Neurosciences Intégratives et Computationnelles - … · Neurosciences Intégratives et Computationnelles CNRS ... V1 Cognisciences The team is interested in the dynamics of neuronal

Section des Unités de recherche

Evaluation report Research unit

Neurosciences Intégratives et Computationnelles

CNRS

February 2009

Section des Unités de recherche

Evaluation report Research unit Neurosciences Intégratives et Computationnelles

CNRS

February 2009

Evaluation report

The research unit :

Name of the research unit : Unité de Neurosciences Integratives et Computationnelles (UNIC)

Requested label : UPR CNRS (Neuroscience, Information et Complexité)

N° in case of renewal : UPR 2191

Head of the research unit : M. Yves FREGNAC

Research organization :

CNRS

Other university or school :

University Paris 11

Date of the visit :

12th January 2009

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Members of the visiting committee

Chairman of the commitee : M. Angus SILVER, University College London, UK

Other committee members : M. Thomas BORAUD, University Bordeaux 2, France

M. David HANSEL, University Paris 5, France

M. Daniel CLESSE, Institut de Neurosciences Cellulaires et Intégratives, Strasbourg, France

CNU, CoNRS, CSS INSERM, INRA, INRIA, IRD representatives : M. Jean-Marie CABELGUEN, CNU representative, Bordeaux, France

M. Clement LENA, CoNRS representative, Paris, France

Observers

AERES scientific representative: M. Erwan BEZARD

University or school representative: M. Alexandre REVCOLEVSCHI, University Paris 11

Research organization representative : Ms. Nathalie LERESCHE, CNRS

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Evaluation report

1 Short presentation of the research unit

— Numbers of full time researchers : 8 — Number of post doctoral fellows : 8 — Number of researcher with teaching duties : 1 — Number of PhD students : 9, all with a fellowship — Number of technicians and administrative assistants : 5 — Numbers of HDR and of HDR who are PhD students avisors : 5 — Numbers of PhD students who have obtained their PhD during the past 4 years : 9 — Average thesis duration 4.3 years — Numbers of lab members who have been granted a PEDR : 0 — Numbers of “publishing” lab members : 12 of 16 (including 4 postdocs)

2 Preparation and execution of the visit

The visit occurred on the 12th January 2009. The preparation and execution of the visit was as specified in the Aeres guidelines. The visit went smoothly with all aspects of the evaluation covered satisfactorily.

Time : from 9 :00 to 9 :30 Time length : 30 minutes Door-closed meeting : Committee members and AERES representative

Time : from 9 :30 to 10 :00 Time length: 30 minutes including questions Presentation by Dr. Fregnac : past activity and projects

Time : from 10 :15 to 11 :00 Time length: 45 minutes including questions Presentation by the leader of team #1: past activity and projects



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Lunch from 13 :15 to 13 :45 Lunch



Time : from 15 :15 to 15 :45 Time length : 30 minutes Two meetings at the same time

• Meeting with PhD students and postdoctoral fellows • Meeting with engineers, technicians and administrative assistants

Time : from 15 :45 to 16 :15 Time length : 30 minutes Door-closed meeting : Committee members, AERES representative, University and Research Organization representatives

Time : from 16 :15 to 17 :45 Time length : 90 minutes Door-closed meeting : Committee members, AERES representative

3 Overall appreciation of the activity of the research unit, of its links with local, national and international partners

This research unit has an excellent international reputation. It has produced an impressive volume of world class science and developed important new methods over the last 4 years. A new unit called “Unite de Neuroscience Information and Complexite” is proposed, thereby keeping the same internationally recogniced UNIC acronym. The new unit will have an additonal team which will work on the newly emerging field of neuroinformatics. The proposed program of work for the unit is world class and the technological development is important and promising.

4 Specific appreciation team by team and/or project by project

Team 1. V1 Cognisciences

The team is interested in the dynamics of neuronal activity in the primary visual cortex. This team is particularly involved in the demonstration that horizontal connections in the cortex and inhibitory/excitatory balance play a major role in shaping the neuronal activity in paradigms less trivial than the classical moving bars or gratings. The team has taken the approach of using subthreshold membrane potential fluctuations, hence the incoming synaptic activity into individual neurons, to access the dynamics of the network.

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This requires extremely difficult and demanding intracellular recordings in vivo in the cat. The team also contributes to international efforts of cortical neurons’ classification and database construction. A member of the team more specifically involved in the past four years in simulations and in the elaboration of a meta-simulator is applying to form an independent team in the lab. The strengths of this team are in the ambition and originality of projects in terms of paradigms and approaches. This requires constant technical developments for stimuli generation, recording techniques and data analysis (e.g. active electrode compensation, time-resolved separation of excitatory and inhibitory conductances), which are possible notably because of the excellent technical support in the lab. The team is well funded. Students and post-docs feel supported and are satisfied by their training. 4 students have defended their thesis in the last four years. The team has a relatively low rate of publication, but this is for a large part due to the technically challenging and highly innovative approaches taken. The main weakness of the team comes from the lack of permanent researchers, while the team leader has substantial local and international administrative responsibilities. Therefore, the experimental training of students on a daily basis critically relies on a single senior postdoc and/or interactions with members of other teams.

Note de l’équipe

Qualité scientifique et production

Rayonnement et

attractivité, intégration dans l’environnement

Stratégie,

gouvernance et vie du laboratoire

Appréciation du

projet

A+

A+

A

A

A+

Team 2 Neuromodulation and Neuronal Plasticity

This group (leader plus a post doc, 3 PhD students and 1 Master student) addressed the question of the neuronal coding of complex natural patterns of sensory inputs in the barrel cortex of rodents. Their approach is based on the working hypothesis that the cortical responses depend on the context of the tactile discrimination and of the physical constraints of the whiskers (mechanic transduction, distortion, vibration, contact statistics…). In this framework they study the spatio-temporal dynamic properties of the neuronal activity in the barrel cortex and the thalamus. For this purpose, the group leader developed several original tools. The most emblematic is a new multiwhisker piezoelectric stimulator able to synthesize genuine “tactile scenes” mimicking the movement of multiple whiskers. This device will be shortly patented. The development of this technology was very time consuming, taking 4 years of design and development. This explains the relatively low number of papers produced by the team in the last 4 years (3 papers in 4 years). However, his efforts were recently rewarded by a very high quality paper in Neuron (2008). His team have now acquired all the tools and expertise he needs to address the question of somatosensory neuronal processing. He has also established national collaborations on the topic. The review committee considered that it is a very interesting and highly innovative project for the next 4 years based on an original working hypothesis. The quality of the previous work provided by the investigators bodes well for future success. The strengths of Team 2 are that the scientific questions are well addressed, the approach is of high quality and originality, the design of the experiments is good, there is a solid theoretical and experimental background and the publications are of very good quality. The only weakness is a relatively low publication rate but this is, at least partially, due to the time devoted to design and develop a new experimental setup.

Note de l’équipe


Rayonnement et


Stratégie,


Appréciation du

projet

A

A

A

A

A+

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Team 3. Dynamics of sensory processing

The team (1 DR2 CNRS; 1 CR1 CNRS ” Emérite”, 1 IE) investigates the active electric sense used by weakly electric fish for communicating and detecting obstacles/partners in the environment (“electroception”). The team has accumulated a lot of anatomical and functional data about the neural networks underlying electroception and those generating the electromotor commands over the last 20 years. However, active electrolocation is a complex dynamic phenomenon that implies “closed loop” interactions between several neural components with the environment. Therefore, although the data obtained by the team are clearly valuable and needed, understanding the active electrolocation (and electrocommunication) is a problem that fundamentally requires a comprehensive and interdisciplinary approach. This is the reason why the team has recently developed collaboration with mathematicians and engineers in France and abroad (Uruguay, Germany, Italy, and Switzerland). The collaborative project, aims at understanding the complex dynamics of active electrolocation by combining electrophysiological recordings in the animal with numerical modeling and implementation in a robot. This interdisciplinary approach (supported by ANR and EU) should strengthen their approach and allow more difficult questions to be addressed, with modeling work suggesting new experiments and predicting their outcomes. The team also plans to study the development of the electric system in mormyrid fish by using anatomical, electrophysiological and behavioural techniques (in vivo and in vitro). This aspect of the research deviates significantly from the main interest (“dynamics of neuronal activities”) of UNIC raising the question of whether the focus of research on the electric sense could be more complementary and synergistic with the work being carried out in UNIC. The team has produced 10 publications during the 2004-2008 period in journals of record, with medium impact factor. A single student has defended his thesis in the last four years.

Note de l’équipe


Rayonnement et


Stratégie,


Appréciation du

projet

B

B

C

B

C

Team 4. Thalamo-cortical Cybernetics

This group (1 principal investigator, a postdoc and a PhD student), focuses on how individual neurons integrate synaptic input within thalamocortical networks, with a view to understanding visual processing and neuronal behaviour during slow wave sleep and potentially during pathological disorders such as absence epilepsy. Over the last 4 years Team 4, has developed some highly original electrophysiological methods that allow better quality recordings to be made through active compensation of the electrical properties of the electrode (Neuron 2008). The group, in collaboration with team 5, has developed a method for extracting the underling excitatory and inhibitory synaptic conductances for voltage measurements and has used it to study the conductances that proceed spikes. The group has used dynamic clamp to show that synaptic noise has a large effect on the input ouput relationship of thalamic neurons (Nat. Neurosci. 2005). The work is of very good international standard and the method development is world leading. The proposed program of work is very promising with further method development, combining neuron-based models and dynamic clamp, thereby allowing synaptic integration to be studied in vitro, under conditions that mimic those observed in vivo. Moreover, extension of the active electrode compensation will have a major impact in improving voltage clamp and dynamic clamp recordings in vivo. The group has published 7 articles in referred international journals and two of those were in high impact neuroscience Journals. The strengths of the group are that the research is original, exiting and world class with future projects focused on important problems. The team has developed a number of important new technologies and collaborates extensively with several of the other teams in UNIC. Nevertheless, some of the proposed experiments using conductance extraction and reinjection may be pushing the methods to their limit. In these cases, it would be good to revaluate the robustness of the assumptions/limitations for the most exacting applications. In particular focus on the inability of the method to

8

account for nonlinear voltage gated conductances in dendrites and the fact that the reinjected conductances are at the soma rather than being distributed over the dendritic tree.

Note de l’équipe


Rayonnement et


Stratégie,


Appréciation du

projet

A

A

A

A

A+

Team 5. Computational Neurosciences

The team focuses on computational neuroscience and consists of two permanent researchers, (1 DR2, 1 CR1), two non-permanent researchers, currently supported by an ANR grant and a European grant, one Ph.D student and one master student. The size of the team is therefore reasonable. The team addresses a variety of questions. It focuses on modeling issues in neuroscience, from cellular levels (ion channels, and synaptic plasticity) to large network dynamics. The techniques used relies mostly on numerical simulations and, to a smaller extent, on analytical approaches. A great part of the research is devoted to studying the integrative properties of neurons using compartmental models. Another central activity of the leader and his collaborators makes use of modeling to design new methods to estimate the excitatory and inhibitory synaptic conductances from intracellular recordings in the cerebral cortex. The team also collaborates with the team 4 at UNIC to develop new methods for dynamic clamp in vivo. The research of team 5 is at the leading edge of the Computational Neuroscience internationally, and its achievements are very significant. The impact of this activity is high, as testified by the regularity of the publications in high profile peer reviewed scientific journals and by invited presentations in international scientific conferences worldwide. In the past four years, the team leader has also made a significant contribution to the organization of scientific conferences and schools. Last but not least, the members of the team are very satisfied with its management. This is a very successful group with an impressive international profile. The only potential weaknesses arise from its very success. The wide range of topics and high publication output may limit the time that the group leader can spend on each project, and as for team 4, some of the techniques may be being pushed close to their limit in terms of the information that can be extracted/predicted. Further tests of these important methods should be encouraged in the future.

Note de l’équipe


Rayonnement et


Stratégie,


Appréciation du

projet

A+

A+

A+

A+

A+

Team 6 Neuroinformatics

In this group, (principal investigator and two postdocs on FACETS and a PhD student) work in the newly emerging field of neuroinformatics. This involves both data driven neural modeling and the development of new software tools for modeling and creating databases of neuroscience data. Unlike systems biology,

9

computational neuroscience is much less standardized. Key issues in the field of neuroinformatics are therefore interoperability and reproducibility of models and the difficulty of making experimental data available. Team 6 is addressing these needs through the development of PyNN a python-based application for specification of neuronal network models which can be used with different simulators, which is part of the FACETS project. This is a very flexible solution to the interoperability problem and this will be extended further with the plans to make PyNN compliant with the XML-based simulator independent model description language NeuroML. They are also developing a database that will allow various kinds of data (e.g. electrophysiological, anatomical, metadata) to be stored and searched. This interfaces with the electrophysiological acquisition and analysis software developed in the unit. Model quality is also an important aspect of neuroscience modeling and the group are developing new benchmarks that provide a quantitative comparison between data and models under similar conditions. The scientific application proposed for the next four years focuses on network modeling of the visual system, collaborating with team 1. The team intends to extend their well received previous work on spike-timing dependent plasticity and will also model olfactory system. Lastly, the team will continue their work on multisensory integration. The strengths of the team are that the leader is already well known in the international neuroinformatics community and is well integrated through the FACETS project. The proposed neuroinformatics projects are timely and the approaches taken are likely to benefit the community. However, It is important that the team do not spend all their time on developing tools (especially the database) as these will only lead to limited publications. The team should allocate at least 50% of time on scientific questions to ensure students and postdocs have sufficient publications in appropriate journals to enable sustainability.

Note de l’équipe


Rayonnement et


Stratégie,


Appréciation du

projet

B

B

B

A

A

5 Appreciation of resources and of the life of the research unit We encountered no problems with the permanent academic and technical staff within the unit. The unit seems to be running smoothly with the present management structure and implementation. The only issues relate to some of the groups relying on senior postdocs for day to day management of projects because, although they are essential members of the team they have not managed to get permanent CNRS positions. This is a particular issue for team 1. However, this does not reflect the active promotion of young researchers, since those that have tenure are being promoted (e.g. promotion of Andrew Davidson to team leader). There is a refreshingly high level of collaboration between groups within UNIC and the technical infrastructure appears excellent, which is essential for the development of new methods.

6 Recommendations and advice

— Strong points :

This unit is a scientific powerhouse that has a excellent international reputation and produces top quality neuroscience that is world leading. It also develops a range of new and important methods that will have a wide impact in this and related fields. The unit attracts significant external funding and is well connected internationally. UNIC is well managed and the staff is satisfied with it.

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— Weak points :

There is little to criticize, but a lot of responsibility is placed on some senior postdocs who do not have tenure. However, this likely results from the very small number of permanent positions open in national institutions, especially in the field of computational neurosciences. More could be done to ensure that the methods developed are accessible to the wider scientific community. Several of the research groups are quite small.

— Recommendations :

It would be good to disseminate the methods developed in the unit more widely through the release of the designs and software and by running international workshops. Encouraging the smaller groups to apply for funds to increase the number of researchers would be beneficial.

Note de l’unité


Rayonnement et


Stratégie,


Appréciation du

projet

A

A

A

A

A+

11

UNIVERSITEPARIS-SUD 11

Le Président de l'Université Paris-Sud 11

Monsieur Pierre GLORIEUXDirecteur de la section des unités de rechercheAERES20, rue Vivienne75002 Paris

Orsay, le 7 avril 2009.

N/Réf. : 113/09/GCo/LM/LS

Objet : Rapport d'évaluation d'unité de rechercheN° S2100025556

Monsieur le Directeur,

Vous m'avez transmis le vingt mars dernier, le rapport d'évaluation de l'unité de recherche « Unité deNeurosciences, de l'Information et de la Complexité » - UNIC - UPR 2191, et je vous en remercie.

L'université prend bonne note de l'appréciation et des suggestions faites par le Comité.

La réponse du directeur d'unité vous parviendra par l'intermédiaire du CNRS.

Je vous prie d'agréer, Monsieur le Directeur, l'expression de ma sincère considération.

Guy COL

Pr. Guy COUARRAZE - Université Paris-Sud 11 Bât. 300 - 91405-Orsay-cedexTel : 01 69 15 74 06 - Fax : 01 69 15 61 03 - e-mail : presidenttg.u-psud.fr

Siège : Université Paris-Sud 1 I - 91405 Orsay cedex - http://www.u-psud.fr

U N I T É D E N E U R O S C I E N C E S

I N T É G R A T I V E S E T C O M P U T A T I O N N E L L E S

CNRS-UPR 2191 Directeur: Yves Frégnac

U N I T É D E N E U R O S C I E N C E S I N T É G R A T I V E S E T C O M P U T A T I O N N E L L E S ( U N I C )

I n s t i t u t d e N e u r o b i o l o g i e A l f r e d F e s s a r d C e n t r e N a t i o n a l d e l a R e c h e r c h e S c i e n t i f i q u e

A v e n u e d e l a T e r r a s s e , F - 9 1 1 9 8 G i f s u r Y v e t t e C e d e x F r a n c e T e l : ( 3 3 ) 1 6 9 8 2 3 4 1 5 F a x : ( 3 3 ) 1 6 9 8 2 3 4 2 7

E - m a i l : f r e g n a c @ u n i c . c n r s - g i f . f r h t t p : / / w w w . u n i c . c n r s - g i f . f r

Dr. Yves Frégnac à Comité d’évaluation de l’AERES et Direction de l’ISBNC Objet: Rapport AERES suite à l’examen du projet d’Unité UNIC Gif-sur-Yvette, le 30 Mars 2009 Monsieur le Président, Chers collègues, en tant que directeur et représentant de l’UNIC, je n’ai pas de remarques particulières à faire sur le rapport du comité d’évaluation scientifique de l’AERES, que les chefs de groupe et moi-même avons trouvé équilibré. Cordialement, Yves Frégnac Directeur de l’UNIC

Yves

UNIC

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Neurosciences Intégratives et Computationnelles - … · Neurosciences Intégratives et Computationnelles CNRS ... V1 Cognisciences The team is interested in the dynamics of neuronal