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INCF: Would you tell us a little about your background?

Le Franc: My name is Yann Le Franc and I am currently working as freelance scientist/consultant in Neuroinformatics and Computational Neurosciences in Paris, France (Sept. 2012). Since the beginning of my career, I have been acquiring a multi-disciplinary experience covering cellular and molecular neurobiology, neurophysiology, computational neurosciences, computer science and Neuroinformatics. In 2009, I joined the lab of E. De Schutter to work on the development of Neuroinformatics tools and standards for the INCF Multi-Scale Modeling program. I am the lead developer of the Computational Neuroscience Ontology and I have been contributing to the development of NineML as a member and secretary of the Multi-Scale Modeling task force.  In parallel, I am the coordinator of the Belgian INCF node (www.neuroinformatics.be).  As consultant, I am now working with T. Wachtler and the German INCF node (G-Node) to develop an ontology for annotating neurophysiological data and to design a software solution for acquiring, storing and manipulating experimental metadata.

INCF: When did you become interested in Neuroinformatics?

Le Franc: During my first post-doctoral experience, I was a research assistant at the Krasnow Institute (George Mason University, VA, USA) where I met G. Ascoli and the members of his lab who introduced me to their work in Neuroinformatics. In 2008, I have been invited to participate in the Neuroinformatics social event that took place during the SfN meeting in Washington DC. During this event, I learned more about Neuroinformatics and met international researchers in the field, which definitively helped me to apprehend the potential impact of this field on our every day work as experimentalist and modeller.

INCF: How is a regular day in the life of a Neuroinformatics researcher?

Le Franc: It is hard to describe a regular day since every day comes with its share of different issues that often requires to learn and to do something new. However, days usually start with the “holy” mug of coffee and by checking emails. As I am managing collaborative projects, I often check the answer from my colleagues living in different time zone. Then, I spend time reading and learning about new technologies and implementing solutions for the different projects in addition to the different duties of project manager/coordinator.

INCF: Some highlights from 2012...

Le Franc: In 2012, the Computational Neuroscience Ontology has been presented to the Computational Neuroscience community during the CNS meeting in Atlanta and a new version of CNO has been developed in 2012 and released in January 2013. Finally, the course entitled “Imaging the brain at different scales: how to integrate multi-scale structural information?” elaborated together with the Belgian, Dutch, French and Polish node, was awarded by the INCF Training committee in 2012.

INCF: What are your projects for 2013?

Le Franc: I am currently working on the organization of the INCF sponsored course, which will be held in Antwerp from Sept. 2^nd to Sept. 6^th. Applications are currently open on the Belgian node website until April 15^th (www.neuroinformatics.be/NeuroinfCourse/). In parallel, I am coordinating the development of a first version of the Ontology for Experimental Neurophysiology (OEN) and I am designing a software solution to acquire, store and manipulate experimental metadata, based on the different tools developed by the G-Node.  Finally, I created with S.D. Larson (MetaCell LLC, USA), S. Ghosh (MIT, USA) and R. Bakker (Donders institute, Netherlands), the first consulting network in Neuroinformatics and Computational Neurosciences. One of the aims of this network is to promote our activities at an international level and join our different competences to provide short-, medium- and/or long-term support on academic and industry projects. This network named the e-Neuroscience Consulting Network started around the simple idea of sharing our experiences as entrepreneurs and was officially created in December 2012. We are currently working on our website which should be hopefully released soon (www.e-neuroconsulting.net). Our mid-term goal is to create an active community of entrepreneurs/consultants in Neuroinformatics and Computational Neurosciences where any entrepreneur could find some community support, advices and promote its own activities and expertises on the network website.

INCF: Last book you have read...

Le Franc: The english version of “the Hitchhicker’s Guide to the Galaxy” from Douglas Adams (I’ve read it in French long time ago…what an heresy!)

INCF: Last movie you have seen...

Le Franc: A good day to die hard, Argo

INCF: What is your secret hobby?

Le Franc: Learning to play bass guitar, drawing and jigsaw

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NCF: Can you give us some background information about yourself?

Willshaw: I'm Professor of Computational Neurobiology at the University of Edinburgh, UK. My research has focused on neural networks and computational neuroscience, stretching back over 40 years. I've also developed algorithms for combinatorial optimization. Since 1984, I've held long term research support from the UK Medical Research Council and, more recently, the Wellcome Trust. Currently I lead a multi-centre Wellcome Trust funded project combining modelling approaches to investigate the roles of neural activity and molecular signalling in the formation of ordered nerve connections in the mouse retinocollicular system.

I'm the grant holder of the Edinburgh Doctoral Training Centre in Neuroinformatics and Computational Neuroscience. Since 2002, this Centre has trained over 80 PhD students from the physical and informational sciences who are applying quantitative approaches to neuroscience and to neurally inspired computing.

From 1999-2005, I was Editor-in-Chief of the computational neuroscience journal Network: Computation in Neural Systems. With colleagues, in 2012 I published the textbook Principles of Computational Modelling in Neuroscience (Cambridge University Press; 2011).

Since 2001, I have coordinated Neuroinformatics research in the UK.

Currently, I am the UK Node Coordinator and Scientific Representative to INCF. I’ve a special interest in training and now chair the INCF Training Committee. In our first full year of operation, last year we funded three short courses in particular aspects of Neuroinformatics and also ran our own introductory short course.

INCF: When did you become interested in Neuroinformatics?

Willshaw: I've been interested in applying computational modelling techniques to understanding the brain ever since I read books on information theory and cybernetics as a teenager and was then inspired at university by lectures on the neurobiology of vision.

INCF: What is a normal day in the life of a Neuroinformatics researcher?

Willshaw: A combination of meetings about projects and new initiatives plus too little time for research. My most fruitful time to do research is when I’m away from the office; the Elastic Net algorithm for the Travelling Salesman Problem which I developed with Richard Durbin was essentially worked out whilst we were attending a summer school.

INCF: Some highlights from 2012...

Willshaw: I've been analyzing some new imaging data, which gives insights about how the connectivity pattern between the eye and the brain is set up. After spending many hours analyzing the data in the wrong way, finally I succeeded. As a modeller I’m proud of the fact that the results of the analysis are inexplicable on any current model!

INCF: Some projects for 2013...

Willshaw: To get my analysis published and to make sure the UK Node stays on a firm footing.

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INCF:  Tell us a little about your background.

Bhalla:  I started out keenly interested in science, convinced I would do physics. An undergraduate biology course at Cambridge was a revelation, so I switched subjects for my PhD. I worked on the GENESIS neuronal simulator as a grad student at Caltech in the group of Jim Bower, and then adapted it to carry out kinetic simulations as a post-doc in Mount Sinai with Ravi Iyengar. I've combined experiments and models on studying olfactory processing, and memory, ever since. I now work on the MOOSE simulator which brings together many scales of function, from molecules to vast networks, that I am convinced are essential to consider to understand neuronal function.

INCF: When did you become interested in Neuroinformatics?

Bhalla: As a grad student, doing neuronal modeling and development of GENESIS. I had an interesting meeting with Mike Hines back then thinking how we could get GENESIS and NEURON to talk to each other. Still trying to achieve interoperability!

INCF: How is a regular day in the life of a neuroinformatics researcher ?

Bhalla: Cycle in, swim, deal with email, deal with committees, prepare a lecture or grant, do some science with students if possible. Cycle back, get down to quality science time in the evening when the kids have gone to sleep. Unfortunately brain switches off about the same time.

INCF: Some highlights from 2012...

Bhalla: Watching Olympics at midnight. Enjoying wandering about lost in Munich at the INCF Congress. Seeing our lab's first 2-photon in-vivo activity recordings from a whole sheet of pyramidal neurons.

INCF: Projects for 2013...
Bhalla: MOOSE with lots of new features and parallelism. Graduate a lot of students. Multiscale models in hippocampal plasticity.

INCF: Last book you have read...

Bhalla: Anathem by Neal Stephenson.

INCF:  Last movie you have seen...

Bhalla: English Vinglish (2012, directed by Gauri Shinde) 

INCF: What is your secret hobby?

Bhalla: Eat vast amounts of dessert to annoy colleagues who have to watch their weight. But this isn't secret any more!

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For the Fourth Year in a Row, Cajal’s Butterflies of the Soul (Oxford University Press) was the best seller book at the Society for Neuroscience meeting. The author Javier DeFelipe, research professor at Laboratorio Cajal de Circuitos Corticales at the Universidad Politecnica de Madrid and Instituto Cajal (CSIC), talks about the exciting adventure of compiling some of the most beautiful scientific illustrations by Nobel Laureate Santiago Ramón y Cajal. 

INCF:  How did the idea of compiling Cajal's drawings come about?

DeFelipe: The main aim of this work is to demonstrate to the general public that the study of the nervous system is not only important for the many obvious reasons related to brain function in both health and disease, but also for the unexpected natural beauty that it beholds. The illustrations included in this book represent only a small sample of the thousands of figures that were produced during Cajal's time. Of course, I have not been able to go through all the articles and books of the time, thus, only selected figures have been included due to space limitations. This selection reflects my own interests, which may not be fully shared by other readers.

INCF:  Is Ramón y Cajal the illustrator known worldwide?

DeFelipe: In the field of neuroscience, Cajal is well known for his beautiful drawings.  Nevertheless, the artistic skills of Cajal were also shared by Pío del Río-Hortega and Fernando de Castro and also by other famous disciples of Cajal.  There are also many other important pioneers in neuroscience, including Deiters, Kölliker, Meynert, Ranvier, Golgi, Retzius, Dogiel and Alzheimer.

INCF: Who is the target audience for this book?

DeFelipe: Neuroscientists, neurologists, psychiatrists, physicians, artists and the general public. We think this book will be of general interest, not only due to the captivating aesthetic appeal of the illustrations but also because they represent the bases of our current understanding of the nervous system. The reader will find that many of the illustrations can be considered to belong to different artistic movements, such as modernism, surrealism, cubism, abstract art or impressionism.

INCF: Where do the illustrations come from?

DeFelipe: This book contains a collection of more than 300 figures dated from 1859 to 1932. These were obtained from private collections, books, and articles.

INCF: Any future projects? Maybe a part two?

DeFelipe: I am preparing a new book entitle “El jardin de la Neurologia. Reflexiones sobre lo bello, el arte y el cerebro” (The Garden of Neurology. Reflexions on the beauty, art and brain)

• Cajal’s Butterflies of the Soul
• Oxford University Press, USA; 1 edition (November 12, 2009)
• ISBN-10: 0195392701

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The Society for Neuroscience celebrated its annual meeting from 14 to 18th October, in New Orleans, US. As in previous years, INCF offered a series of dual demo sessions of Neuroinformatics tools and software (short demo videos are available  on the INCF YouTube Channel). An open mini-hackathon took place on Wednesday, were developers were welcome to join for on-site coding and discussion. The INCF DATASPACE was launched during SfN, along with the Data Share Award. INCF was located near other Neuroinformatics exhibitors like Neuroscience Information Framework (NIF), Whole Brain Catalogue, Cognitive Atlas, CARMEN and NeuroDevian.

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The 5^th Annual INCF Congress of Neuroinformatics took place September 10-12 at the University Hospital Klinikum rechts der Isar der TU München, in Munich, Germany. It welcomed more than 200 researchers in all fields related to neuroinformatics, including data- and knowledge-bases of the nervous system from molecular to behavioral levels; tools for the acquisition, analysis, and visualization of nervous system data; and theoretical, computational, and simulation environments for modeling the brain. The meeting included a series of keynote speakers, workshops, poster sessions and live demonstrations of neuroinformatics tools.

Dr. Sean Hill, Executive Director of the International Neuroinformatics Coordinating Facility –INCF- explains: “The Annual INCF Neuroinformatics Congress brings together world class scientists and a diverse international research community to exchange tools, techniques and knowledge for the acceleration of our understanding of the brain through data sharing and multilevel analysis, data integration and computational modeling“.

Some highlights of the event included:

• Keynote speakers: Michael Brecht, Sonia Grün, Atushi Miyawaki, Russel Poldrack and Gordon Shepherd.
• On Sunday September 10^th, Yasuo Kawaguchi, Carl Petersen, and Harald Luksch presented their work in a workshop on the “Function-structure relationship in microcircuitry.”
• On Monday September 11^th, Kim “Avrama” Blackwell, Thomas Bartol,  Nicolas Le Novère, and Upinder Bhalla presented in a workshop on the “Systems Biology of the Neuron.”
• On Wednesday September 12^th, Cameron Neylon, Amarnath Gupta, and Mercè Crosas participated in a workshop on “If there is a data deluge, where are the data?”

Immediately following Neuroinformatics 2012, the same venue hosted the Bernstein Conference on Computational Neuroscience, the annual meeting of the National Bernstein Network Computational Neuroscience (NNCN) that represents about 200 research groups from over 20 locations in Germany.

 A full program and further information is available at the website: neuroinformatics2012.org

 The meeting was sponsored by: Bernstein Network, IEEE-EMB, CARMEN, Springer and Columbia University Press and Physion Consulting.

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On May, INCF hosted an open house and networking event. Guests were able to meet INCF Director Stan Griller and Executive Director Sean Hill and other members of INCF Secretariat, who explained neuroscience resources offered by INCF, recently developed software tools and standards and benefits of collaboration with INCF. Head of Programs, Linda Lanyon (right) introduced attendees to INCF Programs. Invitees included scientists in related disciplines and representatives from granting agencies, government and other relevant organizations. 

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Last July, INCF travelled to Barcelona to participate in the Federation of European Neurosciences - FENS-  Meeting. INCF had a large booth where demo sessions took place. On Sunday, Andrey Sobolev introduced guests and attendees to the G-Node Tools and Services for Electrophyisiology Data. On Monday  Daniel K. Wójcik (left) presented the 3D Brain Atlas Reconstructor and Scalable Brain Atlas. Attendees were able as well to learn about each INCF Program and meet the Tasks Forces members and Secretariat.  On Wednesday, everybody was welcome to present and discuss their own neuroinformatics work. 

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This week, the Allen Institute for Brain Science announced that they have a funding commitment for another $300M from philantropist Paul G. Allen,  bringing his total investment in the Institute to half a billion dollars.The funds will be used to cover the first four years of an ambitious ten-year plan for the Institute, during which the current staff will be doubled in size and three new, complementary scientific initiatives will be added to the Institute's already existing endeavors.

"We're now at a crossroads where technology has advanced sufficiently to begin to tackle ever more complex questions at large scale", said Allan Jones, Chief Executive Officer, at the March 21 press conference in Seattle (a video of the press conference is available on the announcement event page).

One of the new efforts is targeted toward understanding the visual system of the mouse, from cells and their connectivity to perception and decision making. The project and its vision is described by Christof Koch and R. Clay Reid in a Comment in this week's issue of Nature, and there is also a nice interview with Christof Koch in this week's issue of Science.

While the results from the Institute's founding in 2003 up until today are impressive on their own - large-scale brain science which has produced several brain atlases in astounding detail and more than a petabyte of data - the truly remarkable part is that all results are open and accessible to the community (see www.brain-map.org), even before publication. This commitment to open science, which is a mandate set up by Paul Allen when the Institute was founded with $100M in seed funding from his foundation, will continue unchanged.

It will be very interesting to see both the results and these projects' effects on the neuroscientific community.

Image: a coronal section of an entire mouse brain, which was stained to delineate anatomical boundaries in many brain regions. Cell bodies are stained in red (NeuN) and axonal projections in green (NF160). Image credit: Allen Institute of Brain Science (it is highly recommended to view the full resolution original image).

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The collaborators just published a paper in Nature Methods (available online January 15) describing how their microscopy method, serial two-photon (STP) tomography, enables automated high-throughput imaging of fluorescently labeled mouse brains. A typical whole mouse brain scan is reported to take 6.5 to 8.5 hours, while a scan at the maximum resolution takes 24 hours - in any case quick enough to potentially, as the researchers put it "transform the emerging field of systematic whole-brain anatomy, until now limited to dedicated atlas-generation initiatives, into a routine methodology".

If this turns out to be a true prediction, we are likely to see many comparably small and diverse data sets in the hands of many different groups and labs, some years from now. And a corresponding increased need to compare data sets with each other and with reference atlases, to integrate data for combined queries, and to describe and publish both data and analysis methods. We of course hope that the tools and services INCF and the Task Forces, especially those in Digital Brain Atlasing and in Datasharing, are developing will be useful in this regard, and that we also can help support and complement the community-developed tools already out there.

Have you identified a problem or barrier that you think we can help you and your scientific field or subfield with? Be sure to let us know in the comments!

(Figure: Figure 1a-c from the paper, showing method scheme and 2D/3D views of the resulting brain scans. Reused with permission from Nature Methods)

 Links:

1. T Ragan et al (2012) "Serial two-photon tomography for automated ex vivo mouse brain imaging" Nature Methods, doi:10.1038/nmeth.1854

 2. Cold Spring Harbor Laboratory press release, January 12, 2012

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