
BiGEst
- Information
- Infrastructure
- Data
- Tools
- Expertise
- Trainings
- Collaborations
- Ouverture
- Imports
- Gerer mes utilisateurs
Adress
Structure(s)
Unit:
Website
BiGEstInfrastructure
Effective storage
Cluster: cores number
CPU/hours a year
Bioinformatic tools number
Users number (last year)
Servers description
The platform also has access to part of the IT infrastructure distributed in the partner institutes of the platform:
• IBMP (Federated IT between IBMP, GMGM, IBMC (ARN, RIDI), Herbier de Strasbourg)
o Infrastructure : platform
o 1 Mac Os X computing cluster with 20 cores (16 to 32 GB RAM) :
• 12 To effective storage for computing + 16 To of passive storage dedicated to bioinformatics.
• 50 sequence analysis tools (Alignment, phylogeny, NGS, smallRNAs, EMBOSS, …).
• About 12 users, including 5 very active). CPU/year unquantified. Access reserved for partner institutes.
o 6 web servers
• public : PlantRNA - Cypedia – ANTHoS
• free access for partners : Omero - GBrowse – ncPRO-seq and Intranet (SGDB : MySQL)
• ICube : BFO, LBGI
o Infrastructure : platform
o Web server (KVM) : 24 cores (128 GB RAM)
o Total effective storage: 7 To
o Bioinformatics tools and databases available : 10
o Free access
• IGBMC : GalaxEast
o Infrastructure : platform
o Number and type of servers :
• nginx web servers (VM) : 2
• posgreSQL server (VM) : 1
• FTP servers (VM) : 2
o Computing farm : 16 nodes : 256 cores
o Total effective storage: 2,5 To
o Bioinformatics tools available: 119
o File manager : GridEngine
o Free access for GalaxEast users
• IGBMC : NGS-QC
o Infrastructure : platform (financed by Gronemeyer team and a maturation project supported by SATT Conectus Alsace.
o Number of servers : 2 servers ; 2 x 40 cores ; 256 GB RAM
o Total effective storage: > 20 To
o Data sets available : 1.
o Bioinformatics tools available: 1
o Free access
Access conditions
Les services sont accessible aux utilisateurs régionaux, ainsi qu’aux partenaires nationaux et internationaux. Pour les utilisateurs académiques, l'accès aux ressources est gratuite. La demande doit être faite en contactant la plateforme par email : https://grand-est.fr/nous-contacter/
![]() Annual visits: 10 200 an
Unique visits: 1 800 an
Quotes: 1
Latest update: Not documented
PlantRNADescriptionDatabase of annotated tRNA sequences from plants. Access conditionsFree Web access : http://plantrna.ibmp.cnrs.fr/ |
![]() Annual visits: Not documented
Unique visits: Not documented
Quotes: 7
Latest update: 01-07-2006
CYPediaDescriptionDatabase of P450 cytochromes from plants. Access conditionsFree Web access : http://www-ibmp.u-strasbg.fr/~CYPedia/ |
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Unique visits: Not documented
Quotes: 22
Latest update: 01-02-2014
OrthoinspectorDescriptionDatabase describing orthology/inparalogy relations and a suite of tools to exploit these data. Access conditionsFree Web or download access |
![]() Annual visits: Not documented
Unique visits: Not documented
Quotes: 1
Latest update: 01-02-2012
EvoluCodeDescriptionEvolutionary barcodes, representing evolutionary histories of the complete human proteome at the vertebrate scale. Access conditionsFree Web access |
![]() Annual visits: Not documented
Unique visits: Not documented
Quotes: 78
Latest update: 01-12-2011
BAliBASEDescriptionDatabase of multiple sequence alignments, used as a benchmark for the comparative evaluation of algorithms. Access conditionsFree Web or download access. |
![]() No website documentedAnnual visits: Not documented
Unique visits: Not documented
Quotes: Not documented
Latest update: 01-06-2013
GxDBDescriptionDatabase of transcriptomic data with automatic and standardized analyses. Access conditionsFree Web access after user identification. |
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Unique visits: Not documented
Quotes: Not documented
Latest update: Not documented
MousePatDescriptionAnalysis of the expression of nuclear receptors in the brains of adult mice. Collection of qPCR and in situ hybridization results. Access conditionsFree Web access : www.ics-mci.fr/mousepat |
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Unique visits: Not documented
Quotes: Not documented
Latest update: 01-11-2015
MouseCreDescriptionDatabase of CreERT2 lines of the ICS, with their characterization in different tissues and organs. Access conditionsFree Web access : www.ics-mci.fr/mousecre |
![]() Annual visits: 10 000 an
Unique visits: 8 000 an
Quotes: Not documented
Latest update: Not documented
ICS Mouse ZooDescriptionDatabase of genetically modified mice lines generated by the ICS. Standardized database of mouse models compatible with international standards, also including phenotypic parameters and metadata. These data are exchanged with the reference centres in the field and we develop statistical analyses in line with our data capture. Access conditionswww.ics-mci.fr/en/resources-and-technologies/eucomm-lines/ |
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Latest update: Not documented
dbSTARDescriptionA reference DataBase of human STructural vARiation from sequencing data Access conditionsTéléchargement libre. http://dbstar.lbgi.fr/dbstar/ |
![]() No website documentedAnnual visits: Not documented
Unique visits: Not documented
Quotes: 21
Downloads: Not documented
Assemble2DescriptionAssemble2 allows the design of RNA 2D structures interactively, creation and assembly of the corresponding RNA 3D modules directly in UCSF Chimera. The available services include 2D prediction, a database of structural motifs, 3D alignment of RNA sequences and annotation of 3D structures. Access conditionsFree Web access |
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Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
GETECDescriptionANALYSIS OF SEQUENCES Access conditions |
![]() No website documentedAnnual visits: Not documented
Unique visits: Not documented
Quotes: 21
Downloads: Not documented
MacsimsDescriptionANALYSIS OF SEQUENCES Access conditionsFree access web site |
![]() Annual visits: Not documented
Unique visits: 1 584 an
Quotes: 6
Downloads: Not documented
MSDADescriptionA software suite and databases for the interpretation of data from proteomic analyses by mass spectrometry (database search tools, de novo sequencing pipeline, extraction of protein functional annotations, extraction of spectra based on spectral quality criteria,...). Access conditionsFree Web access |
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Unique visits: Not documented
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Downloads: Not documented
NGS-QC GeneratorDescriptionANALYSIS OF THE DATA NGS - QUALITY CONTROL OF READINGS Access conditionsFree Web access for the academic research community. Premium access is also available on request. |
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Unique visits: 280 an
Quotes: Not documented
Downloads: Not documented
GalaxEastDescriptionThe objective of GalaxEast (http://www.galaxeast.fr) is to provide a reliable public Galaxy instance, with guaranteed availability and accessibility. GalaxEast offers a catalogue of about a hundred tools, mainly for handling of sequencing data (ChIP-seq, RNA-seq and DNAseq) high speed. The addition of proteomic and spectroscopy data analysis tools is planned for 2014. The tools come from both the official Galaxy toolshed and the developments of bioinformaticians from the local community. The new tools will be made available in the platform toolshed. The platform has a wiki that allows users to find documentation and request the addition of new tools and genomes. Access conditionsOpen access for the French academic research community. |
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Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
PipeAlignDescriptionAn online workflow for Multiple Sequence Alignment.
Plewniak F, et al. PipeAlign: A new toolkit for protein family analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3829-32.
Access conditions |
![]() Annual visits: Not documented
Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
OrthoInspectorDescriptionRapid detection of orthology and inparalogy relations.
Linard B, et al. OrthoInspector: comprehensive orthology analysis and visual exploration. BMC Bioinformatics. 2011 Jan 10;12:11.
Access conditions |
![]() No website documentedAnnual visits: Not documented
Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
GETECDescriptionGenome Evolution by Transformation, Expansion and Contraction. Access conditionshttp://icube-bioinfo.u-strasbg.fr/webMathematica/GETEC/Accueil.jsp |
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Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
VaRankDescriptionComprehensive workflow for annotating and ranking SNVs and indels from next generation sequencing data. Geoffroy V, et al. VaRank: a simple and powerful tool for ranking genetic variants. PeerJ 2015 3:e796 Access conditionsSource code avaiilable : http://www.lbgi.fr/VaRank/ |
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Unique visits: Not documented
Quotes: Not documented
Downloads: Not documented
EASEA CloudDescriptionEASEA (EAsy Specification of Evolutionary Algorithms) is an Artificial Evolution platform to implement evolutionary algorithms. Collet P, et al. EASEA : un langage de spécification pour les algorithmes évolutionnaires. [Rapport de recherche] RR-4218, INRIA. 2001. Access conditionsAvailable at http://easea.unistra.fr/easea/index.php/EASEA_platform |
Domains of activity
- Biomedical
- Agri-food
- Environment
- Biotechnology
- Biology
Description of expertise domains
• Rare genetic diseases (ciliopathies, retinopathies, myopathies,...) structural, functional, comparative genomics
• Development of quantitative methods based on mass spectrometry and their application to biological systems
• Non-coding RNA: architecture, mechanisms of evolution, and roles in pathogenicity
• Study of micro-organisms adapted to extreme environmental conditions
• Trans-disciplinary research at the interface of biology, biochemistry, physics, and medicine
The BISTRO platform regroups several bioinformatics platforms/services in various research institutes in Strasbourg:
Molecular Genetics, Genomics, Microbiology (GMGM)
The study of microorganisms adapted to extreme environmental conditions can reveal unsuspected microbial capabilities. Their understanding, including metabolic functions and biofilm formation involved in the adaptation to specific conditions is a major objective of environmental microbiology. We study these microbial adaptation mechanisms in ecosystems contaminated by toxic elements at 3 levels: (i) isolation of new strains and characterization of their metabolic properties, (ii) study of the adaptive response to toxic metals in laboratory conditions, (iii) study of environments contaminated to understand the functioning of the in-situ microbial communities.
Institute of Molecular and Cellular Biology (IBMC)
The "evolution of yeast non-coding RNA" team focuses on the role and evolution of ncRNA in biological mechanisms. These RNA have been known for a long time, but it was thought they were only "infrastructural components" of the translational machinery, leftovers of an ancestral "all RNA" world: ribosomal RNA, transfer RNA, intron RNA, as well as small nucleolar RNA. Through experimental and bioinformatics approaches, we are particularly interested in: (i) the study of structure-function relationships in certain families of ncRNA (ribosomes, riboswitches,...), (ii) the identification and the study of new ncRNA involved in pathogenicity mechanisms in certain yeast species.
Institute of Plant Molecular Biology (IBMP)
The research activity is dedicated to the study of the fundamental mechanisms of plant life, with applications including notably in the biotechnology or medical research fields. The studied areas are very diverse: (i) biosynthesis of bioactive molecules (involved in the development of materials, cosmetics, aromas or drugs) and their regulation, (ii) plant viruses, (iii) large regulatory pathways enabling the development and reproduction of plants and adaptation to their environment, (iv) the biogenesis of organelles, chloroplasts, and mitochondria, essential for the cells’ energy production and whose malfunction can cause highly deleterious effects with respect to cellular life.
Laboratory of engineering science, computer science and imaging (ICube)
The Complex systems and Translational Bioinformatics (CSTB), covers a broad spectrum of research in computer science: integrative bioinformatics and genomics, theoretical bioinformatics, data mining, knowledge engineering, and stochastic optimization. In the bioinformatics field, we focus primarily on the field of health, notably the study of rare genetic diseases, and the understanding of patho-physiological mechanisms involved in these diseases. These mechanisms often have a potential interest for the understanding of biological processes altered in more common diseases, such as obesity, diabetes or cancer.
Institute of Genetics and Molecular and Cellular Biology (IGBMC)
The objective of the Institute is to develop interdisciplinary research at the interface of biology, biochemistry, physics and medicine. We explore very diverse themes, combining basic and applied research in the field of health. The research work also concerns very diverse topics, ranging from structural analysis of proteins in human genetics, stem cells, biophysics and epigenetics. The scientific results have already allowed significant progress, notably in the understanding of many human diseases such as certain cancers or rare genetic diseases.
Mouse Clinic Institute (ICS - IGBMC)
The ICS IT service has strong computer expertise in the development of data processing protocols related to genetically modified mice: development of tools for phenotyping data capture, appropriate statistical analyses, procedures for interfacing with external resources. They are also developing integrative analyses of these data by cross-referencing them with available public resources (MGI, EMMA...).
Institut Pluridisciplinaire Hubert Curien (IPHC)
The goal of the “bioorganic mass spectrometry laboratory” (LSMBO) is the structural determination of macromolecules, mainly proteins, without any structural ambiguity at the atomic level. In proteomics, we focus on improving the description of structures (from identification to complete characterization), including post-translational modifications. Specific objectives include the description of non-covalent complexes and we are developing supra-molecular MS. We have applied this very innovative methodology to the analysis of biological complexes measuring several millions of Daltons, paving the way for a ‘complexomics’ that can be used in biology in the same way as proteomics.
Keywords:
- NGS data analysis
- Sequence analysis
- Machine learning
- Data curation
- Genomics: Chips
- Proteomics
Formation professionnelle
![]() No website documentedTrainees: Not documented
Training time: Not documented
No upcoming session scheduled
Clinique de la sourisDescriptionCNRS on-going training courses: participation in a general training course on mouse models, with 2 x 1 hour modules: Current phenotyping databases and tools; Statistical analyses of phenotyping. Access conditionsNot documented |
![]() No website documentedTrainees: Not documented
Training time: Not documented
No upcoming session scheduled
Workshop, introduction to JalView editorDescriptionin collaboration with the developers of Jalview Access conditionsOpen access after registration |
![]() No website documentedTrainees: 15 trainees / year
Training time: 1 day(s) / year
No upcoming session scheduled
Galaxy : packages and workflow deploiement.DescriptionNot documentedAccess conditionsNot documented |
![]() No website documentedTrainees: 8 trainees / year
Training time: 1 day(s) / year
No upcoming session scheduled
Infrastructure informatique distribuée de France Grilles: Grilles et CloudDescriptionNot documentedAccess conditionsNot documented |
![]() No website documentedTrainees: 10 trainees / year
Training time: 5 day(s) / year
No upcoming session scheduled
Spectrométrie de masse, analyse protéomique et interprétation des donnéesDescriptionNot documentedAccess conditionsNot documented |
Formation universitaire
![]() No website documentedTrainees: 65 trainees / year
Training time: 2 day(s) / year
No upcoming session scheduled
Analyse protéomique à haut débit, interprétation des données, ESBS / TPS, Strasbourg IllkirchDescriptionNot documentedAccess conditionsNot documented |
Internal publications
Thompson, JD. Statistics for Bioinformatics: Methods for Multiple Sequence Alignment. ISTE Press 2016
External publications
Huck O, Al-Hashemi J, Poidevin L, Poch O, Davideau J-L , Tenenbaum H, Amar S. Identification and Characterization of miRNA differentially expressed in macrophages exposed to Porphyromonas gingivalis infection. Infection and Immunity (in press)
Schartner V, Romero NB, Donkervoort S, Treves S, Munot P, Pierson TM, Dabaj I, Malfatti E, Zaharieva I, Zorzato F, Neto OA, Brochier G, Lornage X, Eymard B, Taratuto AL, Böhm J, Gonorazky H, Ramos-Platt L, Feng L, Phadke R, Bharucha-Goebel D, Sumner CJ, Bui MT, Lacene E, Beuvin M, Labasse C, Dondaine N, Schneider R, Thompson J, Boland A, Deleuze JF, Matthews E, Pakleza AN, Sewry CA, Biancalana V, Quijano-Roy S, Muntoni F, Fardeau M, Bönnemann CG, Laporte J. Dihydropyridine receptor (DHPR) congenital myopathy. Acta Neuropathologica, Springer Verlag (Germany) (in press)
Kole K, Berdugo N, Da Silva C, Aït-Ali N, Blond F, Poidevin L, Ripp R, Fontaine V, Wincker P, Zack D, Sahel J, Poch O, Léveillard T. Identification of an alternative splicing product of the Otx2 gene expressed in the neural retina and retinal pigmented epithelial cells, PLoS ONE 2016 11: e0150758
Krupina K, Kleiss C, Metzger T, Fournane S, Schmucker S, Hofmann K, Fischer B, Paul N, Porter I, Raffelsberger W, Poch O, Swedlow J, Brino L, Sumara I. Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules, Developmental Cell 2016, 36:63-78
Publications with the hosting laboratory
E. Benard, S. Lèbre, C. J. Michel, Genome Evolution by Transformation, Expansion and Contraction (GETEC) Biosystems, 2015
Geoffroy V, Pizot C, Redin C, Piton A, Vasli N, Stoetzel C, Blavier A, Laporte J, Muller J. VaRank: a simple and powerful tool for ranking genetic variants. PeerJ. 2015
Khenoussi W, Vanhoutrève R, Poch O, Thompson JD. SIBIS: a Bayesian model for inconsistent protein sequence estimation. Bioinformatics. 2014
Allot A, Anno YN, Poidevin L, Ripp R, Poch O, Lecompte O. PARSEC: PAtteRn SEarch and Contextualization. Bioinformatics. 2013 29:2643-4.
Romand R, Ripp R, Poidevin L, Boeglin M, Geffers L, Dollé P, Poch O. Integrated annotation and analysis of in situ hybridization images using the ImAnno system: application to the ear and sensory organs of the fetal mouse. PLoS One. 10:e0118024.
Arsène-Ploetze, F., Bertin, P.N., and Carapito, C. Proteomic tools to decipher microbial community structure and functioning., Environ Sci Pollut Res Int. 2015 22(18), 13599-612.
Vaca Jacome, A.-S., Rabilloud, T., Schaeffer-Reiss, C., Rompais, M., Ayoub, D., Lane, L., Bairoch, A., Van Dorsselaer, A., and Carapito, C. N-terminome analysis of the human mitochondrial proteome., Proteomics. 2015 15(14), 2519-2524.
Ethuin, P., Marlard, S., Delosiere, M., Carapito, C., Delalande, F., Van Dorsselaer, A., Dehaut, A., Lencel, V., Duflos, G., and Grard, T. Differentiation between fresh and frozen–thawed sea bass (Dicentrarchus labrax) fillets using two-dimensional gel electrophoresis, Food Chemistry 2015 176:294-301.
Schnell, G., Boeuf, A., Westermann, B., Jaulhac, B., Lipsker, D., Carapito, C., Boulanger, N., and Ehret-Sabatier, L. Discovery and targeted proteomics on cutaneous biopsies infected by borrelia to investigate lyme disease., Mol Cell Proteomics 2015 14(5), 1254-64.
Wasselin, T., Zahn, S., Le Maho, Y., Van Dorsselaer, A., Raclot, T., and Bertile, F. Exacerbated oxidative stress in the fasting liver according to fuel partitioning, Proteomics 2014 14(16), 1905-1921.
Plumel, M.I., Stier, A., Thiersé, D., Van Dorsselaer, A., Criscuolo, F., and Bertile, F. Litter size manipulation in laboratory mice: an example of how proteomic analysis can uncover new mechanisms underlying the cost of reproduction, Frontiers in Zoology 2014 11(41).
Stoetzel, C., S. Bar, J.O. De Craene, S. Scheidecker, C. Etard, J. Chicher, J.R. Reck, I. Perrault, V. Geoffroy, K. Chennen, U. Strahle, P. Hammann, S. Friant, and H. Dollfus, A mutation in VPS15 (PIK3R4) causes a ciliopathy and affects IFT20 release from the cis-Golgi. Nat Commun, 2016. 7: p. 13586.
Prasad, M.K., V. Geoffroy, S. Vicaire, B. Jost, M. Dumas, S. Le Gras, M. Switala, B. Gasse, V. Laugel-Haushalter, M. Paschaki, B. Leheup, D. Droz, A. Dalstein, A. Loing, B. Grollemund, M. Muller-Bolla, S. Lopez-Cazaux, M. Minoux, S. Jung, F. Obry, V. Vogt, J.L. Davideau, T. Davit-Beal, A.S. Kaiser, U. Moog, B. Richard, J.J. Morrier, J.P. Duprez, S. Odent, I. Bailleul-Forestier, M.M. Rousset, L. Merametdijan, A. Toutain, C. Joseph, F. Giuliano, J.C. Dahlet, A. Courval, M. El Alloussi, S. Laouina, S. Soskin, N. Guffon, A. Dieux, B. Doray, S. Feierabend, E. Ginglinger, B. Fournier, M. de la Dure Molla, Y. Alembik, C. Tardieu, F. Clauss, A. Berdal, C. Stoetzel, M.C. Maniere, H. Dollfus, and A. Bloch-Zupan, A targeted next-generation sequencing assay for the molecular diagnosis of genetic disorders with orodental involvement. J Med Genet, 2016. 53(2): p. 98-110.
Scheidecker, S., C. Etard, L. Haren, C. Stoetzel, S. Hull, G. Arno, V. Plagnol, S. Drunat, S. Passemard, A. Toutain, C. Obringer, M. Koob, V. Geoffroy, V. Marion, U. Strahle, P. Ostergaard, A. Verloes, A. Merdes, A.T. Moore, and H. Dollfus, Mutations in TUBGCP4 alter microtubule organization via the gamma-tubulin ring complex in autosomal-recessive microcephaly with chorioretinopathy. Am J Hum Genet, 2015. 96(4): p. 666-74.
Vanhoutreve R, Kress A, Legrand B, Gass H, Poch O, Thompson JD. LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system. BMC Bioinformatics. 2016;17:271.
Aouled El Haj S, Elloumi M, Thompson JD. Discovery of motifs in biological sequences, in Pattern Recognition, S. Ramakrishnan (Eds.), Ramakrishnan, 2016
Development
A patent application has been filed (EP123406478.4) describing the use of the NGS-QC system and the software has been registered at the APP (Paris). In addition, the NGS-QC generator system is currently supported by SATT-Conectus Alsace in the framework of a maturation process that aims to transform this concept into a start-up specialized in the certification of antibodies dedicated to NGS applications.
Users distribution
Explanation about this distribution:
• available only to local users, such as the computing power of BioImage servers and the associated bioinformatics tools, as well as the project hosting and support in terms of data processing or software development.
• available only to the French academic community. This includes the local Galaxy instance (GalaxEast), offering a catalogue of a hundred tools for manipulation of high throughput sequencing data (ChIP-seq, RNA - seq and DNAseq), proteomics and spectroscopy data.
• available to the international academic community. The majority of the databases and software are freely available online via websites listed on bioinfo-bistro.fr.
Platform's own projects
BioImage
- Participation in TerpFactory project (LabCom programme): data analysis on the BioImage computing server. Installation of tools and analysis protocols. Project with PAT private company, Nancy.
Collaborations
National projets
BioImage
- Participation in French ANRs
International and European projects
ICS
- Numerous European projects focused on the generation and phenotyping of mouse models: EUMORPHIA (2002-2006), EUMODIC (2007-2012), EUCOMM (2006-2010), CASIMIR (2007-2010), EMMA (2009 /), IMPC (2011 /). Active role in several workpackages: advice on IT architectures to be installed, statistical analyses, data export.
Projects with industry
- Collaboration established in 2003 for data exchange and specification of phenotyping database for MERCK.
Collaboration projects not founded through an external organism
Provision of services not founded through an external organism
Animations (Workshops, Work-groups, seminars, conferences ... )
• Organisation of Strasbourg bioinformatics meetings: 2 / year. Thematic exchanges.
• Organisation of « bioinfo » seminars: 3 / year (presentation of tools, IT infrastructure, …).
• Organisation of GalaxEast (Galaxy) workgroup, with thte goal of sharing tools developed by bioinformaticians in Strasbourg with the scientific community
• Participation in "Strasbourg microbiology federation meetings", 2 / year
• Participation in organisation of ECCB 2014 conference in Strasbourg