Technical platforms

Bioinformatics

The Bioinformatics platform was recently installed at the IBPC to put its know-how to the service of the IBPC units and to collaborate with the broader scientific community.

Contact: bioinfo@ibpc.fr

Objectives

  • To advise and train IBPC researchers in every-day bioinformatics analyses
  • To develop more sophisticated methods of analysis and new tools as a function of needs
  • To develop collaborative projects with the different teams and research units of the IBPC

Specific themes and expertise

  • NGS (analysis of genomics, transcriptomics, proteomics data)
  • Evolutionary biology
  • Structural bioinformatics

Crystallography

The Crystallography platform has evolved significantly since its inauguration on May 20, 2003 to meet to our current expectations. As of 2014 the platform is equipped with two latest-generation Mosquito pipetting robots allowing manipulation of biological macromolecules in viscous lipid phases and a distribution station (TTPlabtech) to prepare solutions used by the robots. The platform is equipped with incubators (18°C and 4°C), Zeiss microscopes and an automated system for visualizing crystals.

NMR

The IBPC’s biomolecular NMR platform is a platform of the research federation of the IBPC (FRC550). The platform serves the coordination of research in the field of nuclear magnetic resonance spectroscopy (NMR) within the IBPC. The platform provides the researchers, students and engineers of the IBPC with access to state-of-the-art infrastructure for the study of biological macromolecules and their complexes. The platform was installed in 2016 as part of the Equipex CACSICE. It consists of a Bruker Avance III-HD 700 MHz spectrometer and various liquid and solid probes. In 2018, thanks to additional funding from the Île-de-France region and the Labex Dynamo, the platform was equipped with a cryoplateform and a latest-generation liquid cryoprobe.

For autonomous users with adequate training in NMR spectroscopy, the NMR spectrometer time required for their projects is simply made available according to the availability of the machine. For users who do not have sufficient autonomy, expertise and support can be provided through collaborations with experienced users of the platform. Depending on the project, these expertise and support may concern all aspects of NMR studies with biological macromolecules in solution, including know-how in the production of isotopically labelled samples, the implementation of NMR experiments, data analysis and structural calculations. The platform is not able to provide services outside collaborations with experienced users of IBPC, and therefore invites the persons interested in NMR to discuss their projects with them

ACKNOWLEDGEMENTS

Sentence to include in any publication that uses results acquired at the IBPC biomolecular NMR platform :

“The authors acknowledge access to the biomolecular NMR platform of the IBPC that is supported by the CNRS, the Labex DYNAMO (ANR-11-LABX-0011), the Equipex CACSICE (ANR-11-EQPX-0008) and the Conseil Régional d’Île-de-France (SESAME grant)”

Proteomics

The Proteomics platform was installed at the IPBC in 2014 thanks to funding from LabEx DYNAMO and EquipEx CACSICE. Its equipment and know-how are available to the scientific community of the two consortia. 

The objectives of the platform are :

To advise researchers on the techniques available in the platform based on their projects

To analyse samples from their preparation to the exploitation of the results

To develop new analytical techniques as a function of researchers’ needs (e.g. label free quantifiacation)

To train researchers in sample preparation, data analysis and exploitation

The Proteomics platform can function as a service or in collaboration mode as a function of researchers’ preferences.

Equipment

The Proteomics platform is equipped with:

 

Analysis

The Proteomics platform proposes different types of services for sample preparation and analysis:

In-gel digestion of sample (spot or band)

Digestion of sample in solution

Purification of peptides (C18 column)

Identification of purified proteins  (simple peptide mixture)

Identification of proteins in a complex mixture (following chromatographic separation)

Measurement of mass of intact proteins (in solution)

Quantitative proteomics (label free techniques)

 

Protocols

Protocols are provided, but contact with the Proteomics platform is recommended before any sample preparation is undertaken

A reservation schedule for the MALDI-TOF is available on line for trained personnel at the IBPC at https://resa-equipement.ibpc.fr/.

For all external requests for analysis or training, please contact hamon@ibpc.fr.

 

 
 

Visualisation wall

The visualization platform at the IBPC institute offers an 25 MPixel high-resolution high-dimension display wall with stereoscopic 3D representations for a semi-immersive experience allowing researchers to explore and manipulate their data.

The display wall consists of 12 stereoscopic displays arranged in a four column by three row matrix setup with a total dimensions of 4.4m wide by 1.8m high and a resolution of 7680 by 3240 pixels, addressed as a single screen through Windows, Mac OSX or Linux workstations.

It empowers researchers to visualize high resolutions images (from electron, confocal, etc microscopy) and visualize macromolecule structures and simulations trajectories in 3D.

EQUIPMENT

The platform is composed of :

– display wall with stereoscopic representation composed of 12 displays  with a total dimensions of 4.4m wide by 1.8m high and a resolution of 7680 by 3240 pixels

– 3 workstations (Windows, Mac OS X, Linux) connected to the wall with 4 GPU cards in each.

– A control system (tablet, screen, keyboard and gyroscopic mouse) to interact with the wall.

SERVICE

The platform offers to researchers a high dimension and stereoscopic display to explore and manipulate their data. It allows to :

– Display high resolutions images from experimental procedure (Confocal Microscopy, Scanning Electron microscope, …)

– Display structure of macromolecules and trajectories of simulations in 3D (Pymol, Chimera, Coot, VMD, UnityMol, )

– Visualize simoutinlasy different type of data thanks to the high dimension.

– Display at the same time the content of 4 notebooks on the wall to facilitate information sharing during meetings.