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CeSGO project

Overview

En utilisant les Technologies de l’Information et de la Communication (TIC) ainsi que des logiciels et standards internationaux pour la gestion des métadonnées, l’analyse et le partage de données ainsi que la collaboration scientifique, CeSGO propose la mise en place d’une plate-forme e-Science couplée à un environnement virtuel de recherche centré sur les besoins des communautés des sciences de la vie.

SEEK ID: https://research-sharing.cesgo.org/projects/2

Public web page: https://www.cesgo.org

Organisms: Escherichia coli, Lactococcus lactis, Oncorhynchus mykiss

CesGO PALs: No PALs for this Project

Project created: 14th Oct 2016

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maDmp
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Integrating DMP data into Seek

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CeSGO
CeSGO project

The CeSGO project itself. Software development and dissemination activities.
This project will help to gain a better undestanding of the pros and cons of collaborative and scientific data management tools on a bioinformatics facility.

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Detection Of QTL and functional genomics study of osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss)
CeSGO project

Euryhalin teleosts can live in freshwater as well as in seawater. The success of their survival depends then on their osmotic acclimation capacities. The objective of my work is to describe acclimation processes in the salted water at the rainbow trout by a study coupling functional genomic and genetic approaches. From a first differential gill transcriptomic study, a list of candidates genes was established. This study also allowed to investigate the physiological answer to a hyperosmotic kinetics
...

Snapshots: Snapshot 1, Snapshot 2, Snapshot 3

DOI: 10.5072/zenodo.246141

Test investigation
CeSGO project

lorem

Snapshots: No snapshots

CeSGO communication
CeSGO project

Dissemination on the CeSGO project and environment

Person responsible: Olivier Collin

Snapshots: No snapshots

CeSGO usage
CeSGO project

How people are using the CeSGO infrastructure and its different services.

Person responsible: Olivier Collin

Snapshots: No snapshots

Detection Of QTL and eQTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus myhiss)
CeSGO project

There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregulation capacities after transfer to saline water in a nonmigratory captive-bred population of rainbow trout. A QTL design (5 full-sib families, about 200 F2 progeny each) was produced from a
...

Person responsible: Cyril Monjeaud

Snapshots: No snapshots

Time-course study of rainbow trout Oncorhynchus mykiss functional responses during transfer from freshwater to seawater
CeSGO project

90 trouts are transferred from freshwater to seawater during 21 days. Plamsatic ion concentrations and gill transcriptome expression are studied and related to better understand seawater acclimation functional processes on Rainbow trout.

Person responsible: Cyril Monjeaud

Snapshots: No snapshots

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CeSGO resources usage
CeSGO project
No description specified

Submitter: Olivier Collin

Assay type: Software development

Technology type: Information Technology

Snapshots: No snapshots

Transcription profiling
CeSGO project
No description specified

Submitter: Cyril Monjeaud

Assay type: Transcriptional Profiling

Technology type: Microarray

Snapshots: No snapshots

clinical chemistry analysis
CeSGO project
No description specified

Submitter: Cyril Monjeaud

Assay type: Reactomics

Technology type: Chemostat Measurement

Snapshots: No snapshots

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data transformed
CeSGO project
No description specified

Creator: Cyril Monjeaud

Submitter: Cyril Monjeaud

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Data day 2
CeSGO project

Chemical Measuments D2

Creators: Cyril Monjeaud, Yvan Le Bras

Submitter: Cyril Monjeaud

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megablast.out
CeSGO project
No description specified

Creator: Cyril Monjeaud

Submitter: Cyril Monjeaud

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blast_script.sh
CeSGO project
No description specified

Creator: Cyril Monjeaud

Submitter: Cyril Monjeaud

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sequences_COI.fasta
CeSGO project
No description specified

Creator: Cyril Monjeaud

Submitter: Cyril Monjeaud

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Kinetic Model of Lactococcus lactis PYK LightningSimulate Model on JWS
CeSGO project

Kinetic Model of Lactococcus lactis PYK
LightningSimulate Model on JWS

Creator: Cyril Monjeaud

Submitter: Cyril Monjeaud

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E-coli extraction protocol
CeSGO project

SOP for labelled E-coli extraction protocol

Creator: Cyril Monjeaud

Submitter: Cyril Monjeaud

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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
CeSGO project

Abstract (Expand)

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of … data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

Authors: Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R. McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L. Snoep, Stian Soiland-Reyes, Natalie J. Stanford, Neil Swainston, Nicole Washington, Alan R. Williams, Sarala M. Wimalaratne, Lilly M. Winfree, Katherine Wolstencroft, Carole Goble, Christopher J. Mungall, Melissa A. Haendel, Helen Parkinson

Date Published: 29th Jun 2017

Publication Type: Not specified

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads
CeSGO project

Abstract (Expand)

With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of … computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Dedicated to ‘whole-genome assembly-free’ treatments, the Colib’read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. With the Colib’read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.

Authors: Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru, Pierre Peterlongo

Date Published: 1st Dec 2016

Publication Type: Not specified

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
CeSGO project

Abstract (Expand)

BACKGROUND: In this paper, we address the problem of identifying and quantifying polymorphisms in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on … the fundamental idea that each polymorphism corresponds to a recognisable pattern in a De Bruijn graph constructed from the RNA-seq reads, we propose a general model for all polymorphisms in such graphs. We then introduce an exact algorithm, called KISSPLICE, to extract alternative splicing events. RESULTS: We show that KISSPLICE enables to identify more correct events than general purpose transcriptome assemblers. Additionally, on a 71 M reads dataset from human brain and liver tissues, KISSPLICE identified 3497 alternative splicing events, out of which 56% are not present in the annotations, which confirms recent estimates showing that the complexity of alternative splicing has been largely underestimated so far. CONCLUSIONS: We propose new models and algorithms for the detection of polymorphism in RNA-seq data. This opens the way to a new kind of studies on large HTS RNA-seq datasets, where the focus is not the global reconstruction of full-length transcripts, but local assembly of polymorphic regions. KISSPLICE is available for download at http://alcovna.genouest.org/kissplice/.

Authors: G. A. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou, M. F. Sagot, P. Peterlongo, V. Lacroix

Date Published: 2nd May 2012

Publication Type: Not specified

Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss).
CeSGO project

Abstract (Expand)

There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known … about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregulation capacities after transfer to saline water in a nonmigratory captive-bred population of rainbow trout.

Authors: Yvan Le Bras, Nicolas Dechamp, Francine Krieg, Olivier Filangi, René Guyomard, Mekki Boussaha, Henk Bovenhuis, Thomas G Pottinger, Patrick Prunet, Pascale Le Roy, Edwige Quillet

Date Published: 22nd Jun 2011

Publication Type: Not specified

CeSGO meeting with INIST
CeSGO project

Presentation of the CeSGO concepts to the DMP-OPIDoR team

Creator: Olivier Collin

Submitter: Olivier Collin

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