biology concepts. It is used to […]

Cytokinesis leads to the physical separation of daughter cells and concludes cell division. Final abscission occurs close to the midbody (or Flemming body), a prominent structure that matures at the center of the intercellular […]

Immunology at work – resource center Whether you want to review the basics, gain more in-depth knowledge, or discover the latest research tools, this resource hub contains rich and reliable technical content, designed for […]

fq2dna (FASTQ files to de novo assembly) is a command line tool to ease the de novo assembly oƒ archaea, bacteria or virus genomes ƒrom raw high-throughput sequencing (HTS) paired-end (PE) reads. Every data […]

ƒqCleanER (ƒastq Cleaning and Enhancing Routine) is a command line tool to ease the diƒƒerent standard preprocessing steps oƒ short high-throughput sequencing (HTS) reads. Eight standard HTS read processing steps can be carried out […]

We originally developed genetic tools to study adhesion and biofilm formation in commensal and pathogenic E. coli species. These tools are made freely available to the scientific community upon request. • pKOBEG Lambda Red […]

GeneTrek is an online tool that enables users to explore the association of human genes to neurodevelopmental disorders. Users can explore their own gene list or any of the curated gene list. Once queried, […]

Recent progress in sequencing and bioinformatics methods have given access to ancient DNA. The GenEvo project aims at understanding the differential evolutionary pressure on the key proteins implicated in the nervous system, especially those […]

The genomic and nomenclature databases of strains of pathogenic bacterial species are available through the Institut Pasteur BIGSdb portal: http://bigsdb.pasteur.fr. The portal is powered by the Bacterial Isolates Genome Sequence DataBase (BIGSdb) tool developed […]

Guidelines for DC preparation and flow cytometry analysis of mouse nonlymphoid tissues This article is part of the Dendritic Cell Guidelines article series, which provides a collection of state-of-the-art protocols for the preparation, phenotype […]

We developed a clinically relevant in vivo model of catheter-associated biofilm infections to design new and efficient biofilm-eradication approaches applicable to contaminated totally implantable venous access port (TIVAP) catheters.      Key publications •  Chauhan, A., J.M. […]

In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary […]

Integrated bash and R toolbox for linkage analysis using SLURM (TARS Cluster) that include (1) basic quality control of initial file structures, (2) quality control analysis and file preparation by the Alohomora software and […]

What is Live Mouse Tracker ? LMT is designed to track mice on the long term. It has been created with on idea on mind: to provide behaviourist a reliable system to annotate automatically […]

This web application allows the exchange of mouse vocalisation recording files. https://mousetube.pasteur.fr/ You can be part of the community by clicking here.

Easily, reliably, and quantitatively distinguish live and dead cells in minutes New LIVE/DEAD viability dye kits increase options Robust—staining is maintained for multiple weeks and labeled cells can be shipped stained without losing fluorescence […]

We are currently developping new optogenetic tools of interest for System Neuroscience.  Optogenetics is the combination of genetics and optics to control well-defined events within specific cells of living tissue. It includes the discovery and insertion into cells […]

Galaxy is an open source, web-based platform for data intensive biomedical research. It is developed by the Galaxy Team, which is based at the part of the Center for Comparative Genomics and Bioinformatics at […]

PLUMED-NEST is the public repository of the PLUMED consortium. It provides all the data needed to reproduce the results of a PLUMED-enhanced molecular dynamics simulation (or analysis) contained in a published paper. Furthermore, PLUMED-NEST […]

Python-cwlgen is a python library for the generation of CWL programmatically. It supports the generation of CommandLineTool and DockerRequirement. The library works for both Python 2.7.12+ and 3.6.0.

RΕQ is a program ƒor quickly estimating a conƒidence value at each branch oƒ a distance-based phylogenetic tree. Branch support assessment is commonly based on bootstrap procedures (e.g. Felsenstein 1985, Makarenkov et al. 2010, […]

CRISPR polymorphism is a powerful tool to subtype Salmonella strains and is now used in routine for epidemiological investigations. This tool gets a CRISPR profile by identifying the presence of known spacers and direct […]

Warning: This data is old and the site will be discontinued soon. We are working on an alternative. Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial […]

sequana_coverage is a standalone application that reports genomic regions of interest (ROIs) which are significantly over- or under-represented in high throughput sequencing data. Thanks to HTML reports, is allows users to browse the detected […]

Shiny Exploration tool for Transcriptomic Analysis

The single cell transcriptomics, epigenetic and genomics are supported by collaborative effort of the CB UTechS, Biomics and the Hub. The CB UTechS gathers expertise and high-end instrumentation for single cell phenotyping and sorting, single cell […]

Specifically for smartphomes and tablets (Apple and / or Androids), non-exhaustive list of reference or commercial applications on cytometry. Smartphones-Tablets Applications

Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification […]

The traditional spectral viewers are focused on the premise of measuring one fluorochrome in a single detector. With full spectrum flow cytometry becoming the new standard in measuring fluorescence, these systems operate on the premise of […]

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are […]

The database TXSSdb includes all results from our works on the detection of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. It is by far the most complete database […]